Starting phenix.real_space_refine
on Wed Apr 30 20:56:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6n3q_0336/04_2025/6n3q_0336.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6n3q_0336/04_2025/6n3q_0336.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6n3q_0336/04_2025/6n3q_0336.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6n3q_0336/04_2025/6n3q_0336.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6n3q_0336/04_2025/6n3q_0336.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6n3q_0336/04_2025/6n3q_0336.cif"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.010 sd=   0.066
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      38      5.16       5
     C    6495      2.51       5
     N    1678      2.21       5
     O    1720      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9931
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 391, 2960
          Classifications: {'peptide': 391}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 16, 'TRANS': 374}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 84
          Unresolved non-hydrogen angles: 103
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 66
    Chain: "C"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 435
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 2, 'TRANS': 52}
    Chain: "B"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 229
          Classifications: {'peptide': 32}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 3779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 487, 3779
          Classifications: {'peptide': 487}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 28, 'TRANS': 458}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 141
          Unresolved non-hydrogen angles: 178
          Unresolved non-hydrogen dihedrals: 106
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 17, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 13}
          Unresolved non-hydrogen planarities: 124
    Chain: "E"
      Number of atoms: 1095
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1095
          Classifications: {'peptide': 135}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "F"
      Number of atoms: 1433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1433
          Classifications: {'peptide': 190}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 7, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 46
          Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 37
  Time building chain proxies: 6.65, per 1000 atoms: 0.67
  Number of scatterers: 9931
  At special positions: 0
  Unit cell: (105.56, 126.44, 127.6, 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      38     16.00
     O    1720      8.00
     N    1678      7.00
     C    6495      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.43
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2432

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 4 sheets defined
      67.2% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 48
      removed outlier: 3.806A  pdb=" N   ILE A  34 " --> pdb=" O   ASN A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 99
    Processing helix  chain 'A' and resid 107 through 137
    Processing helix  chain 'A' and resid 148 through 173
    Processing helix  chain 'A' and resid 179 through 199
    Processing helix  chain 'A' and resid 213 through 224
      removed outlier: 3.545A  pdb=" N   ALA A 217 " --> pdb=" O   GLY A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 237
    Processing helix  chain 'A' and resid 243 through 261
    Processing helix  chain 'A' and resid 291 through 310
      removed outlier: 3.803A  pdb=" N   LEU A 295 " --> pdb=" O   THR A 291 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   LEU A 305 " --> pdb=" O   SER A 301 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ILE A 306 " --> pdb=" O   ASN A 302 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ILE A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 385
      removed outlier: 4.202A  pdb=" N   GLU A 382 " --> pdb=" O   LYS A 378 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE A 383 " --> pdb=" O   THR A 379 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLY A 385 " --> pdb=" O   ILE A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 399
    Processing helix  chain 'A' and resid 408 through 440
      Proline residue:  A 419  - end of helix
    Processing helix  chain 'A' and resid 444 through 466
    Processing helix  chain 'C' and resid 27 through 38
      removed outlier: 3.883A  pdb=" N   LYS C  38 " --> pdb=" O   GLN C  34 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 79
      removed outlier: 3.839A  pdb=" N   LYS C  49 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ILE C  56 " --> pdb=" O   LYS C  52 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ILE C  68 " --> pdb=" O   ILE C  64 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ILE C  73 " --> pdb=" O   LYS C  69 " (cutoff:3.500A)
      Proline residue:  C  74  - end of helix
    Processing helix  chain 'B' and resid 53 through 82
    Processing helix  chain 'D' and resid 13 through 36
      removed outlier: 3.705A  pdb=" N   ILE D  18 " --> pdb=" O   TRP D  14 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR D  20 " --> pdb=" O   SER D  16 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   VAL D  25 " --> pdb=" O   GLY D  21 " (cutoff:3.500A)
      Proline residue:  D  28  - end of helix
    Processing helix  chain 'D' and resid 58 through 67
      removed outlier: 3.877A  pdb=" N   LEU D  62 " --> pdb=" O   VAL D  58 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   GLU D  64 " --> pdb=" O   LYS D  60 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   GLU D  65 " --> pdb=" O   ASN D  61 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   TYR D  66 " --> pdb=" O   LEU D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 78
    Processing helix  chain 'D' and resid 94 through 113
      removed outlier: 3.646A  pdb=" N   ASN D 113 " --> pdb=" O   ARG D 109 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 218 through 249
      removed outlier: 4.449A  pdb=" N   LEU D 222 " --> pdb=" O   SER D 218 " (cutoff:3.500A)
      Proline residue:  D 236  - end of helix
      removed outlier: 3.541A  pdb=" N   TYR D 249 " --> pdb=" O   ARG D 245 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 268
      removed outlier: 3.777A  pdb=" N   ASN D 268 " --> pdb=" O   SER D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 278 through 285
    Processing helix  chain 'D' and resid 287 through 294
      removed outlier: 3.750A  pdb=" N   LYS D 291 " --> pdb=" O   ALA D 287 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   PHE D 293 " --> pdb=" O   GLU D 289 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 311
      removed outlier: 3.739A  pdb=" N   LYS D 304 " --> pdb=" O   THR D 300 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 318 through 343
      removed outlier: 4.606A  pdb=" N   SER D 331 " --> pdb=" O   ALA D 327 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 345 through 362
      removed outlier: 3.672A  pdb=" N   ALA D 349 " --> pdb=" O   ASN D 345 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 368 through 372
      removed outlier: 3.708A  pdb=" N   ILE D 371 " --> pdb=" O   ASN D 368 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 378 through 386
    Processing helix  chain 'D' and resid 391 through 396
    Processing helix  chain 'D' and resid 401 through 408
      removed outlier: 4.301A  pdb=" N   GLU D 405 " --> pdb=" O   ALA D 401 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL D 406 " --> pdb=" O   LYS D 402 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 411 through 424
      removed outlier: 3.686A  pdb=" N   HIS D 424 " --> pdb=" O   ARG D 420 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 480 through 485
    Processing helix  chain 'D' and resid 487 through 493
      removed outlier: 3.998A  pdb=" N   MET D 491 " --> pdb=" O   PRO D 487 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 541 through 545
    Processing helix  chain 'E' and resid 71 through 86
      removed outlier: 3.591A  pdb=" N   TYR E  75 " --> pdb=" O   ALA E  71 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   PHE E  76 " --> pdb=" O   HIS E  72 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   GLU E  83 " --> pdb=" O   LYS E  79 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   ASN E  84 " --> pdb=" O   GLU E  80 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   LYS E  86 " --> pdb=" O   SER E  82 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 88 through 124
      removed outlier: 3.746A  pdb=" N   LEU E  96 " --> pdb=" O   LEU E  92 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU E  97 " --> pdb=" O   LYS E  93 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ASN E  98 " --> pdb=" O   ALA E  94 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ARG E  99 " --> pdb=" O   ALA E  95 " (cutoff:3.500A)
      Proline residue:  E 115  - end of helix
    Processing helix  chain 'E' and resid 127 through 156
      removed outlier: 3.543A  pdb=" N   TRP E 131 " --> pdb=" O   GLY E 127 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 161 through 182
      removed outlier: 4.177A  pdb=" N   MET E 165 " --> pdb=" O   GLN E 161 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 182 through 195
    Processing helix  chain 'F' and resid 21 through 42
      removed outlier: 3.526A  pdb=" N   ASN F  27 " --> pdb=" O   SER F  23 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   GLY F  40 " --> pdb=" O   THR F  36 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   THR F  42 " --> pdb=" O   LEU F  38 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 51 through 71
    Processing helix  chain 'F' and resid 73 through 91
    Processing helix  chain 'F' and resid 97 through 120
      Proline residue:  F 103  - end of helix
      removed outlier: 3.712A  pdb=" N   ILE F 118 " --> pdb=" O   ASP F 114 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 121 through 136
      removed outlier: 3.646A  pdb=" N   ALA F 125 " --> pdb=" O   LYS F 121 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   GLY F 136 " --> pdb=" O   LEU F 132 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 139 through 153
      removed outlier: 3.551A  pdb=" N   PHE F 143 " --> pdb=" O   GLN F 139 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ARG F 145 " --> pdb=" O   ASP F 141 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 155 through 168
      removed outlier: 3.592A  pdb=" N   ALA F 161 " --> pdb=" O   GLU F 157 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 173 through 192
      removed outlier: 3.812A  pdb=" N   ARG F 177 " --> pdb=" O   ASP F 173 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA F 178 " --> pdb=" O   MET F 174 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 211
      removed outlier: 3.832A  pdb=" N   ASN A 204 " --> pdb=" O   SER D 205 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   SER D 205 " --> pdb=" O   ASN A 204 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 281
      removed outlier: 3.627A  pdb=" N   GLY A 279 " --> pdb=" O   ILE A 269 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TYR A 281 " --> pdb=" O   LEU A 267 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LEU A 267 " --> pdb=" O   TYR A 281 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 430 through 436
      removed outlier: 4.910A  pdb=" N   LYS D 432 " --> pdb=" O   LYS D 454 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LYS D 454 " --> pdb=" O   LYS D 432 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ASP D 434 " --> pdb=" O   SER D 452 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 530 through 532
      removed outlier: 3.863A  pdb=" N   GLY D 584 " --> pdb=" O   VAL D 610 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   VAL D 610 " --> pdb=" O   GLY D 584 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   PHE D 586 " --> pdb=" O   MET D 608 " (cutoff:3.500A)

    631 hydrogen bonds defined for protein.
    1866 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: 2.93

  Time building geometry restraints manager: 2.84 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: 2909
        1.34 -     1.46: 1541
        1.46 -     1.57: 5620
        1.57 -     1.69: 0
        1.69 -     1.81: 59
  Bond restraints: 10129
  Sorted by residual:
  bond pdb=" C   LEU D 235 "
       pdb=" N   PRO D 236 "
    ideal  model  delta    sigma   weight residual
    1.336  1.379 -0.043 1.20e-02 6.94e+03 1.26e+01
  bond pdb=" C   THR A 291 "
       pdb=" N   PRO A 292 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.049 2.34e-02 1.83e+03 4.34e+00
  bond pdb=" CB  CYS E 167 "
       pdb=" SG  CYS E 167 "
    ideal  model  delta    sigma   weight residual
    1.808  1.740  0.068 3.30e-02 9.18e+02 4.29e+00
  bond pdb=" CG1 ILE D 280 "
       pdb=" CD1 ILE D 280 "
    ideal  model  delta    sigma   weight residual
    1.513  1.449  0.064 3.90e-02 6.57e+02 2.68e+00
  bond pdb=" C   ALA E 114 "
       pdb=" N   PRO E 115 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.20e-02 6.94e+03 2.45e+00
  ... (remaining 10124 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 13110
        2.14 -     4.29: 507
        4.29 -     6.43: 73
        6.43 -     8.57: 39
        8.57 -    10.71: 9
  Bond angle restraints: 13738
  Sorted by residual:
  angle pdb=" C   THR A  98 "
        pdb=" N   GLN A  99 "
        pdb=" CA  GLN A  99 "
      ideal   model   delta    sigma   weight residual
     122.74  129.32   -6.58 1.44e+00 4.82e-01 2.09e+01
  angle pdb=" C   ILE A 417 "
        pdb=" N   ILE A 418 "
        pdb=" CA  ILE A 418 "
      ideal   model   delta    sigma   weight residual
     120.33  123.96   -3.63 8.00e-01 1.56e+00 2.05e+01
  angle pdb=" C   ILE C  79 "
        pdb=" N   VAL C  80 "
        pdb=" CA  VAL C  80 "
      ideal   model   delta    sigma   weight residual
     121.70  128.70   -7.00 1.80e+00 3.09e-01 1.51e+01
  angle pdb=" CA  GLY A 178 "
        pdb=" C   GLY A 178 "
        pdb=" O   GLY A 178 "
      ideal   model   delta    sigma   weight residual
     122.22  119.78    2.44 6.50e-01 2.37e+00 1.41e+01
  angle pdb=" N   GLN A  99 "
        pdb=" CA  GLN A  99 "
        pdb=" C   GLN A  99 "
      ideal   model   delta    sigma   weight residual
     112.58  108.19    4.39 1.22e+00 6.72e-01 1.30e+01
  ... (remaining 13733 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.28: 5657
       15.28 -    30.55: 318
       30.55 -    45.83: 93
       45.83 -    61.11: 2
       61.11 -    76.38: 6
  Dihedral angle restraints: 6076
    sinusoidal: 2332
      harmonic: 3744
  Sorted by residual:
  dihedral pdb=" CA  LEU F 137 "
           pdb=" C   LEU F 137 "
           pdb=" N   ILE F 138 "
           pdb=" CA  ILE F 138 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -143.35  -36.65     0      5.00e+00 4.00e-02 5.37e+01
  dihedral pdb=" CA  PHE D 501 "
           pdb=" C   PHE D 501 "
           pdb=" N   ALA D 502 "
           pdb=" CA  ALA D 502 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.62  -23.38     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" CA  PRO D 463 "
           pdb=" C   PRO D 463 "
           pdb=" N   LEU D 464 "
           pdb=" CA  LEU D 464 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.34   22.66     0      5.00e+00 4.00e-02 2.05e+01
  ... (remaining 6073 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1062
       0.044 -    0.089: 418
       0.089 -    0.133: 126
       0.133 -    0.177: 28
       0.177 -    0.222: 9
  Chirality restraints: 1643
  Sorted by residual:
  chirality pdb=" CB  ILE A  49 "
            pdb=" CA  ILE A  49 "
            pdb=" CG1 ILE A  49 "
            pdb=" CG2 ILE A  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  LEU D 235 "
            pdb=" N   LEU D 235 "
            pdb=" C   LEU D 235 "
            pdb=" CB  LEU D 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.89e-01
  chirality pdb=" CB  THR A 453 "
            pdb=" CA  THR A 453 "
            pdb=" OG1 THR A 453 "
            pdb=" CG2 THR A 453 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.20 2.00e-01 2.50e+01 9.52e-01
  ... (remaining 1640 not shown)

  Planarity restraints: 1703
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU F 137 "    0.015 2.00e-02 2.50e+03   3.00e-02 8.99e+00
        pdb=" C   LEU F 137 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   LEU F 137 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ILE F 138 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F  47 "    0.040 5.00e-02 4.00e+02   5.99e-02 5.74e+00
        pdb=" N   PRO F  48 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO F  48 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO F  48 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 141 "    0.039 5.00e-02 4.00e+02   5.93e-02 5.62e+00
        pdb=" N   PRO A 142 "   -0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO A 142 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 142 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1700 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2967
        2.83 -     3.34: 9609
        3.34 -     3.86: 16151
        3.86 -     4.38: 16894
        4.38 -     4.90: 29885
  Nonbonded interactions: 75506
  Sorted by model distance:
  nonbonded pdb=" O   SER D 512 "
            pdb=" OG1 THR D 595 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   GLY D  27 "
            pdb=" OG1 THR D  30 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OD1 ASN A 204 "
            pdb=" OG  SER D 205 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   LYS E  79 "
            pdb=" OG  SER E  82 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" O   PHE A 198 "
            pdb=" OH  TYR C  66 "
     model   vdw
     2.334 3.040
  ... (remaining 75501 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.430
  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:          0.470
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     25.730
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  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:3.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
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      :  0.006   0.068  10129  Z= 0.253
  Angle     :  1.032  10.714  13738  Z= 0.547
  Chirality :  0.053   0.222   1643
  Planarity :  0.008   0.060   1703
  Dihedral  : 10.912  76.383   3644
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  5.47 %
    Favored  : 93.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.32 (0.18), residues: 1264
  helix: -1.92 (0.13), residues: 817
  sheet: -2.55 (0.56), residues: 64
  loop : -2.34 (0.27), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP D 242 
 HIS   0.008   0.002   HIS C  72 
 PHE   0.029   0.003   PHE D 290 
 TYR   0.026   0.002   TYR A 175 
 ARG   0.017   0.001   ARG E  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13132 (  631)
  hydrogen bonds       : angle       6.34952 ( 1866)
  covalent geometry    : bond        0.00563 (10129)
  covalent geometry    : angle       1.03208 (13738)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 342
  time to evaluate  : 1.314 
Fit side-chains
REVERT: A   30 ASN cc_start: 0.8289 (t0) cc_final: 0.8071 (t0)
REVERT: A   45 ILE cc_start: 0.8985 (tt) cc_final: 0.8781 (tt)
REVERT: A  162 LEU cc_start: 0.9112 (tm) cc_final: 0.8889 (tp)
REVERT: A  168 ASP cc_start: 0.8373 (t0) cc_final: 0.7936 (t0)
REVERT: A  188 ASN cc_start: 0.8384 (t0) cc_final: 0.8125 (t0)
REVERT: A  212 GLU cc_start: 0.7937 (tt0) cc_final: 0.7262 (mt-10)
REVERT: A  244 MET cc_start: 0.7318 (tmm) cc_final: 0.7072 (ttp)
REVERT: A  376 PHE cc_start: 0.7766 (m-80) cc_final: 0.7215 (m-10)
REVERT: A  424 PHE cc_start: 0.8019 (t80) cc_final: 0.7808 (t80)
REVERT: C   30 ARG cc_start: 0.7156 (ttm-80) cc_final: 0.6643 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8650 (mtmp) cc_final: 0.8237 (mttp)
REVERT: C   52 LYS cc_start: 0.7668 (ttmt) cc_final: 0.7269 (ttmt)
REVERT: D   16 SER cc_start: 0.8921 (m) cc_final: 0.8609 (t)
REVERT: D  100 TRP cc_start: 0.7541 (m100) cc_final: 0.7200 (m100)
REVERT: D  222 LEU cc_start: 0.8266 (tp) cc_final: 0.7523 (mm)
REVERT: D  272 SER cc_start: 0.8517 (m) cc_final: 0.8164 (p)
REVERT: D  282 HIS cc_start: 0.8258 (t70) cc_final: 0.7903 (t70)
REVERT: D  444 THR cc_start: 0.9188 (t) cc_final: 0.8892 (p)
REVERT: E  146 LYS cc_start: 0.8398 (ttmt) cc_final: 0.8169 (tptt)
REVERT: E  147 ASP cc_start: 0.8891 (t0) cc_final: 0.8658 (t0)
REVERT: E  148 THR cc_start: 0.9156 (p) cc_final: 0.8801 (p)
REVERT: E  150 GLN cc_start: 0.7871 (tt0) cc_final: 0.7044 (tm-30)
REVERT: E  165 MET cc_start: 0.7251 (tpt) cc_final: 0.6980 (tpp)
REVERT: F   10 SER cc_start: 0.8787 (t) cc_final: 0.8429 (p)
REVERT: F   49 GLN cc_start: 0.8762 (pp30) cc_final: 0.8520 (pp30)
REVERT: F   91 LYS cc_start: 0.8858 (mmtp) cc_final: 0.8625 (mmmm)
REVERT: F  108 MET cc_start: 0.8502 (mtm) cc_final: 0.8089 (mtt)
REVERT: F  112 LYS cc_start: 0.9223 (tttt) cc_final: 0.8940 (tttp)
  outliers start: 7
  outliers final: 1
  residues processed: 346
  average time/residue: 0.2370
  time to fit residues: 110.4108
Evaluate side-chains
  196 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 96 optimal weight:    0.4980
   chunk 53 optimal weight:    7.9990
   chunk 32 optimal weight:    0.0010
   chunk 64 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 99 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 115 optimal weight:    0.8980
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 115 GLN
A 192 GLN
A 204 ASN
D 345 ASN
D 494 GLN
D 539 ASN
** D 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  98 ASN
E 174 GLN
F  30 GLN
F  71 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.135386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.119268 restraints weight = 19075.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.122090 restraints weight = 9731.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.123725 restraints weight = 6090.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10129  Z= 0.149
  Angle     :  0.663   8.293  13738  Z= 0.332
  Chirality :  0.042   0.275   1643
  Planarity :  0.005   0.048   1703
  Dihedral  :  4.913  22.856   1364
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 13.92 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.22), residues: 1264
  helix:  0.20 (0.17), residues: 817
  sheet: -1.86 (0.59), residues: 69
  loop : -1.73 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  35 
 HIS   0.008   0.001   HIS D 288 
 PHE   0.031   0.002   PHE A  16 
 TYR   0.022   0.002   TYR A 237 
 ARG   0.008   0.001   ARG F 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04386 (  631)
  hydrogen bonds       : angle       4.51022 ( 1866)
  covalent geometry    : bond        0.00337 (10129)
  covalent geometry    : angle       0.66293 (13738)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 237
  time to evaluate  : 1.162 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 LEU cc_start: 0.8796 (tp) cc_final: 0.8495 (tt)
REVERT: A  100 LEU cc_start: 0.8432 (mt) cc_final: 0.8226 (tt)
REVERT: A  162 LEU cc_start: 0.9332 (tm) cc_final: 0.9101 (tp)
REVERT: A  168 ASP cc_start: 0.8570 (t0) cc_final: 0.8091 (t0)
REVERT: A  188 ASN cc_start: 0.8697 (t0) cc_final: 0.8257 (t0)
REVERT: A  204 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7355 (t0)
REVERT: A  447 SER cc_start: 0.8601 (m) cc_final: 0.8372 (p)
REVERT: A  456 TYR cc_start: 0.8148 (t80) cc_final: 0.7911 (t80)
REVERT: C   30 ARG cc_start: 0.6992 (ttm-80) cc_final: 0.6541 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8395 (mtmp) cc_final: 0.8077 (mttp)
REVERT: C   52 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7522 (ttmt)
REVERT: C   66 TYR cc_start: 0.8475 (t80) cc_final: 0.7653 (t80)
REVERT: D  222 LEU cc_start: 0.8076 (tp) cc_final: 0.7595 (mm)
REVERT: D  288 HIS cc_start: 0.7926 (t70) cc_final: 0.7661 (t-170)
REVERT: E  147 ASP cc_start: 0.8459 (t0) cc_final: 0.8244 (t0)
REVERT: E  150 GLN cc_start: 0.7236 (tt0) cc_final: 0.6906 (tm-30)
REVERT: E  153 GLU cc_start: 0.7428 (tp30) cc_final: 0.7057 (tt0)
REVERT: F   49 GLN cc_start: 0.8846 (pp30) cc_final: 0.8638 (pp30)
REVERT: F   71 GLN cc_start: 0.8669 (mt0) cc_final: 0.7955 (tm-30)
REVERT: F   86 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8223 (tp30)
REVERT: F  108 MET cc_start: 0.8213 (mtm) cc_final: 0.7681 (mtt)
REVERT: F  124 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7711 (tm-30)
REVERT: F  152 LYS cc_start: 0.8848 (tppt) cc_final: 0.8198 (tptt)
  outliers start: 41
  outliers final: 22
  residues processed: 265
  average time/residue: 0.2133
  time to fit residues: 81.2871
Evaluate side-chains
  211 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 188
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  204 ASN
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  419 LEU
Chi-restraints excluded: chain D residue  497 VAL
Chi-restraints excluded: chain D residue  526 LEU
Chi-restraints excluded: chain D residue  543 ASP
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  112 GLU
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain F residue   29 ASP
Chi-restraints excluded: chain F residue  181 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 87 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 50 optimal weight:    7.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 309 HIS
** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.129396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.110469 restraints weight = 20055.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.113310 restraints weight = 10632.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.115078 restraints weight = 6847.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.3109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10129  Z= 0.171
  Angle     :  0.655   9.965  13738  Z= 0.325
  Chirality :  0.042   0.190   1643
  Planarity :  0.004   0.045   1703
  Dihedral  :  4.631  20.903   1363
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 16.12 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.23), residues: 1264
  helix:  0.98 (0.18), residues: 816
  sheet: -1.50 (0.63), residues: 69
  loop : -1.51 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  14 
 HIS   0.007   0.001   HIS D 288 
 PHE   0.018   0.002   PHE A  16 
 TYR   0.020   0.002   TYR A 237 
 ARG   0.005   0.001   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04160 (  631)
  hydrogen bonds       : angle       4.23912 ( 1866)
  covalent geometry    : bond        0.00395 (10129)
  covalent geometry    : angle       0.65532 (13738)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 206
  time to evaluate  : 1.120 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 TRP cc_start: 0.8551 (m100) cc_final: 0.8304 (m100)
REVERT: A  188 ASN cc_start: 0.8731 (t0) cc_final: 0.8254 (t0)
REVERT: A  204 ASN cc_start: 0.7912 (t0) cc_final: 0.7366 (t0)
REVERT: A  212 GLU cc_start: 0.7932 (tt0) cc_final: 0.7356 (mt-10)
REVERT: A  244 MET cc_start: 0.7881 (ttp) cc_final: 0.7389 (ttp)
REVERT: A  376 PHE cc_start: 0.7861 (m-80) cc_final: 0.7043 (m-10)
REVERT: A  447 SER cc_start: 0.8904 (m) cc_final: 0.8197 (p)
REVERT: C   30 ARG cc_start: 0.7194 (ttm-80) cc_final: 0.6650 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8501 (mtmp) cc_final: 0.8095 (mttp)
REVERT: C   46 GLU cc_start: 0.8389 (tp30) cc_final: 0.8179 (tp30)
REVERT: C   52 LYS cc_start: 0.7740 (ttmt) cc_final: 0.7524 (ttmt)
REVERT: D  222 LEU cc_start: 0.8138 (tp) cc_final: 0.7658 (mm)
REVERT: E  130 TYR cc_start: 0.8744 (t80) cc_final: 0.8478 (t80)
REVERT: E  150 GLN cc_start: 0.7465 (tt0) cc_final: 0.6900 (tm-30)
REVERT: F   49 GLN cc_start: 0.8827 (pp30) cc_final: 0.8588 (pp30)
REVERT: F   71 GLN cc_start: 0.8762 (mt0) cc_final: 0.7897 (tm-30)
REVERT: F  124 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7731 (tm-30)
REVERT: F  152 LYS cc_start: 0.8941 (tppt) cc_final: 0.8290 (tptt)
  outliers start: 59
  outliers final: 40
  residues processed: 247
  average time/residue: 0.2032
  time to fit residues: 73.2635
Evaluate side-chains
  221 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 181
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue   16 SER
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  272 SER
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  419 LEU
Chi-restraints excluded: chain D residue  425 ILE
Chi-restraints excluded: chain D residue  497 VAL
Chi-restraints excluded: chain D residue  514 CYS
Chi-restraints excluded: chain D residue  526 LEU
Chi-restraints excluded: chain D residue  543 ASP
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  123 ASN
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain F residue   13 ILE
Chi-restraints excluded: chain F residue   29 ASP
Chi-restraints excluded: chain F residue  162 THR
Chi-restraints excluded: chain F residue  181 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0970
   chunk 24 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   chunk 104 optimal weight:    0.5980
   chunk 98 optimal weight:    0.7980
   chunk 91 optimal weight:    0.5980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 539 ASN
** E  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.120429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.105725 restraints weight = 18641.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.107646 restraints weight = 11904.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.109153 restraints weight = 7500.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.3386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10129  Z= 0.131
  Angle     :  0.631  10.331  13738  Z= 0.302
  Chirality :  0.040   0.193   1643
  Planarity :  0.004   0.041   1703
  Dihedral  :  4.345  20.204   1363
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 19.19 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.24), residues: 1264
  helix:  1.40 (0.18), residues: 815
  sheet: -1.31 (0.61), residues: 73
  loop : -1.34 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F 156 
 HIS   0.006   0.001   HIS D 288 
 PHE   0.015   0.001   PHE D 290 
 TYR   0.018   0.001   TYR A 237 
 ARG   0.005   0.000   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03827 (  631)
  hydrogen bonds       : angle       4.01856 ( 1866)
  covalent geometry    : bond        0.00297 (10129)
  covalent geometry    : angle       0.63052 (13738)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 202
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 ASN cc_start: 0.8635 (t0) cc_final: 0.8205 (t0)
REVERT: A  204 ASN cc_start: 0.7535 (t0) cc_final: 0.6922 (t0)
REVERT: A  212 GLU cc_start: 0.7823 (tt0) cc_final: 0.7365 (mt-10)
REVERT: A  244 MET cc_start: 0.7730 (ttp) cc_final: 0.7246 (ttp)
REVERT: C   30 ARG cc_start: 0.6914 (ttm-80) cc_final: 0.6537 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8268 (mtmp) cc_final: 0.8000 (mttp)
REVERT: C   46 GLU cc_start: 0.7873 (tp30) cc_final: 0.7578 (tp30)
REVERT: D  222 LEU cc_start: 0.7783 (tp) cc_final: 0.7453 (mm)
REVERT: E  150 GLN cc_start: 0.7100 (tt0) cc_final: 0.6863 (tm-30)
REVERT: F   71 GLN cc_start: 0.8280 (mt0) cc_final: 0.7814 (tm-30)
REVERT: F  124 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7578 (tm-30)
REVERT: F  152 LYS cc_start: 0.8588 (tppt) cc_final: 0.8269 (tptt)
  outliers start: 50
  outliers final: 28
  residues processed: 238
  average time/residue: 0.1826
  time to fit residues: 63.6051
Evaluate side-chains
  205 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 177
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  272 SER
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  419 LEU
Chi-restraints excluded: chain D residue  425 ILE
Chi-restraints excluded: chain D residue  497 VAL
Chi-restraints excluded: chain D residue  543 ASP
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  160 VAL
Chi-restraints excluded: chain F residue  181 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 50 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 390 HIS
** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 539 ASN
** E  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.116881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.101582 restraints weight = 18787.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.103647 restraints weight = 11593.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.105065 restraints weight = 8099.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10129  Z= 0.174
  Angle     :  0.661  15.709  13738  Z= 0.319
  Chirality :  0.041   0.196   1643
  Planarity :  0.004   0.041   1703
  Dihedral  :  4.271  20.480   1363
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 19.67 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.24), residues: 1264
  helix:  1.56 (0.18), residues: 815
  sheet: -1.31 (0.61), residues: 74
  loop : -1.30 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A  35 
 HIS   0.005   0.001   HIS D 288 
 PHE   0.029   0.002   PHE F  62 
 TYR   0.020   0.001   TYR F 190 
 ARG   0.005   0.000   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03960 (  631)
  hydrogen bonds       : angle       4.01801 ( 1866)
  covalent geometry    : bond        0.00404 (10129)
  covalent geometry    : angle       0.66100 (13738)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 194
  time to evaluate  : 1.169 
Fit side-chains
REVERT: A  100 LEU cc_start: 0.8290 (mp) cc_final: 0.7829 (tt)
REVERT: A  188 ASN cc_start: 0.8647 (t0) cc_final: 0.8104 (t0)
REVERT: A  204 ASN cc_start: 0.7640 (t0) cc_final: 0.7037 (t0)
REVERT: A  212 GLU cc_start: 0.7746 (tt0) cc_final: 0.7301 (mt-10)
REVERT: A  244 MET cc_start: 0.7849 (ttp) cc_final: 0.7443 (ttp)
REVERT: A  376 PHE cc_start: 0.7534 (m-80) cc_final: 0.6878 (m-10)
REVERT: C   30 ARG cc_start: 0.6898 (ttm-80) cc_final: 0.6536 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8311 (mtmp) cc_final: 0.8009 (mttp)
REVERT: D  222 LEU cc_start: 0.7866 (tp) cc_final: 0.7498 (mm)
REVERT: E  150 GLN cc_start: 0.7179 (tt0) cc_final: 0.6866 (tm-30)
REVERT: E  165 MET cc_start: 0.6697 (tpp) cc_final: 0.6459 (tpt)
REVERT: F   71 GLN cc_start: 0.8236 (mt0) cc_final: 0.7769 (tm-30)
REVERT: F  107 PHE cc_start: 0.8185 (t80) cc_final: 0.7919 (t80)
REVERT: F  124 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7606 (tm-30)
REVERT: F  152 LYS cc_start: 0.8770 (tppt) cc_final: 0.8383 (tptt)
  outliers start: 57
  outliers final: 48
  residues processed: 236
  average time/residue: 0.1914
  time to fit residues: 66.2150
Evaluate side-chains
  218 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 170
  time to evaluate  : 1.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  100 TRP
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  272 SER
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  337 LEU
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  419 LEU
Chi-restraints excluded: chain D residue  425 ILE
Chi-restraints excluded: chain D residue  430 ILE
Chi-restraints excluded: chain D residue  456 LEU
Chi-restraints excluded: chain D residue  497 VAL
Chi-restraints excluded: chain D residue  514 CYS
Chi-restraints excluded: chain D residue  543 ASP
Chi-restraints excluded: chain D residue  594 SER
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  123 ASN
Chi-restraints excluded: chain E residue  160 VAL
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain F residue   13 ILE
Chi-restraints excluded: chain F residue  113 ILE
Chi-restraints excluded: chain F residue  162 THR
Chi-restraints excluded: chain F residue  181 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 122 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 93 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.114633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.099347 restraints weight = 18831.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.101339 restraints weight = 11511.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.102770 restraints weight = 8130.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.3901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  10129  Z= 0.202
  Angle     :  0.705  14.527  13738  Z= 0.339
  Chirality :  0.043   0.207   1643
  Planarity :  0.004   0.041   1703
  Dihedral  :  4.288  20.133   1363
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 20.63 %
    Favored  : 73.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.24), residues: 1264
  helix:  1.55 (0.18), residues: 815
  sheet: -1.21 (0.62), residues: 74
  loop : -1.27 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A  35 
 HIS   0.004   0.001   HIS D 288 
 PHE   0.016   0.002   PHE D  74 
 TYR   0.021   0.002   TYR F 190 
 ARG   0.005   0.000   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04062 (  631)
  hydrogen bonds       : angle       4.05604 ( 1866)
  covalent geometry    : bond        0.00474 (10129)
  covalent geometry    : angle       0.70465 (13738)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 182
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 LEU cc_start: 0.8355 (mp) cc_final: 0.7897 (tt)
REVERT: A  188 ASN cc_start: 0.8645 (t0) cc_final: 0.7990 (t0)
REVERT: A  204 ASN cc_start: 0.7702 (t0) cc_final: 0.6951 (t0)
REVERT: A  212 GLU cc_start: 0.7861 (tt0) cc_final: 0.7444 (mt-10)
REVERT: A  244 MET cc_start: 0.7881 (ttp) cc_final: 0.7469 (ttp)
REVERT: A  376 PHE cc_start: 0.7624 (m-80) cc_final: 0.6886 (m-10)
REVERT: C   30 ARG cc_start: 0.6876 (ttm-80) cc_final: 0.6551 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8339 (mtmp) cc_final: 0.8009 (mttp)
REVERT: D  336 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8753 (tp)
REVERT: E  150 GLN cc_start: 0.7235 (tt0) cc_final: 0.6960 (tm-30)
REVERT: F   71 GLN cc_start: 0.8313 (mt0) cc_final: 0.7810 (tm-30)
REVERT: F  124 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7655 (tm-30)
REVERT: F  151 LEU cc_start: 0.9084 (mm) cc_final: 0.8882 (mt)
REVERT: F  152 LYS cc_start: 0.8829 (tppt) cc_final: 0.8450 (tmtt)
  outliers start: 58
  outliers final: 48
  residues processed: 224
  average time/residue: 0.1897
  time to fit residues: 62.6537
Evaluate side-chains
  213 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 164
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  100 TRP
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  272 SER
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  336 LEU
Chi-restraints excluded: chain D residue  337 LEU
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  419 LEU
Chi-restraints excluded: chain D residue  425 ILE
Chi-restraints excluded: chain D residue  456 LEU
Chi-restraints excluded: chain D residue  497 VAL
Chi-restraints excluded: chain D residue  514 CYS
Chi-restraints excluded: chain D residue  543 ASP
Chi-restraints excluded: chain D residue  594 SER
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  123 ASN
Chi-restraints excluded: chain E residue  160 VAL
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain F residue   13 ILE
Chi-restraints excluded: chain F residue   67 LYS
Chi-restraints excluded: chain F residue  113 ILE
Chi-restraints excluded: chain F residue  162 THR
Chi-restraints excluded: chain F residue  181 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 119 optimal weight:    0.8980
   chunk 111 optimal weight:    3.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 192 GLN
A 220 HIS
** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 539 ASN
** E  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.115993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.101284 restraints weight = 18973.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.103052 restraints weight = 12443.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.104731 restraints weight = 8047.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.4044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10129  Z= 0.158
  Angle     :  0.690  13.768  13738  Z= 0.327
  Chirality :  0.041   0.223   1643
  Planarity :  0.004   0.042   1703
  Dihedral  :  4.229  19.528   1363
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 22.17 %
    Favored  : 72.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.24), residues: 1264
  helix:  1.62 (0.18), residues: 816
  sheet: -1.14 (0.64), residues: 74
  loop : -1.28 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A  35 
 HIS   0.004   0.001   HIS D 288 
 PHE   0.012   0.001   PHE F  98 
 TYR   0.017   0.001   TYR F 190 
 ARG   0.005   0.000   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03898 (  631)
  hydrogen bonds       : angle       3.95476 ( 1866)
  covalent geometry    : bond        0.00370 (10129)
  covalent geometry    : angle       0.69012 (13738)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 175
  time to evaluate  : 1.141 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 LEU cc_start: 0.8106 (mp) cc_final: 0.7721 (tt)
REVERT: A  204 ASN cc_start: 0.7677 (t0) cc_final: 0.6921 (t0)
REVERT: A  212 GLU cc_start: 0.7798 (tt0) cc_final: 0.7386 (mt-10)
REVERT: A  244 MET cc_start: 0.7760 (ttp) cc_final: 0.7393 (ttp)
REVERT: A  376 PHE cc_start: 0.7531 (m-80) cc_final: 0.6855 (m-10)
REVERT: C   30 ARG cc_start: 0.6828 (ttm-80) cc_final: 0.6519 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8292 (mtmp) cc_final: 0.8035 (mttp)
REVERT: D  336 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8735 (tp)
REVERT: F   71 GLN cc_start: 0.8287 (mt0) cc_final: 0.7784 (tm-30)
REVERT: F  124 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7813 (tm-30)
REVERT: F  151 LEU cc_start: 0.9084 (mm) cc_final: 0.8814 (mt)
REVERT: F  152 LYS cc_start: 0.8779 (tppt) cc_final: 0.8331 (tptt)
  outliers start: 51
  outliers final: 45
  residues processed: 211
  average time/residue: 0.1947
  time to fit residues: 60.1716
Evaluate side-chains
  212 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 166
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  100 TRP
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  272 SER
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  336 LEU
Chi-restraints excluded: chain D residue  337 LEU
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  419 LEU
Chi-restraints excluded: chain D residue  425 ILE
Chi-restraints excluded: chain D residue  456 LEU
Chi-restraints excluded: chain D residue  497 VAL
Chi-restraints excluded: chain D residue  514 CYS
Chi-restraints excluded: chain D residue  543 ASP
Chi-restraints excluded: chain D residue  594 SER
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  160 VAL
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain F residue   67 LYS
Chi-restraints excluded: chain F residue  113 ILE
Chi-restraints excluded: chain F residue  162 THR
Chi-restraints excluded: chain F residue  181 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 99 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9990
   chunk 122 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 539 ASN
** F  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.117619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.102229 restraints weight = 18763.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.104366 restraints weight = 11469.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.105803 restraints weight = 8052.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10129  Z= 0.152
  Angle     :  0.693  13.459  13738  Z= 0.328
  Chirality :  0.041   0.241   1643
  Planarity :  0.004   0.040   1703
  Dihedral  :  4.195  19.417   1363
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 22.36 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.24), residues: 1264
  helix:  1.69 (0.18), residues: 816
  sheet: -1.15 (0.65), residues: 74
  loop : -1.21 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  35 
 HIS   0.004   0.001   HIS D 288 
 PHE   0.012   0.001   PHE F  98 
 TYR   0.018   0.001   TYR F 190 
 ARG   0.007   0.000   ARG F 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03831 (  631)
  hydrogen bonds       : angle       3.92382 ( 1866)
  covalent geometry    : bond        0.00356 (10129)
  covalent geometry    : angle       0.69290 (13738)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 175
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 LEU cc_start: 0.8247 (mp) cc_final: 0.7788 (tt)
REVERT: A  204 ASN cc_start: 0.7668 (t0) cc_final: 0.6920 (t0)
REVERT: A  244 MET cc_start: 0.7765 (ttp) cc_final: 0.7423 (ttp)
REVERT: A  376 PHE cc_start: 0.7417 (m-80) cc_final: 0.6819 (m-10)
REVERT: C   30 ARG cc_start: 0.6924 (ttm-80) cc_final: 0.6602 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8284 (mtmp) cc_final: 0.7996 (mttp)
REVERT: C   40 LYS cc_start: 0.7829 (tmtt) cc_final: 0.7270 (tmtt)
REVERT: D  336 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8725 (tp)
REVERT: F   71 GLN cc_start: 0.8171 (mt0) cc_final: 0.7671 (tm-30)
REVERT: F  102 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8555 (tt)
REVERT: F  124 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7879 (tm-30)
REVERT: F  151 LEU cc_start: 0.9042 (mm) cc_final: 0.8799 (mt)
REVERT: F  152 LYS cc_start: 0.8762 (tppt) cc_final: 0.8281 (tptt)
  outliers start: 58
  outliers final: 48
  residues processed: 218
  average time/residue: 0.2313
  time to fit residues: 69.9693
Evaluate side-chains
  214 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 164
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue   14 TRP
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  100 TRP
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  272 SER
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  336 LEU
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  419 LEU
Chi-restraints excluded: chain D residue  425 ILE
Chi-restraints excluded: chain D residue  456 LEU
Chi-restraints excluded: chain D residue  497 VAL
Chi-restraints excluded: chain D residue  514 CYS
Chi-restraints excluded: chain D residue  543 ASP
Chi-restraints excluded: chain D residue  594 SER
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  160 VAL
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain F residue   67 LYS
Chi-restraints excluded: chain F residue  102 LEU
Chi-restraints excluded: chain F residue  113 ILE
Chi-restraints excluded: chain F residue  162 THR
Chi-restraints excluded: chain F residue  181 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 85 optimal weight:    0.8980
   chunk 108 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 113 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0010
   overall best weight:    0.8988

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

Flipped N/Q/H residues before XYZ refinement:
** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 539 ASN
** E  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.117601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.102915 restraints weight = 18700.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.104607 restraints weight = 12221.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.106425 restraints weight = 8044.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.4345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10129  Z= 0.153
  Angle     :  0.703  13.256  13738  Z= 0.332
  Chirality :  0.041   0.246   1643
  Planarity :  0.004   0.040   1703
  Dihedral  :  4.152  19.024   1363
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 22.55 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.24), residues: 1264
  helix:  1.77 (0.18), residues: 814
  sheet: -1.23 (0.59), residues: 84
  loop : -1.19 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP F  95 
 HIS   0.004   0.001   HIS D 288 
 PHE   0.011   0.001   PHE D 586 
 TYR   0.017   0.001   TYR F 190 
 ARG   0.009   0.001   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  631)
  hydrogen bonds       : angle       3.89560 ( 1866)
  covalent geometry    : bond        0.00358 (10129)
  covalent geometry    : angle       0.70341 (13738)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 167
  time to evaluate  : 1.105 
Fit side-chains
REVERT: A  192 GLN cc_start: 0.8505 (tp40) cc_final: 0.8017 (tp-100)
REVERT: A  204 ASN cc_start: 0.7673 (t0) cc_final: 0.7077 (t0)
REVERT: A  244 MET cc_start: 0.7760 (ttp) cc_final: 0.7426 (ttp)
REVERT: A  376 PHE cc_start: 0.7397 (m-80) cc_final: 0.6846 (m-10)
REVERT: C   30 ARG cc_start: 0.6845 (ttm-80) cc_final: 0.6514 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8299 (mtmp) cc_final: 0.8018 (mttp)
REVERT: D  336 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8420 (tt)
REVERT: F   71 GLN cc_start: 0.8231 (mt0) cc_final: 0.7820 (tm-30)
REVERT: F  124 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7834 (tm-30)
REVERT: F  152 LYS cc_start: 0.8677 (tppt) cc_final: 0.8297 (tptt)
REVERT: F  177 ARG cc_start: 0.8915 (mtp85) cc_final: 0.8617 (mtt-85)
  outliers start: 55
  outliers final: 48
  residues processed: 207
  average time/residue: 0.1935
  time to fit residues: 58.8812
Evaluate side-chains
  213 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 164
  time to evaluate  : 1.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue   14 TRP
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  100 TRP
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  272 SER
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  336 LEU
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  419 LEU
Chi-restraints excluded: chain D residue  425 ILE
Chi-restraints excluded: chain D residue  456 LEU
Chi-restraints excluded: chain D residue  497 VAL
Chi-restraints excluded: chain D residue  514 CYS
Chi-restraints excluded: chain D residue  543 ASP
Chi-restraints excluded: chain D residue  594 SER
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  160 VAL
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain F residue  113 ILE
Chi-restraints excluded: chain F residue  162 THR
Chi-restraints excluded: chain F residue  181 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 123 optimal weight:    2.9990
   chunk 120 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 107 optimal weight:    0.7980
   chunk 116 optimal weight:    0.6980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN
** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 539 ASN
E 123 ASN
** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.120519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.106293 restraints weight = 18486.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.107758 restraints weight = 11771.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.109281 restraints weight = 7940.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.4392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  10129  Z= 0.145
  Angle     :  0.712  13.121  13738  Z= 0.336
  Chirality :  0.041   0.248   1643
  Planarity :  0.004   0.040   1703
  Dihedral  :  4.148  21.812   1363
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 23.61 %
    Favored  : 71.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.24), residues: 1264
  helix:  1.81 (0.18), residues: 815
  sheet: -1.22 (0.60), residues: 84
  loop : -1.18 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP F  95 
 HIS   0.010   0.001   HIS F 106 
 PHE   0.026   0.001   PHE F  98 
 TYR   0.015   0.001   TYR F 190 
 ARG   0.011   0.001   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03766 (  631)
  hydrogen bonds       : angle       3.89179 ( 1866)
  covalent geometry    : bond        0.00339 (10129)
  covalent geometry    : angle       0.71166 (13738)

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

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

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2528 Ramachandran restraints generated.
    1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 176
  time to evaluate  : 1.187 
Fit side-chains
REVERT: A  192 GLN cc_start: 0.8431 (tp-100) cc_final: 0.7708 (tp-100)
REVERT: A  204 ASN cc_start: 0.7678 (t0) cc_final: 0.7079 (t0)
REVERT: A  212 GLU cc_start: 0.7809 (tt0) cc_final: 0.7431 (mt-10)
REVERT: A  244 MET cc_start: 0.7727 (ttp) cc_final: 0.7386 (ttp)
REVERT: A  376 PHE cc_start: 0.7488 (m-80) cc_final: 0.6898 (m-10)
REVERT: C   30 ARG cc_start: 0.6848 (ttm-80) cc_final: 0.6528 (mmm-85)
REVERT: D   57 GLU cc_start: 0.8448 (mp0) cc_final: 0.8229 (mp0)
REVERT: D  336 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8419 (tt)
REVERT: E  165 MET cc_start: 0.6708 (tpp) cc_final: 0.6434 (tpt)
REVERT: F   67 LYS cc_start: 0.8322 (mtmm) cc_final: 0.8115 (ptpp)
REVERT: F   71 GLN cc_start: 0.8220 (mt0) cc_final: 0.7820 (tm-30)
REVERT: F  124 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7894 (tm-30)
REVERT: F  152 LYS cc_start: 0.8657 (tppt) cc_final: 0.8193 (tptt)
REVERT: F  177 ARG cc_start: 0.8923 (mtp85) cc_final: 0.8613 (mtt-85)
  outliers start: 52
  outliers final: 48
  residues processed: 213
  average time/residue: 0.2086
  time to fit residues: 65.0622
Evaluate side-chains
  215 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 166
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  121 CYS
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue   14 TRP
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  100 TRP
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  272 SER
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  314 ASP
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  336 LEU
Chi-restraints excluded: chain D residue  366 THR
Chi-restraints excluded: chain D residue  419 LEU
Chi-restraints excluded: chain D residue  425 ILE
Chi-restraints excluded: chain D residue  456 LEU
Chi-restraints excluded: chain D residue  497 VAL
Chi-restraints excluded: chain D residue  514 CYS
Chi-restraints excluded: chain D residue  543 ASP
Chi-restraints excluded: chain D residue  594 SER
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  160 VAL
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain F residue  113 ILE
Chi-restraints excluded: chain F residue  162 THR
Chi-restraints excluded: chain F residue  181 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 90 optimal weight:    0.0170
   chunk 1 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 27 optimal weight:    9.9990
   chunk 58 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0970
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.6016

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

Flipped N/Q/H residues before XYZ refinement:
** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 539 ASN
** E  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 123 ASN
** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.119693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.105211 restraints weight = 18561.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.106837 restraints weight = 12090.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.108548 restraints weight = 8031.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.4475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10129  Z= 0.139
  Angle     :  0.717  12.931  13738  Z= 0.336
  Chirality :  0.041   0.240   1643
  Planarity :  0.004   0.040   1703
  Dihedral  :  4.096  21.679   1363
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 23.90 %
    Favored  : 71.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.24), residues: 1264
  helix:  1.85 (0.18), residues: 817
  sheet: -1.18 (0.60), residues: 84
  loop : -1.17 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP F  95 
 HIS   0.006   0.001   HIS F 106 
 PHE   0.021   0.001   PHE F  98 
 TYR   0.015   0.001   TYR E 121 
 ARG   0.010   0.001   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03710 (  631)
  hydrogen bonds       : angle       3.84805 ( 1866)
  covalent geometry    : bond        0.00322 (10129)
  covalent geometry    : angle       0.71652 (13738)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3395.11 seconds
wall clock time: 60 minutes 10.19 seconds (3610.19 seconds total)