Starting phenix.real_space_refine
on Fri Feb 14 06:49:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6n3q_0336/02_2025/6n3q_0336.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6n3q_0336/02_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_0336/02_2025/6n3q_0336.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6n3q_0336/02_2025/6n3q_0336.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6n3q_0336/02_2025/6n3q_0336.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6n3q_0336/02_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-5592/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: 5.81, per 1000 atoms: 0.59
  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: 2.25
  Conformation dependent library (CDL) restraints added in 1.2 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: 0.91
  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: 2.80

  Time building geometry restraints manager: 2.65 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:             0.700
  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:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.420
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.590
-------------------------------------------------------------------------------
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= 0.359
  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 

*********************** 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  : 1.091 
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: 0.2424
  time to fit residues: 112.6706
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  : 1.120 
-------------------------------------------------------------------------------
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 = 0.135385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.119270 restraints weight = 19075.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.122078 restraints weight = 9729.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.123714 restraints weight = 6112.544|
|-----------------------------------------------------------------------------|
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= 0.212
  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 

*********************** 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  : 1.120 
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: 0.8434 (mt) cc_final: 0.8228 (tt)
REVERT: A  162 LEU cc_start: 0.9330 (tm) cc_final: 0.9100 (tp)
REVERT: A  168 ASP cc_start: 0.8570 (t0) cc_final: 0.8091 (t0)
REVERT: A  188 ASN cc_start: 0.8698 (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: 0.8603 (m) cc_final: 0.8373 (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: 0.6540 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8394 (mtmp) cc_final: 0.8077 (mttp)
REVERT: C   52 LYS cc_start: 0.7870 (ttmt) cc_final: 0.7522 (ttmt)
REVERT: C   66 TYR cc_start: 0.8476 (t80) cc_final: 0.7654 (t80)
REVERT: D  222 LEU cc_start: 0.8077 (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: 0.7237 (tt0) cc_final: 0.6907 (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: 0.8637 (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: 0.7682 (mtt)
REVERT: F  124 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7712 (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: 0.1972
  time to fit residues: 74.8069
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  : 1.242 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 50 optimal weight:    7.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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**
E  98 ASN
** 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 = 0.3812 r_free = 0.3812 target = 0.130136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.111289 restraints weight = 20038.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.114110 restraints weight = 10593.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.115981 restraints weight = 6842.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.3100

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= 0.245
  Angle     :  0.657   9.954  13738  Z= 0.326
  Chirality :  0.042   0.189   1643
  Planarity :  0.004   0.045   1703
  Dihedral  :  4.629  20.769   1363
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 16.03 %
    Favored  : 78.41 %
  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:  0.11 (0.23), residues: 1264
  helix:  0.97 (0.18), residues: 817
  sheet: -1.50 (0.63), residues: 69
  loop : -1.52 (0.31), residues: 378

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   0.021   0.002   TYR A 237 
 ARG   0.006   0.001   ARG F  90 

*********************** 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
  264 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 206
  time to evaluate  : 1.121 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 TRP cc_start: 0.8548 (m100) cc_final: 0.8318 (m100)
REVERT: A  188 ASN cc_start: 0.8804 (t0) cc_final: 0.8317 (t0)
REVERT: A  204 ASN cc_start: 0.7852 (t0) cc_final: 0.7340 (t0)
REVERT: A  212 GLU cc_start: 0.7878 (tt0) cc_final: 0.7360 (mt-10)
REVERT: A  244 MET cc_start: 0.7872 (ttp) cc_final: 0.7397 (ttp)
REVERT: A  447 SER cc_start: 0.8855 (m) cc_final: 0.8183 (p)
REVERT: C   30 ARG cc_start: 0.7076 (ttm-80) cc_final: 0.6576 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8409 (mtmp) cc_final: 0.8063 (mttp)
REVERT: C   46 GLU cc_start: 0.8252 (tp30) cc_final: 0.8046 (tp30)
REVERT: C   52 LYS cc_start: 0.7831 (ttmt) cc_final: 0.7618 (ttmt)
REVERT: D  222 LEU cc_start: 0.8044 (tp) cc_final: 0.7610 (mm)
REVERT: E  129 ASP cc_start: 0.8353 (p0) cc_final: 0.8145 (p0)
REVERT: E  130 TYR cc_start: 0.8733 (t80) cc_final: 0.8488 (t80)
REVERT: E  150 GLN cc_start: 0.7292 (tt0) cc_final: 0.6859 (tm-30)
REVERT: F   49 GLN cc_start: 0.8786 (pp30) cc_final: 0.8586 (pp30)
REVERT: F   71 GLN cc_start: 0.8551 (mt0) cc_final: 0.7832 (tm-30)
REVERT: F  124 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7644 (tm-30)
REVERT: F  152 LYS cc_start: 0.8849 (tppt) cc_final: 0.8312 (tptt)
  outliers start: 58
  outliers final: 39
  residues processed: 247
  average time/residue: 0.1945
  time to fit residues: 69.9129
Evaluate side-chains
  218 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 179
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
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  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:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 104 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 204 ASN
** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 520 GLN ** 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 = 0.3548 r_free = 0.3548 target = 0.116869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.102610 restraints weight = 18569.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.104106 restraints weight = 11783.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.105833 restraints weight = 7987.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10129  Z= 0.248
  Angle     :  0.661  10.670  13738  Z= 0.319
  Chirality :  0.041   0.196   1643
  Planarity :  0.004   0.042   1703
  Dihedral  :  4.404  20.955   1363
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  6.24 %
    Allowed  : 17.56 %
    Favored  : 76.20 %
  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:  0.59 (0.24), residues: 1264
  helix:  1.36 (0.18), residues: 813
  sheet: -1.45 (0.63), residues: 69
  loop : -1.35 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F 156 
 HIS   0.005   0.001   HIS D 288 
 PHE   0.016   0.002   PHE D 290 
 TYR   0.020   0.002   TYR A 237 
 ARG   0.005   0.001   ARG F 154 

*********************** 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
  264 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 199
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 LEU cc_start: 0.9005 (tp) cc_final: 0.8790 (tt)
REVERT: A  188 ASN cc_start: 0.8632 (t0) cc_final: 0.8194 (t0)
REVERT: A  204 ASN cc_start: 0.7486 (OUTLIER) cc_final: 0.7003 (t0)
REVERT: A  212 GLU cc_start: 0.7738 (tt0) cc_final: 0.7309 (mt-10)
REVERT: A  244 MET cc_start: 0.7837 (ttp) cc_final: 0.7335 (ttp)
REVERT: A  376 PHE cc_start: 0.7475 (m-80) cc_final: 0.6746 (m-10)
REVERT: C   30 ARG cc_start: 0.6849 (ttm-80) cc_final: 0.6497 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8283 (mtmp) cc_final: 0.8000 (mttp)
REVERT: C   46 GLU cc_start: 0.7873 (tp30) cc_final: 0.7560 (tp30)
REVERT: D  222 LEU cc_start: 0.7797 (tp) cc_final: 0.7458 (mm)
REVERT: E  129 ASP cc_start: 0.8094 (p0) cc_final: 0.7822 (p0)
REVERT: E  150 GLN cc_start: 0.7141 (tt0) cc_final: 0.6864 (tm-30)
REVERT: F   71 GLN cc_start: 0.8226 (mt0) cc_final: 0.7770 (tm-30)
REVERT: F  137 LEU cc_start: 0.7320 (tt) cc_final: 0.7020 (tp)
REVERT: F  151 LEU cc_start: 0.8920 (mm) cc_final: 0.8691 (mt)
REVERT: F  152 LYS cc_start: 0.8755 (tppt) cc_final: 0.8279 (tptt)
  outliers start: 65
  outliers final: 40
  residues processed: 247
  average time/residue: 0.1905
  time to fit residues: 68.4783
Evaluate side-chains
  215 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 174
  time to evaluate  : 1.985 
-------------------------------------------------------------------------------
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  133 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  204 ASN
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  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  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  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  543 ASP
Chi-restraints excluded: chain D residue  594 SER
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  110 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 110 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.9580

-------------------------------------------------------------------------------
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 156 GLN
** 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
** F  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.116782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.101580 restraints weight = 18813.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.103606 restraints weight = 11498.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.104885 restraints weight = 8121.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.3705

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= 0.230
  Angle     :  0.657  14.809  13738  Z= 0.314
  Chirality :  0.041   0.203   1643
  Planarity :  0.004   0.040   1703
  Dihedral  :  4.281  19.717   1363
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 20.25 %
    Favored  : 74.76 %
  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:  0.80 (0.24), residues: 1264
  helix:  1.53 (0.18), residues: 815
  sheet: -1.35 (0.61), residues: 73
  loop : -1.29 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  35 
 HIS   0.005   0.001   HIS D 288 
 PHE   0.012   0.001   PHE D 290 
 TYR   0.017   0.001   TYR F 190 
 ARG   0.005   0.000   ARG F  90 

*********************** 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
  253 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 201
  time to evaluate  : 1.233 
Fit side-chains
REVERT: A   41 LEU cc_start: 0.8981 (tp) cc_final: 0.8772 (tt)
REVERT: A  100 LEU cc_start: 0.8341 (mp) cc_final: 0.7894 (tt)
REVERT: A  188 ASN cc_start: 0.8628 (t0) cc_final: 0.8082 (t0)
REVERT: A  204 ASN cc_start: 0.7105 (t0) cc_final: 0.6779 (t0)
REVERT: A  212 GLU cc_start: 0.7767 (tt0) cc_final: 0.7349 (mt-10)
REVERT: A  244 MET cc_start: 0.7810 (ttp) cc_final: 0.7413 (ttp)
REVERT: A  376 PHE cc_start: 0.7591 (m-80) cc_final: 0.6850 (m-10)
REVERT: C   30 ARG cc_start: 0.6915 (ttm-80) cc_final: 0.6550 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8318 (mtmp) cc_final: 0.8015 (mttp)
REVERT: D  222 LEU cc_start: 0.7843 (tp) cc_final: 0.7490 (mm)
REVERT: E  129 ASP cc_start: 0.8188 (p0) cc_final: 0.7882 (p0)
REVERT: E  150 GLN cc_start: 0.7165 (tt0) cc_final: 0.6890 (tm-30)
REVERT: E  165 MET cc_start: 0.6672 (tpp) cc_final: 0.6439 (tpt)
REVERT: F   62 PHE cc_start: 0.8132 (t80) cc_final: 0.7803 (t80)
REVERT: F   71 GLN cc_start: 0.8270 (mt0) cc_final: 0.7776 (tm-30)
REVERT: F  107 PHE cc_start: 0.8163 (t80) cc_final: 0.7843 (t80)
REVERT: F  124 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7671 (tm-30)
REVERT: F  152 LYS cc_start: 0.8710 (tppt) cc_final: 0.8243 (tptt)
  outliers start: 52
  outliers final: 44
  residues processed: 238
  average time/residue: 0.1936
  time to fit residues: 67.4840
Evaluate side-chains
  223 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 179
  time to evaluate  : 1.260 
-------------------------------------------------------------------------------
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 D residue   31 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  543 ASP
Chi-restraints excluded: chain D residue  594 SER
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  110 LEU
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  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:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 93 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.3588

-------------------------------------------------------------------------------
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 ** 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 173 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 = 0.3520 r_free = 0.3520 target = 0.115003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.099698 restraints weight = 18850.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.101714 restraints weight = 11595.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.103072 restraints weight = 8184.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.3904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10129  Z= 0.284
  Angle     :  0.695  13.946  13738  Z= 0.335
  Chirality :  0.042   0.211   1643
  Planarity :  0.004   0.040   1703
  Dihedral  :  4.285  20.476   1363
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 20.83 %
    Favored  : 73.13 %
  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:  0.85 (0.24), residues: 1264
  helix:  1.56 (0.18), residues: 814
  sheet: -1.25 (0.62), residues: 74
  loop : -1.24 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A  35 
 HIS   0.005   0.001   HIS D 288 
 PHE   0.017   0.002   PHE D 435 
 TYR   0.021   0.002   TYR F 190 
 ARG   0.006   0.000   ARG F  90 

*********************** 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
  254 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 191
  time to evaluate  : 1.065 
Fit side-chains
REVERT: A   41 LEU cc_start: 0.9002 (tp) cc_final: 0.8763 (tt)
REVERT: A  100 LEU cc_start: 0.8306 (mp) cc_final: 0.7873 (tt)
REVERT: A  188 ASN cc_start: 0.8635 (t0) cc_final: 0.8010 (t0)
REVERT: A  192 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8362 (tp40)
REVERT: A  204 ASN cc_start: 0.7504 (t0) cc_final: 0.6993 (t0)
REVERT: A  212 GLU cc_start: 0.7864 (tt0) cc_final: 0.7394 (mt-10)
REVERT: A  244 MET cc_start: 0.7855 (ttp) cc_final: 0.7452 (ttp)
REVERT: A  376 PHE cc_start: 0.7633 (m-80) cc_final: 0.6867 (m-10)
REVERT: C   30 ARG cc_start: 0.6888 (ttm-80) cc_final: 0.6564 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8344 (mtmp) cc_final: 0.8028 (mttp)
REVERT: C   40 LYS cc_start: 0.7795 (tmtt) cc_final: 0.7267 (tmtt)
REVERT: D  336 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8741 (tp)
REVERT: E  129 ASP cc_start: 0.8226 (p0) cc_final: 0.7900 (p0)
REVERT: E  150 GLN cc_start: 0.7220 (tt0) cc_final: 0.6956 (tm-30)
REVERT: F   25 GLU cc_start: 0.8675 (tp30) cc_final: 0.8451 (tp30)
REVERT: F   71 GLN cc_start: 0.8284 (mt0) cc_final: 0.7810 (tm-30)
REVERT: F  107 PHE cc_start: 0.8213 (t80) cc_final: 0.7921 (t80)
REVERT: F  124 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7678 (tm-30)
REVERT: F  152 LYS cc_start: 0.8772 (tppt) cc_final: 0.8295 (tptt)
  outliers start: 63
  outliers final: 50
  residues processed: 238
  average time/residue: 0.2245
  time to fit residues: 75.2053
Evaluate side-chains
  217 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 165
  time to evaluate  : 2.063 
-------------------------------------------------------------------------------
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  192 GLN
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 A residue  441 THR
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  543 ASP
Chi-restraints excluded: chain D residue  594 SER
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 120 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 119 optimal weight:    0.7980
   chunk 111 optimal weight:    3.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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
** 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 173 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 = 0.3547 r_free = 0.3547 target = 0.116892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.102330 restraints weight = 18987.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.104029 restraints weight = 12130.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.105804 restraints weight = 8045.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.4095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10129  Z= 0.223
  Angle     :  0.682  13.413  13738  Z= 0.324
  Chirality :  0.041   0.232   1643
  Planarity :  0.004   0.040   1703
  Dihedral  :  4.204  19.494   1363
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 21.98 %
    Favored  : 72.36 %
  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:  0.97 (0.24), residues: 1264
  helix:  1.67 (0.18), residues: 813
  sheet: -1.22 (0.63), residues: 74
  loop : -1.23 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   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   0.008   0.001   ARG A 264 

*********************** 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
  242 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 183
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 LEU cc_start: 0.8171 (mp) cc_final: 0.7787 (tt)
REVERT: A  192 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8143 (tp-100)
REVERT: A  204 ASN cc_start: 0.7432 (t0) cc_final: 0.6901 (t0)
REVERT: A  212 GLU cc_start: 0.7734 (tt0) cc_final: 0.7344 (mt-10)
REVERT: A  244 MET cc_start: 0.7770 (ttp) cc_final: 0.7406 (ttp)
REVERT: A  376 PHE cc_start: 0.7563 (m-80) cc_final: 0.6850 (m-10)
REVERT: C   30 ARG cc_start: 0.6954 (ttm-80) cc_final: 0.6612 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8388 (mtmp) cc_final: 0.8058 (mttp)
REVERT: D  336 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8742 (tp)
REVERT: E  129 ASP cc_start: 0.8139 (p0) cc_final: 0.7817 (p0)
REVERT: E  150 GLN cc_start: 0.7153 (tt0) cc_final: 0.6916 (tm-30)
REVERT: F   71 GLN cc_start: 0.8405 (mt0) cc_final: 0.7814 (tm-30)
REVERT: F  107 PHE cc_start: 0.8171 (t80) cc_final: 0.7951 (t80)
REVERT: F  124 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7538 (tm-30)
REVERT: F  152 LYS cc_start: 0.8711 (tppt) cc_final: 0.8320 (tptt)
  outliers start: 59
  outliers final: 51
  residues processed: 223
  average time/residue: 0.1932
  time to fit residues: 63.1981
Evaluate side-chains
  222 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 169
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
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  192 GLN
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   31 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  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  517 VAL
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  110 LEU
Chi-restraints excluded: chain E residue  149 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  115 LEU
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:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 122 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A  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
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.116934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.101798 restraints weight = 18846.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.103862 restraints weight = 11393.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.105095 restraints weight = 8001.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.4219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10129  Z= 0.230
  Angle     :  0.697  13.057  13738  Z= 0.330
  Chirality :  0.041   0.237   1643
  Planarity :  0.004   0.039   1703
  Dihedral  :  4.182  19.975   1363
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 22.55 %
    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:  1.04 (0.24), residues: 1264
  helix:  1.72 (0.18), residues: 813
  sheet: -1.24 (0.63), residues: 74
  loop : -1.18 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A  35 
 HIS   0.004   0.001   HIS D 288 
 PHE   0.011   0.001   PHE F  98 
 TYR   0.018   0.001   TYR F 190 
 ARG   0.009   0.001   ARG A 264 

*********************** 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
  234 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 171
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 LEU cc_start: 0.8290 (mp) cc_final: 0.7843 (tt)
REVERT: A  204 ASN cc_start: 0.7490 (t0) cc_final: 0.6916 (t0)
REVERT: A  244 MET cc_start: 0.7783 (ttp) cc_final: 0.7417 (ttp)
REVERT: A  376 PHE cc_start: 0.7484 (m-80) cc_final: 0.6853 (m-10)
REVERT: C   30 ARG cc_start: 0.6974 (ttm-80) cc_final: 0.6641 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8398 (mtmp) cc_final: 0.8101 (mttp)
REVERT: D  336 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8737 (tp)
REVERT: E  129 ASP cc_start: 0.8161 (p0) cc_final: 0.7840 (p0)
REVERT: E  150 GLN cc_start: 0.7165 (tt0) cc_final: 0.6923 (tm-30)
REVERT: F   71 GLN cc_start: 0.8249 (mt0) cc_final: 0.7721 (tm-30)
REVERT: F  102 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8571 (tt)
REVERT: F  107 PHE cc_start: 0.8179 (t80) cc_final: 0.7952 (t80)
REVERT: F  124 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7806 (tm-30)
REVERT: F  152 LYS cc_start: 0.8706 (tppt) cc_final: 0.8319 (tptt)
  outliers start: 63
  outliers final: 52
  residues processed: 218
  average time/residue: 0.2003
  time to fit residues: 63.5802
Evaluate side-chains
  222 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 168
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
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   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  517 VAL
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  110 LEU
Chi-restraints excluded: chain E residue  149 LEU
Chi-restraints excluded: chain E residue  160 VAL
Chi-restraints excluded: chain E residue  189 VAL
Chi-restraints excluded: chain F residue  102 LEU
Chi-restraints excluded: chain F residue  113 ILE
Chi-restraints excluded: chain F residue  115 LEU
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:    0.6980
   chunk 7 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   chunk 108 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 113 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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  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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.118157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.103815 restraints weight = 18458.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.105634 restraints weight = 11996.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.107382 restraints weight = 7718.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.4311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10129  Z= 0.214
  Angle     :  0.693  12.868  13738  Z= 0.326
  Chirality :  0.041   0.245   1643
  Planarity :  0.004   0.041   1703
  Dihedral  :  4.116  19.254   1363
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 22.26 %
    Favored  : 72.26 %
  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:  1.16 (0.24), residues: 1264
  helix:  1.81 (0.18), residues: 814
  sheet: -1.26 (0.63), residues: 74
  loop : -1.13 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP A  35 
 HIS   0.004   0.001   HIS D 288 
 PHE   0.011   0.001   PHE F  98 
 TYR   0.016   0.001   TYR F 190 
 ARG   0.007   0.001   ARG F 154 

*********************** 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
  236 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 179
  time to evaluate  : 1.148 
Fit side-chains
REVERT: A  100 LEU cc_start: 0.8070 (mp) cc_final: 0.7672 (tt)
REVERT: A  204 ASN cc_start: 0.7481 (t0) cc_final: 0.6901 (t0)
REVERT: A  244 MET cc_start: 0.7758 (ttp) cc_final: 0.7409 (ttp)
REVERT: A  376 PHE cc_start: 0.7382 (m-80) cc_final: 0.6816 (m-10)
REVERT: C   30 ARG cc_start: 0.6877 (ttm-80) cc_final: 0.6542 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8411 (mtmp) cc_final: 0.8104 (mttp)
REVERT: D   57 GLU cc_start: 0.8478 (mp0) cc_final: 0.8258 (mp0)
REVERT: D  336 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8418 (tt)
REVERT: E  129 ASP cc_start: 0.8115 (p0) cc_final: 0.7813 (p0)
REVERT: E  150 GLN cc_start: 0.7122 (tt0) cc_final: 0.6892 (tm-30)
REVERT: F   63 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8180 (mm-30)
REVERT: F   71 GLN cc_start: 0.8257 (mt0) cc_final: 0.7845 (tm-30)
REVERT: F  107 PHE cc_start: 0.8172 (t80) cc_final: 0.7898 (t80)
REVERT: F  152 LYS cc_start: 0.8725 (tppt) cc_final: 0.8308 (tptt)
  outliers start: 57
  outliers final: 53
  residues processed: 221
  average time/residue: 0.2000
  time to fit residues: 63.5312
Evaluate side-chains
  222 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 168
  time to evaluate  : 1.340 
-------------------------------------------------------------------------------
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  253 ILE
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   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  517 VAL
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  110 LEU
Chi-restraints excluded: chain E residue  149 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  115 LEU
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:    0.3980
   chunk 74 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 123 optimal weight:    0.8980
   chunk 120 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9990
   chunk 116 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 156 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.118158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.104023 restraints weight = 18508.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.105894 restraints weight = 11792.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.107376 restraints weight = 7704.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.4381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10129  Z= 0.218
  Angle     :  0.706  12.645  13738  Z= 0.333
  Chirality :  0.041   0.246   1643
  Planarity :  0.004   0.040   1703
  Dihedral  :  4.111  19.158   1363
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 22.94 %
    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:  1.18 (0.24), residues: 1264
  helix:  1.82 (0.18), residues: 817
  sheet: -1.28 (0.62), residues: 74
  loop : -1.12 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A  35 
 HIS   0.004   0.001   HIS D 288 
 PHE   0.012   0.001   PHE F  98 
 TYR   0.016   0.001   TYR F 190 
 ARG   0.009   0.001   ARG A 264 

********************** 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
  229 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 173
  time to evaluate  : 1.210 
Fit side-chains
REVERT: A  100 LEU cc_start: 0.8046 (mp) cc_final: 0.7679 (tt)
REVERT: A  204 ASN cc_start: 0.7551 (t0) cc_final: 0.6955 (t0)
REVERT: A  244 MET cc_start: 0.7745 (ttp) cc_final: 0.7393 (ttp)
REVERT: A  376 PHE cc_start: 0.7465 (m-80) cc_final: 0.6883 (m-10)
REVERT: C   30 ARG cc_start: 0.6885 (ttm-80) cc_final: 0.6548 (mmm-85)
REVERT: C   38 LYS cc_start: 0.8404 (mtmp) cc_final: 0.8116 (mttp)
REVERT: D   57 GLU cc_start: 0.8468 (mp0) cc_final: 0.8241 (mp0)
REVERT: D  336 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8429 (tt)
REVERT: E  129 ASP cc_start: 0.8164 (p0) cc_final: 0.7853 (p0)
REVERT: E  150 GLN cc_start: 0.7097 (tt0) cc_final: 0.6881 (tm-30)
REVERT: E  165 MET cc_start: 0.6742 (tpp) cc_final: 0.6474 (tpt)
REVERT: F   71 GLN cc_start: 0.8219 (mt0) cc_final: 0.7832 (tm-30)
REVERT: F  152 LYS cc_start: 0.8633 (tppt) cc_final: 0.8197 (tptt)
  outliers start: 56
  outliers final: 48
  residues processed: 214
  average time/residue: 0.2012
  time to fit residues: 63.0857
Evaluate side-chains
  219 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 170
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
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 D residue   14 TRP
Chi-restraints excluded: chain D residue   31 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  517 VAL
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  149 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  115 LEU
Chi-restraints excluded: chain F residue  162 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 92 optimal weight:    0.0470
   chunk 27 optimal weight:    9.9990
   chunk 58 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 76 optimal weight:    0.6980
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
D 334 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 = 0.3584 r_free = 0.3584 target = 0.120147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.106096 restraints weight = 18358.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.107938 restraints weight = 11676.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.108957 restraints weight = 7634.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.4441

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= 0.195
  Angle     :  0.713  13.377  13738  Z= 0.332
  Chirality :  0.041   0.243   1643
  Planarity :  0.004   0.041   1703
  Dihedral  :  4.054  18.342   1363
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 23.61 %
    Favored  : 71.59 %
  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:  1.22 (0.25), residues: 1264
  helix:  1.88 (0.18), residues: 817
  sheet: -1.29 (0.58), residues: 84
  loop : -1.15 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A  35 
 HIS   0.004   0.001   HIS D 288 
 PHE   0.012   0.001   PHE F  98 
 TYR   0.014   0.001   TYR F 190 
 ARG   0.008   0.001   ARG D 485 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3033.23 seconds
wall clock time: 55 minutes 12.03 seconds (3312.03 seconds total)