Starting phenix.real_space_refine
on Wed Mar  4 01:15:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kb5_22787/03_2026/7kb5_22787.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kb5_22787/03_2026/7kb5_22787.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kb5_22787/03_2026/7kb5_22787.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kb5_22787/03_2026/7kb5_22787.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kb5_22787/03_2026/7kb5_22787.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kb5_22787/03_2026/7kb5_22787.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.016
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      40      5.16       5
     C    6382      2.51       5
     N    1645      2.21       5
     O    1710      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9777
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3269
          Classifications: {'peptide': 427}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 19, 'TRANS': 407}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 78
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 48
    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: {'ASP:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 9
    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: "D"
      Number of atoms: 3244
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 410, 3244
          Classifications: {'peptide': 410}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 24, 'TRANS': 385}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 6, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 68
    Chain: "E"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1129
          Classifications: {'peptide': 138}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 2, 'TRANS': 135}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "F"
      Number of atoms: 1471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1471
          Classifications: {'peptide': 190}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
  Time building chain proxies: 2.30, per 1000 atoms: 0.24
  Number of scatterers: 9777
  At special positions: 0
  Unit cell: (99, 124.2, 135.9, 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      40     16.00
     O    1710      8.00
     N    1645      7.00
     C    6382      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: 0.81
  Conformation dependent library (CDL) restraints added in 599.2 milliseconds
  

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2364

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 7 sheets defined
      67.3% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 49
      removed outlier: 3.591A  pdb=" N   GLN A  48 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ILE A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 70
      removed outlier: 3.742A  pdb=" N   ALA A  68 " --> pdb=" O   TYR A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 98
      removed outlier: 3.557A  pdb=" N   THR A  98 " --> pdb=" O   PHE A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 137
      removed outlier: 3.619A  pdb=" N   LEU A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 174
      removed outlier: 3.655A  pdb=" N   VAL A 164 " --> pdb=" O   ALA A 160 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   GLY A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 198
      removed outlier: 3.672A  pdb=" N   LEU A 183 " --> pdb=" O   SER A 179 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   THR A 185 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 225
      removed outlier: 3.643A  pdb=" N   ALA A 223 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 238
      removed outlier: 3.676A  pdb=" N   VAL A 233 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   TYR A 237 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ARG A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 262
      removed outlier: 3.632A  pdb=" N   VAL A 247 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   TYR A 259 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU A 260 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLN A 261 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   GLY A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 314
    Processing helix  chain 'A' and resid 317 through 324
    Processing helix  chain 'A' and resid 341 through 347
      removed outlier: 3.661A  pdb=" N   TYR A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 358
      removed outlier: 3.830A  pdb=" N   ASP A 358 " --> pdb=" O   GLU A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 385
      removed outlier: 3.636A  pdb=" N   THR A 362 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   CYS A 373 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS A 378 " --> pdb=" O   ALA A 374 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   GLU A 382 " --> pdb=" O   LYS A 378 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE A 383 " --> pdb=" O   THR A 379 " (cutoff:3.500A)
      removed outlier: 3.682A  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 406 through 440
      removed outlier: 3.564A  pdb=" N   ILE A 410 " --> pdb=" O   ARG A 406 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   TYR A 411 " --> pdb=" O   GLU A 407 " (cutoff:3.500A)
      Proline residue:  A 419  - end of helix
    Processing helix  chain 'A' and resid 444 through 466
      removed outlier: 4.036A  pdb=" N   ILE A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   LEU A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 82
    Processing helix  chain 'C' and resid 27 through 39
    Processing helix  chain 'C' and resid 43 through 80
      removed outlier: 3.732A  pdb=" N   TYR C  47 " --> pdb=" O   ASP C  43 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LYS C  49 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ILE C  73 " --> pdb=" O   LYS C  69 " (cutoff:3.500A)
      Proline residue:  C  74  - end of helix
    Processing helix  chain 'D' and resid 68 through 78
    Processing helix  chain 'D' and resid 221 through 233
    Processing helix  chain 'D' and resid 234 through 249
    Processing helix  chain 'D' and resid 255 through 268
      removed outlier: 3.784A  pdb=" N   ALA D 259 " --> pdb=" O   HIS D 255 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   ASN D 268 " --> pdb=" O   SER D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 276 through 285
      removed outlier: 3.633A  pdb=" N   ILE D 280 " --> pdb=" O   THR D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 311
    Processing helix  chain 'D' and resid 318 through 343
      removed outlier: 4.125A  pdb=" N   ARG D 324 " --> pdb=" O   ASN D 320 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   HIS D 330 " --> pdb=" O   VAL D 326 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   SER D 331 " --> pdb=" O   ALA D 327 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU D 332 " --> pdb=" O   LYS D 328 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 346 through 362
    Processing helix  chain 'D' and resid 378 through 386
      removed outlier: 4.416A  pdb=" N   THR D 384 " --> pdb=" O   GLU D 380 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 391 through 397
    Processing helix  chain 'D' and resid 399 through 408
      removed outlier: 3.578A  pdb=" N   ILE D 403 " --> pdb=" O   GLU D 399 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   GLY D 404 " --> pdb=" O   ASP D 400 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 411 through 423
      removed outlier: 4.365A  pdb=" N   GLU D 417 " --> pdb=" O   ALA D 413 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 466 through 470
    Processing helix  chain 'D' and resid 480 through 486
      removed outlier: 3.650A  pdb=" N   ASP D 486 " --> pdb=" O   GLU D 482 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 487 through 492
      removed outlier: 4.409A  pdb=" N   MET D 491 " --> pdb=" O   PRO D 487 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 537 through 541
      removed outlier: 3.691A  pdb=" N   ASN D 541 " --> pdb=" O   LYS D 538 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 554 through 558
    Processing helix  chain 'E' and resid 72 through 86
      removed outlier: 3.773A  pdb=" N   PHE E  76 " --> pdb=" O   HIS E  72 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ASN E  84 " --> pdb=" O   GLU E  80 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   LYS E  86 " --> pdb=" O   SER E  82 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 88 through 124
      removed outlier: 4.197A  pdb=" N   LEU E  92 " --> pdb=" O   HIS E  88 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LYS E  93 " --> pdb=" O   GLU E  89 " (cutoff:3.500A)
      Proline residue:  E 115  - end of helix
    Processing helix  chain 'E' and resid 128 through 156
      removed outlier: 3.855A  pdb=" N   LYS E 132 " --> pdb=" O   GLU E 128 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LYS E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLU E 142 " --> pdb=" O   VAL E 138 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 162 through 182
      removed outlier: 4.008A  pdb=" N   PHE E 172 " --> pdb=" O   LYS E 168 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 182 through 195
      removed outlier: 5.080A  pdb=" N   GLU E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   VAL E 189 " --> pdb=" O   LYS E 185 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   CYS E 190 " --> pdb=" O   ARG E 186 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ILE E 191 " --> pdb=" O   LYS E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 199 through 203
      removed outlier: 3.549A  pdb=" N   GLY E 202 " --> pdb=" O   ASN E 199 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ARG E 203 " --> pdb=" O   ASN E 200 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 199 through 203'
    Processing helix  chain 'F' and resid 21 through 41
    Processing helix  chain 'F' and resid 52 through 67
    Processing helix  chain 'F' and resid 68 through 70
      No H-bonds generated for 'chain 'F' and resid 68 through 70'
    Processing helix  chain 'F' and resid 75 through 91
      removed outlier: 3.727A  pdb=" N   LYS F  79 " --> pdb=" O   ASN F  75 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 101 through 120
      removed outlier: 3.637A  pdb=" N   LEU F 105 " --> pdb=" O   GLN F 101 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   SER F 111 " --> pdb=" O   PHE F 107 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 122 through 135
    Processing helix  chain 'F' and resid 139 through 153
      removed outlier: 3.940A  pdb=" N   VAL F 144 " --> pdb=" O   PRO F 140 " (cutoff:3.500A)
      removed outlier: 5.268A  pdb=" N   ARG F 145 " --> pdb=" O   ASP F 141 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 156 through 168
    Processing helix  chain 'F' and resid 175 through 192
    Processing sheet with id=AA1, first strand: chain 'A' and resid 278 through 284
    Processing sheet with id=AA2, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA3, first strand: chain 'D' and resid 426 through 427
    Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 434
      removed outlier: 4.005A  pdb=" N   LYS D 432 " --> pdb=" O   LYS D 454 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ASP D 434 " --> pdb=" O   SER D 452 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER D 452 " --> pdb=" O   ASP D 434 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532
      removed outlier: 3.511A  pdb=" N   ILE D 604 " --> pdb=" O   VAL D 590 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU D 602 " --> pdb=" O   VAL D 592 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 530 through 532
    Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 6

    609 hydrogen bonds defined for protein.
    1779 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 1.11 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: 3069
        1.34 -     1.46: 1891
        1.46 -     1.58: 4948
        1.58 -     1.69: 0
        1.69 -     1.81: 63
  Bond restraints: 9971
  Sorted by residual:
  bond pdb=" CB  CYS E 167 "
       pdb=" SG  CYS E 167 "
    ideal  model  delta    sigma   weight residual
    1.808  1.762  0.046 3.30e-02 9.18e+02 1.96e+00
  bond pdb=" C   ILE A 418 "
       pdb=" N   PRO A 419 "
    ideal  model  delta    sigma   weight residual
    1.335  1.352 -0.016 1.36e-02 5.41e+03 1.44e+00
  bond pdb=" CB  GLN F 155 "
       pdb=" CG  GLN F 155 "
    ideal  model  delta    sigma   weight residual
    1.520  1.488  0.032 3.00e-02 1.11e+03 1.14e+00
  bond pdb=" C   THR D 595 "
       pdb=" N   ASP D 596 "
    ideal  model  delta    sigma   weight residual
    1.333  1.319  0.014 1.41e-02 5.03e+03 9.83e-01
  bond pdb=" C   ILE D 531 "
       pdb=" N   ILE D 532 "
    ideal  model  delta    sigma   weight residual
    1.335  1.321  0.014 1.41e-02 5.03e+03 9.69e-01
  ... (remaining 9966 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 13237
        1.88 -     3.75: 227
        3.75 -     5.63: 36
        5.63 -     7.51: 4
        7.51 -     9.38: 1
  Bond angle restraints: 13505
  Sorted by residual:
  angle pdb=" N   VAL E 205 "
        pdb=" CA  VAL E 205 "
        pdb=" C   VAL E 205 "
      ideal   model   delta    sigma   weight residual
     112.17  108.28    3.89 9.50e-01 1.11e+00 1.68e+01
  angle pdb=" N   ILE E 126 "
        pdb=" CA  ILE E 126 "
        pdb=" C   ILE E 126 "
      ideal   model   delta    sigma   weight residual
     113.71  110.11    3.60 9.50e-01 1.11e+00 1.44e+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  122.80   -2.47 8.00e-01 1.56e+00 9.52e+00
  angle pdb=" C   PRO F  94 "
        pdb=" N   TRP F  95 "
        pdb=" CA  TRP F  95 "
      ideal   model   delta    sigma   weight residual
     122.56  117.83    4.73 1.72e+00 3.38e-01 7.57e+00
  angle pdb=" CA  TYR F 190 "
        pdb=" CB  TYR F 190 "
        pdb=" CG  TYR F 190 "
      ideal   model   delta    sigma   weight residual
     113.90  118.77   -4.87 1.80e+00 3.09e-01 7.33e+00
  ... (remaining 13500 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.72: 5362
       16.72 -    33.43: 526
       33.43 -    50.15: 111
       50.15 -    66.87: 9
       66.87 -    83.58: 8
  Dihedral angle restraints: 6016
    sinusoidal: 2376
      harmonic: 3640
  Sorted by residual:
  dihedral pdb=" CA  VAL D 437 "
           pdb=" C   VAL D 437 "
           pdb=" N   PRO D 438 "
           pdb=" CA  PRO D 438 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.46   21.54     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  ASP D 545 "
           pdb=" CB  ASP D 545 "
           pdb=" CG  ASP D 545 "
           pdb=" OD1 ASP D 545 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.94   58.94     1      2.00e+01 2.50e-03 1.16e+01
  dihedral pdb=" CA  ASN E  84 "
           pdb=" C   ASN E  84 "
           pdb=" N   GLU E  85 "
           pdb=" CA  GLU E  85 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.25  -16.75     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 6013 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 860
       0.027 -    0.054: 499
       0.054 -    0.081: 136
       0.081 -    0.108: 82
       0.108 -    0.135: 20
  Chirality restraints: 1597
  Sorted by residual:
  chirality pdb=" CA  ILE D 470 "
            pdb=" N   ILE D 470 "
            pdb=" C   ILE D 470 "
            pdb=" CB  ILE D 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.55e-01
  chirality pdb=" CA  ILE D 389 "
            pdb=" N   ILE D 389 "
            pdb=" C   ILE D 389 "
            pdb=" CB  ILE D 389 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.44e-01
  chirality pdb=" CA  PRO F  94 "
            pdb=" N   PRO F  94 "
            pdb=" C   PRO F  94 "
            pdb=" CB  PRO F  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.20e-01
  ... (remaining 1594 not shown)

  Planarity restraints: 1677
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F  47 "    0.029 5.00e-02 4.00e+02   4.39e-02 3.09e+00
        pdb=" N   PRO F  48 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO F  48 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO F  48 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 437 "   -0.028 5.00e-02 4.00e+02   4.22e-02 2.85e+00
        pdb=" N   PRO D 438 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO D 438 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO D 438 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F  93 "   -0.028 5.00e-02 4.00e+02   4.22e-02 2.85e+00
        pdb=" N   PRO F  94 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO F  94 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO F  94 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1674 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 285
        2.71 -     3.26: 10117
        3.26 -     3.81: 14954
        3.81 -     4.35: 17322
        4.35 -     4.90: 29626
  Nonbonded interactions: 72304
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN D 370 "
            pdb=" OG1 THR D 391 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" OG  SER A 271 "
            pdb=" O   VAL A 274 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   PRO F 171 "
            pdb=" NH2 ARG F 177 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" O   PRO A  18 "
            pdb=" NZ  LYS A 119 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" O   SER D 423 "
            pdb=" OG  SER D 423 "
     model   vdw
     2.271 3.040
  ... (remaining 72299 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.260
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9971  Z= 0.190
  Angle     :  0.635   9.382  13505  Z= 0.354
  Chirality :  0.040   0.135   1597
  Planarity :  0.004   0.044   1677
  Dihedral  : 13.760  83.585   3652
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.22), residues: 1228
  helix: -0.09 (0.17), residues: 753
  sheet: -2.43 (0.54), residues: 85
  loop : -2.26 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  99 
 TYR   0.022   0.002   TYR F 190 
 PHE   0.019   0.001   PHE D 356 
 TRP   0.007   0.001   TRP F 156 
 HIS   0.004   0.001   HIS D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 9971)
  covalent geometry    : angle       0.63539 (13505)
  hydrogen bonds       : bond        0.14114 (  599)
  hydrogen bonds       : angle       5.02546 ( 1779)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  400 MET cc_start: 0.9334 (mmm) cc_final: 0.8861 (mmm)
REVERT: B   71 LEU cc_start: 0.9403 (mt) cc_final: 0.9151 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1014
  time to fit residues: 11.1427
Evaluate side-chains
  48 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    7.9990
   chunk 117 optimal weight:    0.9980
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 188 ASN
A 317 ASN
A 336 GLN
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 390 HIS
D 484 GLN
D 520 GLN
E  88 HIS
E 181 GLN
F  68 ASN
F  71 GLN
F  89 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.051385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.036577 restraints weight = 68884.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.037597 restraints weight = 36295.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.038300 restraints weight = 24711.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.038638 restraints weight = 19399.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.038998 restraints weight = 16914.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9971  Z= 0.182
  Angle     :  0.593   7.156  13505  Z= 0.299
  Chirality :  0.039   0.136   1597
  Planarity :  0.004   0.048   1677
  Dihedral  :  3.846  20.838   1328
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.67 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.24), residues: 1228
  helix:  1.48 (0.19), residues: 759
  sheet: -1.93 (0.57), residues: 82
  loop : -1.77 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 485 
 TYR   0.018   0.001   TYR D 227 
 PHE   0.009   0.001   PHE D 343 
 TRP   0.008   0.001   TRP F 156 
 HIS   0.006   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 9971)
  covalent geometry    : angle       0.59299 (13505)
  hydrogen bonds       : bond        0.04349 (  599)
  hydrogen bonds       : angle       3.90300 ( 1779)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.8438 (tpp) cc_final: 0.8227 (tpp)
REVERT: A  249 MET cc_start: 0.9401 (mmm) cc_final: 0.9166 (mmm)
REVERT: A  400 MET cc_start: 0.9451 (mmm) cc_final: 0.8809 (mmm)
REVERT: B   71 LEU cc_start: 0.9368 (mt) cc_final: 0.9141 (tp)
REVERT: C   47 TYR cc_start: 0.8564 (t80) cc_final: 0.8329 (t80)
REVERT: D  330 HIS cc_start: 0.8452 (OUTLIER) cc_final: 0.8246 (t-90)
REVERT: F   87 MET cc_start: 0.9293 (ttt) cc_final: 0.9027 (tmm)
  outliers start: 15
  outliers final: 10
  residues processed: 64
  average time/residue: 0.0746
  time to fit residues: 7.6271
Evaluate side-chains
  57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  330 HIS
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  126 ILE
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain E residue  198 ILE
Chi-restraints excluded: chain F residue  162 THR
Chi-restraints excluded: chain F residue  183 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 94 optimal weight:    7.9990
   chunk 122 optimal weight:    3.9990
   chunk 0 optimal weight:   30.0000
   chunk 119 optimal weight:    2.9990
   chunk 110 optimal weight:    9.9990
   chunk 83 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 181 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.050802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.035940 restraints weight = 69321.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.036963 restraints weight = 36690.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.037464 restraints weight = 25048.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.038024 restraints weight = 20573.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.038353 restraints weight = 17364.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9971  Z= 0.185
  Angle     :  0.582   8.028  13505  Z= 0.291
  Chirality :  0.039   0.132   1597
  Planarity :  0.004   0.049   1677
  Dihedral  :  3.776  21.196   1328
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 15.97 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.25), residues: 1228
  helix:  2.09 (0.19), residues: 759
  sheet: -1.65 (0.58), residues: 81
  loop : -1.51 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  99 
 TYR   0.019   0.001   TYR F 190 
 PHE   0.024   0.001   PHE B  64 
 TRP   0.009   0.001   TRP F 156 
 HIS   0.006   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 9971)
  covalent geometry    : angle       0.58226 (13505)
  hydrogen bonds       : bond        0.04143 (  599)
  hydrogen bonds       : angle       3.72718 ( 1779)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 49
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 MET cc_start: 0.8971 (tmm) cc_final: 0.8758 (tmm)
REVERT: A  400 MET cc_start: 0.9455 (mmm) cc_final: 0.8836 (mmm)
REVERT: B   71 LEU cc_start: 0.9364 (mt) cc_final: 0.9143 (tp)
REVERT: C   47 TYR cc_start: 0.8502 (t80) cc_final: 0.8221 (t80)
REVERT: D  330 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.8090 (t-90)
REVERT: E  126 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9152 (pt)
REVERT: F   87 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.9047 (tmm)
  outliers start: 26
  outliers final: 15
  residues processed: 71
  average time/residue: 0.0695
  time to fit residues: 7.9687
Evaluate side-chains
  63 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 45
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 HIS
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  555 LEU
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  126 ILE
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain E residue  198 ILE
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue  162 THR
Chi-restraints excluded: chain F residue  163 CYS
Chi-restraints excluded: chain F residue  183 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 94 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 59 optimal weight:    9.9990
   chunk 111 optimal weight:   10.0000
   chunk 100 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
D 330 HIS
E 181 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.051584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.036800 restraints weight = 69330.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.037895 restraints weight = 36044.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.038612 restraints weight = 24150.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.039062 restraints weight = 18762.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.039375 restraints weight = 16119.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9971  Z= 0.110
  Angle     :  0.531   8.158  13505  Z= 0.260
  Chirality :  0.037   0.134   1597
  Planarity :  0.003   0.049   1677
  Dihedral  :  3.565  20.157   1328
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.02 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.25), residues: 1228
  helix:  2.40 (0.19), residues: 758
  sheet: -1.47 (0.59), residues: 82
  loop : -1.29 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  99 
 TYR   0.019   0.001   TYR D 227 
 PHE   0.023   0.001   PHE B  64 
 TRP   0.008   0.001   TRP F  95 
 HIS   0.006   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 9971)
  covalent geometry    : angle       0.53056 (13505)
  hydrogen bonds       : bond        0.03625 (  599)
  hydrogen bonds       : angle       3.39577 ( 1779)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 49
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.8448 (tpp) cc_final: 0.8222 (tpp)
REVERT: A  165 MET cc_start: 0.8983 (tmm) cc_final: 0.8641 (tmm)
REVERT: A  249 MET cc_start: 0.9371 (mmm) cc_final: 0.9155 (ptp)
REVERT: A  350 MET cc_start: 0.8606 (mmp) cc_final: 0.8403 (mmp)
REVERT: A  400 MET cc_start: 0.9469 (mmm) cc_final: 0.8885 (mmm)
REVERT: D  330 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.7407 (t70)
REVERT: D  414 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8945 (mtpp)
REVERT: F   87 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.9012 (tmm)
  outliers start: 24
  outliers final: 15
  residues processed: 69
  average time/residue: 0.0729
  time to fit residues: 8.1031
Evaluate side-chains
  63 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 45
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  330 HIS
Chi-restraints excluded: chain D residue  414 LYS
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain E residue  198 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   87 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 113 optimal weight:    8.9990
   chunk 96 optimal weight:    8.9990
   chunk 117 optimal weight:    0.0670
   chunk 13 optimal weight:    5.9990
   chunk 75 optimal weight:    0.6980
   chunk 70 optimal weight:    7.9990
   chunk 52 optimal weight:    9.9990
   chunk 58 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 112 optimal weight:    4.9990
   overall best weight:    2.1524

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

Flipped N/Q/H residues before XYZ refinement:
D 330 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.051246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.036546 restraints weight = 69740.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.037602 restraints weight = 36177.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.038306 restraints weight = 24372.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.038703 restraints weight = 19056.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.039023 restraints weight = 16457.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9971  Z= 0.130
  Angle     :  0.543   8.302  13505  Z= 0.265
  Chirality :  0.037   0.133   1597
  Planarity :  0.003   0.048   1677
  Dihedral  :  3.518  20.268   1328
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 17.69 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.26), residues: 1228
  helix:  2.47 (0.19), residues: 765
  sheet: -1.32 (0.59), residues: 81
  loop : -1.15 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  99 
 TYR   0.016   0.001   TYR F 190 
 PHE   0.023   0.001   PHE C  58 
 TRP   0.007   0.001   TRP F 156 
 HIS   0.005   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9971)
  covalent geometry    : angle       0.54347 (13505)
  hydrogen bonds       : bond        0.03627 (  599)
  hydrogen bonds       : angle       3.38724 ( 1779)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 47
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.8417 (tpp) cc_final: 0.8174 (tpp)
REVERT: A  135 MET cc_start: 0.8169 (mmm) cc_final: 0.7686 (mtp)
REVERT: A  165 MET cc_start: 0.9033 (tmm) cc_final: 0.8612 (tmm)
REVERT: A  350 MET cc_start: 0.8587 (mmp) cc_final: 0.8376 (mmp)
REVERT: A  400 MET cc_start: 0.9406 (mmm) cc_final: 0.8877 (mmm)
REVERT: B   66 PHE cc_start: 0.8997 (t80) cc_final: 0.8568 (t80)
REVERT: C   70 LEU cc_start: 0.9674 (tt) cc_final: 0.9425 (mt)
REVERT: F   87 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8961 (tmm)
  outliers start: 22
  outliers final: 17
  residues processed: 65
  average time/residue: 0.0674
  time to fit residues: 6.8837
Evaluate side-chains
  62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 44
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  414 LYS
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain E residue  198 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   87 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 105 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 45 optimal weight:    8.9990
   chunk 38 optimal weight:   30.0000
   chunk 16 optimal weight:    8.9990
   chunk 34 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 92 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
D 307 GLN
E 181 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.050664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.035829 restraints weight = 69446.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.036863 restraints weight = 36534.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.037547 restraints weight = 24784.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.037962 restraints weight = 19459.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.038271 restraints weight = 16813.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9971  Z= 0.157
  Angle     :  0.562   8.845  13505  Z= 0.275
  Chirality :  0.038   0.134   1597
  Planarity :  0.003   0.049   1677
  Dihedral  :  3.540  19.884   1328
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.26 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.26), residues: 1228
  helix:  2.52 (0.19), residues: 765
  sheet: -1.28 (0.59), residues: 81
  loop : -1.08 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  99 
 TYR   0.026   0.001   TYR C  47 
 PHE   0.010   0.001   PHE D 356 
 TRP   0.008   0.001   TRP F 156 
 HIS   0.004   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 9971)
  covalent geometry    : angle       0.56235 (13505)
  hydrogen bonds       : bond        0.03767 (  599)
  hydrogen bonds       : angle       3.45490 ( 1779)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 45
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.8372 (tpp) cc_final: 0.8133 (tpp)
REVERT: A  165 MET cc_start: 0.9044 (tmm) cc_final: 0.8592 (tmm)
REVERT: A  194 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8943 (t80)
REVERT: A  350 MET cc_start: 0.8619 (mmp) cc_final: 0.8403 (mmp)
REVERT: A  400 MET cc_start: 0.9419 (mmm) cc_final: 0.8935 (mmm)
REVERT: B   66 PHE cc_start: 0.8982 (t80) cc_final: 0.8546 (t80)
REVERT: C   47 TYR cc_start: 0.9118 (t80) cc_final: 0.8665 (t80)
REVERT: C   70 LEU cc_start: 0.9674 (tt) cc_final: 0.9433 (mt)
REVERT: D  228 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7924 (t)
REVERT: F   57 MET cc_start: 0.8984 (ptp) cc_final: 0.8767 (ptp)
REVERT: F   87 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8960 (tmm)
  outliers start: 24
  outliers final: 20
  residues processed: 66
  average time/residue: 0.0674
  time to fit residues: 7.4011
Evaluate side-chains
  67 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 44
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  228 VAL
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  414 LYS
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain E residue  198 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue  163 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 42 optimal weight:    8.9990
   chunk 82 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
F 155 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.051325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.036707 restraints weight = 69185.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.037777 restraints weight = 36458.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.038462 restraints weight = 24635.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.038932 restraints weight = 19328.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.039156 restraints weight = 16563.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9971  Z= 0.127
  Angle     :  0.544   9.232  13505  Z= 0.263
  Chirality :  0.038   0.151   1597
  Planarity :  0.003   0.049   1677
  Dihedral  :  3.469  19.919   1328
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.55 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.93 (0.26), residues: 1228
  helix:  2.62 (0.19), residues: 765
  sheet: -1.25 (0.58), residues: 86
  loop : -0.98 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  99 
 TYR   0.020   0.001   TYR C  47 
 PHE   0.023   0.001   PHE C  58 
 TRP   0.006   0.001   TRP F 156 
 HIS   0.004   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9971)
  covalent geometry    : angle       0.54426 (13505)
  hydrogen bonds       : bond        0.03505 (  599)
  hydrogen bonds       : angle       3.30086 ( 1779)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 46
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A   69 MET cc_start: 0.8431 (tpp) cc_final: 0.8203 (tpp)
REVERT: A  165 MET cc_start: 0.9069 (tmm) cc_final: 0.8601 (tmm)
REVERT: A  350 MET cc_start: 0.8572 (mmp) cc_final: 0.8358 (mmp)
REVERT: A  400 MET cc_start: 0.9440 (mmm) cc_final: 0.8967 (mmm)
REVERT: B   66 PHE cc_start: 0.8979 (t80) cc_final: 0.8531 (t80)
REVERT: C   47 TYR cc_start: 0.9133 (t80) cc_final: 0.8653 (t80)
REVERT: C   70 LEU cc_start: 0.9690 (tt) cc_final: 0.9433 (mt)
REVERT: D  414 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8985 (mtpp)
REVERT: D  533 GLU cc_start: 0.7902 (tp30) cc_final: 0.7667 (tp30)
REVERT: F   87 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8952 (tmm)
REVERT: F  155 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7730 (mm-40)
  outliers start: 25
  outliers final: 18
  residues processed: 68
  average time/residue: 0.0694
  time to fit residues: 7.7622
Evaluate side-chains
  66 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 45
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  359 ILE
Chi-restraints excluded: chain D residue  414 LYS
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain E residue  198 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue  155 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 34 optimal weight:   20.0000
   chunk 12 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   chunk 94 optimal weight:    0.9990
   chunk 82 optimal weight:    8.9990
   chunk 79 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   chunk 84 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 30 optimal weight:   20.0000
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
F 155 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.051300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.036714 restraints weight = 69241.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.037759 restraints weight = 36371.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.038457 restraints weight = 24677.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.038879 restraints weight = 19402.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.039192 restraints weight = 16720.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9971  Z= 0.128
  Angle     :  0.561   9.853  13505  Z= 0.268
  Chirality :  0.038   0.146   1597
  Planarity :  0.003   0.044   1677
  Dihedral  :  3.468  19.581   1328
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.64 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.97 (0.26), residues: 1228
  helix:  2.63 (0.19), residues: 765
  sheet: -1.21 (0.58), residues: 86
  loop : -0.94 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 154 
 TYR   0.023   0.001   TYR D 227 
 PHE   0.010   0.001   PHE E 134 
 TRP   0.006   0.001   TRP F  95 
 HIS   0.004   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9971)
  covalent geometry    : angle       0.56064 (13505)
  hydrogen bonds       : bond        0.03486 (  599)
  hydrogen bonds       : angle       3.29353 ( 1779)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 46
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A   69 MET cc_start: 0.8425 (tpp) cc_final: 0.8207 (tpp)
REVERT: A  135 MET cc_start: 0.8081 (mmm) cc_final: 0.7644 (mtp)
REVERT: A  165 MET cc_start: 0.9078 (tmm) cc_final: 0.8589 (tmm)
REVERT: A  194 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8964 (t80)
REVERT: A  350 MET cc_start: 0.8578 (mmp) cc_final: 0.8366 (mmp)
REVERT: A  400 MET cc_start: 0.9446 (mmm) cc_final: 0.8975 (mmm)
REVERT: B   66 PHE cc_start: 0.9007 (t80) cc_final: 0.8520 (t80)
REVERT: C   47 TYR cc_start: 0.9137 (t80) cc_final: 0.8699 (t80)
REVERT: C   70 LEU cc_start: 0.9689 (tt) cc_final: 0.9418 (mt)
REVERT: D  414 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.9009 (mtpp)
REVERT: D  533 GLU cc_start: 0.7903 (tp30) cc_final: 0.7666 (tp30)
REVERT: D  547 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8127 (t80)
REVERT: F   57 MET cc_start: 0.8937 (ptp) cc_final: 0.8706 (ptp)
REVERT: F   87 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8960 (tmm)
  outliers start: 24
  outliers final: 19
  residues processed: 67
  average time/residue: 0.0675
  time to fit residues: 7.4304
Evaluate side-chains
  68 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 45
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  359 ILE
Chi-restraints excluded: chain D residue  414 LYS
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  532 ILE
Chi-restraints excluded: chain D residue  547 PHE
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain E residue  198 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue  179 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 87 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 94 optimal weight:    6.9990
   chunk 8 optimal weight:   40.0000
   chunk 0 optimal weight:   30.0000
   overall best weight:    3.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.050739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.036123 restraints weight = 70007.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.037159 restraints weight = 37396.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.037830 restraints weight = 25510.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.038283 restraints weight = 20111.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.038396 restraints weight = 17288.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9971  Z= 0.175
  Angle     :  0.595  10.158  13505  Z= 0.286
  Chirality :  0.038   0.140   1597
  Planarity :  0.003   0.043   1677
  Dihedral  :  3.530  19.766   1328
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 18.64 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.26), residues: 1228
  helix:  2.65 (0.19), residues: 765
  sheet: -1.32 (0.57), residues: 86
  loop : -0.97 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  99 
 TYR   0.021   0.001   TYR D 227 
 PHE   0.027   0.001   PHE C  58 
 TRP   0.013   0.001   TRP F 156 
 HIS   0.005   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 9971)
  covalent geometry    : angle       0.59544 (13505)
  hydrogen bonds       : bond        0.03729 (  599)
  hydrogen bonds       : angle       3.41992 ( 1779)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 46
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.8469 (tpp) cc_final: 0.8245 (tpp)
REVERT: A   90 MET cc_start: 0.9524 (tmm) cc_final: 0.9220 (ppp)
REVERT: A  165 MET cc_start: 0.9095 (tmm) cc_final: 0.8617 (tmm)
REVERT: A  194 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8935 (t80)
REVERT: A  350 MET cc_start: 0.8602 (mmp) cc_final: 0.8388 (mmp)
REVERT: A  400 MET cc_start: 0.9450 (mmm) cc_final: 0.9006 (mmm)
REVERT: B   66 PHE cc_start: 0.9026 (t80) cc_final: 0.8558 (t80)
REVERT: C   47 TYR cc_start: 0.9115 (t80) cc_final: 0.8758 (t80)
REVERT: C   70 LEU cc_start: 0.9708 (tt) cc_final: 0.9467 (mt)
REVERT: D  547 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8163 (t80)
REVERT: F   87 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8966 (tmm)
  outliers start: 27
  outliers final: 21
  residues processed: 70
  average time/residue: 0.0707
  time to fit residues: 8.0078
Evaluate side-chains
  68 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 44
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  359 ILE
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  532 ILE
Chi-restraints excluded: chain D residue  547 PHE
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain E residue  198 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue  179 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 51 optimal weight:    8.9990
   chunk 44 optimal weight:    7.9990
   chunk 59 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 122 optimal weight:    3.9990
   chunk 120 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 56 optimal weight:    0.6980
   chunk 114 optimal weight:    3.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
** D 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.050918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.036712 restraints weight = 68788.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.037763 restraints weight = 35149.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.038287 restraints weight = 22429.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.038379 restraints weight = 21251.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.038399 restraints weight = 18028.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9971  Z= 0.150
  Angle     :  0.609  13.982  13505  Z= 0.288
  Chirality :  0.038   0.198   1597
  Planarity :  0.003   0.044   1677
  Dihedral  :  3.538  19.465   1328
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 19.02 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (0.26), residues: 1228
  helix:  2.65 (0.19), residues: 766
  sheet: -1.31 (0.57), residues: 86
  loop : -0.93 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  99 
 TYR   0.021   0.001   TYR D 227 
 PHE   0.010   0.001   PHE E 134 
 TRP   0.009   0.001   TRP F 156 
 HIS   0.004   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 9971)
  covalent geometry    : angle       0.60908 (13505)
  hydrogen bonds       : bond        0.03651 (  599)
  hydrogen bonds       : angle       3.36438 ( 1779)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 46
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.8505 (tpp) cc_final: 0.8288 (tpp)
REVERT: A   90 MET cc_start: 0.9528 (tmm) cc_final: 0.9217 (ppp)
REVERT: A  165 MET cc_start: 0.9084 (tmm) cc_final: 0.8593 (tmm)
REVERT: A  194 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8968 (t80)
REVERT: A  350 MET cc_start: 0.8580 (mmp) cc_final: 0.8371 (mmp)
REVERT: A  400 MET cc_start: 0.9507 (mmm) cc_final: 0.9024 (mmm)
REVERT: B   66 PHE cc_start: 0.9009 (t80) cc_final: 0.8549 (t80)
REVERT: C   70 LEU cc_start: 0.9699 (tt) cc_final: 0.9444 (mt)
REVERT: D  491 MET cc_start: 0.8931 (ttm) cc_final: 0.8446 (tpp)
REVERT: D  533 GLU cc_start: 0.7956 (tp30) cc_final: 0.7714 (tp30)
REVERT: D  547 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8097 (t80)
REVERT: D  555 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8174 (mp)
REVERT: F   87 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8969 (tmm)
  outliers start: 26
  outliers final: 21
  residues processed: 69
  average time/residue: 0.0645
  time to fit residues: 7.4838
Evaluate side-chains
  70 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 45
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  194 PHE
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  341 CYS
Chi-restraints excluded: chain D residue  359 ILE
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain D residue  532 ILE
Chi-restraints excluded: chain D residue  547 PHE
Chi-restraints excluded: chain D residue  555 LEU
Chi-restraints excluded: chain D residue  606 MET
Chi-restraints excluded: chain E residue  165 MET
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain E residue  198 ILE
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   87 MET
Chi-restraints excluded: chain F residue  179 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 115 optimal weight:    0.9990
   chunk 31 optimal weight:    8.9990
   chunk 11 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 47 optimal weight:    0.4980
   chunk 91 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 1 optimal weight:    7.9990
   chunk 97 optimal weight:    8.9990
   chunk 10 optimal weight:    0.8980
   chunk 29 optimal weight:    7.9990
   overall best weight:    2.8786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.050826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.036785 restraints weight = 70233.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.037761 restraints weight = 37231.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.037997 restraints weight = 24278.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.038356 restraints weight = 22668.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.038351 restraints weight = 21223.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9971  Z= 0.155
  Angle     :  0.609  12.948  13505  Z= 0.289
  Chirality :  0.039   0.197   1597
  Planarity :  0.003   0.043   1677
  Dihedral  :  3.524  19.639   1328
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 19.12 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.01 (0.26), residues: 1228
  helix:  2.68 (0.19), residues: 766
  sheet: -1.31 (0.57), residues: 86
  loop : -0.92 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  99 
 TYR   0.017   0.001   TYR F 190 
 PHE   0.026   0.001   PHE C  58 
 TRP   0.010   0.001   TRP F 156 
 HIS   0.004   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 9971)
  covalent geometry    : angle       0.60938 (13505)
  hydrogen bonds       : bond        0.03645 (  599)
  hydrogen bonds       : angle       3.36162 ( 1779)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1578.86 seconds
wall clock time: 28 minutes 0.89 seconds (1680.89 seconds total)