Starting phenix.real_space_refine
on Wed Mar  4 03:01:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ngh_12314/03_2026/7ngh_12314.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ngh_12314/03_2026/7ngh_12314.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ngh_12314/03_2026/7ngh_12314.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ngh_12314/03_2026/7ngh_12314.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ngh_12314/03_2026/7ngh_12314.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ngh_12314/03_2026/7ngh_12314.map"
  }
  resolution = 3.5
  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=   0.000 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    6785      2.51       5
     N    1672      2.21       5
     O    1806      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 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: 10315
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3108
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 18, 'TRANS': 396}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3178
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 18, 'TRANS': 407}
    Chain: "C"
      Number of atoms: 3108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3108
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 18, 'TRANS': 396}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 894
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 894
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 3, 'TRANS': 111}
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "C"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 2.49, per 1000 atoms: 0.24
  Number of scatterers: 10315
  At special positions: 0
  Unit cell: (102.212, 109.296, 103.224, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1806      8.00
     N    1672      7.00
     C    6785      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  26 " - pdb=" SG  CYS D 100 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 480.3 milliseconds
  

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2464

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 3 sheets defined
      80.2% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 12
      removed outlier: 3.732A  pdb=" N   TYR A  12 " --> pdb=" O   TYR A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 13 through 35
      removed outlier: 3.816A  pdb=" N   GLY A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 45
    Processing helix  chain 'A' and resid 45 through 73
      removed outlier: 3.663A  pdb=" N   GLY A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LEU A  59 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   VAL A  60 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   MET A  61 " --> pdb=" O   LYS A  57 " (cutoff:3.500A)
      Proline residue:  A  62  - end of helix
    Processing helix  chain 'A' and resid 76 through 110
      removed outlier: 3.643A  pdb=" N   TYR A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 138
    Processing helix  chain 'A' and resid 143 through 151
    Processing helix  chain 'A' and resid 152 through 172
      removed outlier: 3.933A  pdb=" N   ASN A 172 " --> pdb=" O   THR A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 222
      removed outlier: 3.714A  pdb=" N   SER A 181 " --> pdb=" O   ARG A 177 " (cutoff:3.500A)
      Proline residue:  A 208  - end of helix
    Processing helix  chain 'A' and resid 228 through 256
      removed outlier: 3.948A  pdb=" N   LYS A 232 " --> pdb=" O   GLY A 228 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL A 234 " --> pdb=" O   LEU A 230 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLY A 235 " --> pdb=" O   ALA A 231 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   PHE A 250 " --> pdb=" O   VAL A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 278
      removed outlier: 5.202A  pdb=" N   ASP A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   ALA A 270 " --> pdb=" O   LYS A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 282
      No H-bonds generated for 'chain 'A' and resid 280 through 282'
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 298 through 313
      removed outlier: 5.614A  pdb=" N   PHE A 304 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
      Proline residue:  A 307  - end of helix
      removed outlier: 3.712A  pdb=" N   THR A 311 " --> pdb=" O   PRO A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 332
    Processing helix  chain 'A' and resid 337 through 355
      removed outlier: 3.831A  pdb=" N   LEU A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL A 349 " --> pdb=" O   VAL A 345 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   LEU A 350 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 373
      removed outlier: 4.177A  pdb=" N   ALA A 367 " --> pdb=" O   ALA A 363 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   MET A 368 " --> pdb=" O   ILE A 364 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   VAL A 369 " --> pdb=" O   MET A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 420
      removed outlier: 3.593A  pdb=" N   LEU A 385 " --> pdb=" O   SER A 381 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ILE A 393 " --> pdb=" O   MET A 389 " (cutoff:3.500A)
      removed outlier: 4.939A  pdb=" N   ALA A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 5.817A  pdb=" N   ILE A 396 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLY A 400 " --> pdb=" O   ILE A 396 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   MET A 403 " --> pdb=" O   MET A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 429
      removed outlier: 3.699A  pdb=" N   TRP A 428 " --> pdb=" O   ASP A 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 12
    Processing helix  chain 'B' and resid 13 through 36
    Processing helix  chain 'B' and resid 37 through 45
    Processing helix  chain 'B' and resid 45 through 58
      removed outlier: 3.821A  pdb=" N   GLY B  49 " --> pdb=" O   ILE B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 72
    Processing helix  chain 'B' and resid 76 through 110
      removed outlier: 3.655A  pdb=" N   TYR B  90 " --> pdb=" O   LYS B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 138
    Processing helix  chain 'B' and resid 143 through 150
    Processing helix  chain 'B' and resid 152 through 172
      removed outlier: 3.854A  pdb=" N   VAL B 156 " --> pdb=" O   GLU B 152 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ASN B 172 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 222
      Proline residue:  B 208  - end of helix
    Processing helix  chain 'B' and resid 228 through 257
      removed outlier: 3.788A  pdb=" N   LYS B 232 " --> pdb=" O   GLY B 228 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   PHE B 250 " --> pdb=" O   VAL B 246 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ILE B 251 " --> pdb=" O   ILE B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 278
      removed outlier: 5.860A  pdb=" N   ASP B 269 " --> pdb=" O   ARG B 265 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   ALA B 270 " --> pdb=" O   LYS B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 282
      No H-bonds generated for 'chain 'B' and resid 280 through 282'
    Processing helix  chain 'B' and resid 283 through 294
    Processing helix  chain 'B' and resid 298 through 313
      removed outlier: 3.583A  pdb=" N   PHE B 302 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   PHE B 304 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
      Proline residue:  B 307  - end of helix
      removed outlier: 3.700A  pdb=" N   THR B 311 " --> pdb=" O   PRO B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 333
    Processing helix  chain 'B' and resid 337 through 355
      removed outlier: 4.443A  pdb=" N   LEU B 346 " --> pdb=" O   LEU B 342 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL B 349 " --> pdb=" O   VAL B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 373
      removed outlier: 4.149A  pdb=" N   ALA B 367 " --> pdb=" O   ALA B 363 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   MET B 368 " --> pdb=" O   ILE B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 392
      removed outlier: 3.782A  pdb=" N   LEU B 385 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA B 386 " --> pdb=" O   PRO B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 420
      removed outlier: 3.850A  pdb=" N   GLY B 400 " --> pdb=" O   ILE B 396 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   MET B 403 " --> pdb=" O   MET B 399 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL B 404 " --> pdb=" O   GLY B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 424 through 429
    Processing helix  chain 'C' and resid 13 through 36
    Processing helix  chain 'C' and resid 37 through 45
    Processing helix  chain 'C' and resid 45 through 58
      removed outlier: 3.719A  pdb=" N   GLY C  49 " --> pdb=" O   ILE C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 75
      removed outlier: 3.666A  pdb=" N   ILE C  75 " --> pdb=" O   GLY C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 110
      removed outlier: 3.596A  pdb=" N   TYR C  90 " --> pdb=" O   LYS C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 138
    Processing helix  chain 'C' and resid 143 through 151
    Processing helix  chain 'C' and resid 153 through 171
    Processing helix  chain 'C' and resid 175 through 222
      Proline residue:  C 208  - end of helix
    Processing helix  chain 'C' and resid 228 through 256
      removed outlier: 4.323A  pdb=" N   PHE C 250 " --> pdb=" O   VAL C 246 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 278
      removed outlier: 5.639A  pdb=" N   ASP C 269 " --> pdb=" O   ARG C 265 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   ALA C 270 " --> pdb=" O   LYS C 266 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 282
      No H-bonds generated for 'chain 'C' and resid 280 through 282'
    Processing helix  chain 'C' and resid 283 through 295
    Processing helix  chain 'C' and resid 298 through 313
      removed outlier: 3.540A  pdb=" N   PHE C 302 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   PHE C 304 " --> pdb=" O   GLY C 300 " (cutoff:3.500A)
      Proline residue:  C 307  - end of helix
    Processing helix  chain 'C' and resid 314 through 333
      removed outlier: 3.787A  pdb=" N   GLY C 333 " --> pdb=" O   ALA C 329 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 354
      removed outlier: 4.569A  pdb=" N   LEU C 346 " --> pdb=" O   LEU C 342 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   VAL C 349 " --> pdb=" O   VAL C 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 360 through 365
    Processing helix  chain 'C' and resid 365 through 373
      removed outlier: 3.873A  pdb=" N   VAL C 369 " --> pdb=" O   MET C 365 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 381 through 420
      removed outlier: 4.025A  pdb=" N   LEU C 385 " --> pdb=" O   SER C 381 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ILE C 393 " --> pdb=" O   MET C 389 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ALA C 395 " --> pdb=" O   LEU C 391 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   ILE C 396 " --> pdb=" O   GLY C 392 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLY C 400 " --> pdb=" O   ILE C 396 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   MET C 403 " --> pdb=" O   MET C 399 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 424 through 428
    Processing helix  chain 'D' and resid 66 through 69
    Processing helix  chain 'D' and resid 91 through 95
    Processing sheet with id=AA1, first strand: chain 'D' and resid 8 through 11
    Processing sheet with id=AA2, first strand: chain 'D' and resid 14 through 16
      removed outlier: 6.172A  pdb=" N   GLY D  14 " --> pdb=" O   THR D 116 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   MET D  38 " --> pdb=" O   ILE D  55 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   ARG D  42 " --> pdb=" O   TRP D  51 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   TRP D  51 " --> pdb=" O   ARG D  42 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 14 through 16
      removed outlier: 6.172A  pdb=" N   GLY D  14 " --> pdb=" O   THR D 116 " (cutoff:3.500A)

    805 hydrogen bonds defined for protein.
    2367 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: 1.74

  Time building geometry restraints manager: 1.15 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: 3212
        1.34 -     1.46: 1954
        1.46 -     1.57: 5240
        1.57 -     1.69: 0
        1.69 -     1.81: 102
  Bond restraints: 10508
  Sorted by residual:
  bond pdb=" C   VAL B 140 "
       pdb=" N   PRO B 141 "
    ideal  model  delta    sigma   weight residual
    1.334  1.314  0.019 1.11e-02 8.12e+03 3.07e+00
  bond pdb=" C   ASP A 259 "
       pdb=" N   PRO A 260 "
    ideal  model  delta    sigma   weight residual
    1.336  1.318  0.018 1.20e-02 6.94e+03 2.29e+00
  bond pdb=" CA  VAL B 358 "
       pdb=" CB  VAL B 358 "
    ideal  model  delta    sigma   weight residual
    1.546  1.534  0.013 8.80e-03 1.29e+04 2.06e+00
  bond pdb=" N   VAL C 226 "
       pdb=" CA  VAL C 226 "
    ideal  model  delta    sigma   weight residual
    1.474  1.456  0.019 1.57e-02 4.06e+03 1.41e+00
  bond pdb=" CA  ASN A 313 "
       pdb=" CB  ASN A 313 "
    ideal  model  delta    sigma   weight residual
    1.525  1.509  0.016 1.47e-02 4.63e+03 1.14e+00
  ... (remaining 10503 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 13871
        1.55 -     3.11: 349
        3.11 -     4.66: 53
        4.66 -     6.21: 17
        6.21 -     7.76: 5
  Bond angle restraints: 14295
  Sorted by residual:
  angle pdb=" N   VAL C 227 "
        pdb=" CA  VAL C 227 "
        pdb=" C   VAL C 227 "
      ideal   model   delta    sigma   weight residual
     113.71  109.09    4.62 9.50e-01 1.11e+00 2.36e+01
  angle pdb=" N   LEU B  59 "
        pdb=" CA  LEU B  59 "
        pdb=" C   LEU B  59 "
      ideal   model   delta    sigma   weight residual
     114.62  110.76    3.86 1.14e+00 7.69e-01 1.15e+01
  angle pdb=" C   VAL B 246 "
        pdb=" N   ILE B 247 "
        pdb=" CA  ILE B 247 "
      ideal   model   delta    sigma   weight residual
     122.63  118.76    3.87 1.19e+00 7.06e-01 1.06e+01
  angle pdb=" N   ALA A 207 "
        pdb=" CA  ALA A 207 "
        pdb=" C   ALA A 207 "
      ideal   model   delta    sigma   weight residual
     109.81  116.42   -6.61 2.21e+00 2.05e-01 8.96e+00
  angle pdb=" N   ALA C 207 "
        pdb=" CA  ALA C 207 "
        pdb=" C   ALA C 207 "
      ideal   model   delta    sigma   weight residual
     109.81  116.31   -6.50 2.21e+00 2.05e-01 8.66e+00
  ... (remaining 14290 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 5686
       17.82 -    35.65: 427
       35.65 -    53.47: 62
       53.47 -    71.30: 7
       71.30 -    89.12: 2
  Dihedral angle restraints: 6184
    sinusoidal: 2304
      harmonic: 3880
  Sorted by residual:
  dihedral pdb=" CA  GLN B 128 "
           pdb=" C   GLN B 128 "
           pdb=" N   PRO B 129 "
           pdb=" CA  PRO B 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.98   22.02     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  LEU A  59 "
           pdb=" C   LEU A  59 "
           pdb=" N   VAL A  60 "
           pdb=" CA  VAL A  60 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.00  -20.00     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  VAL D 104 "
           pdb=" C   VAL D 104 "
           pdb=" N   GLY D 105 "
           pdb=" CA  GLY D 105 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.77  -19.23     0      5.00e+00 4.00e-02 1.48e+01
  ... (remaining 6181 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1003
       0.028 -    0.055: 462
       0.055 -    0.083: 178
       0.083 -    0.110: 96
       0.110 -    0.138: 20
  Chirality restraints: 1759
  Sorted by residual:
  chirality pdb=" CA  ASN D  81 "
            pdb=" N   ASN D  81 "
            pdb=" C   ASN D  81 "
            pdb=" CB  ASN D  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.77e-01
  chirality pdb=" CA  PRO C 208 "
            pdb=" N   PRO C 208 "
            pdb=" C   PRO C 208 "
            pdb=" CB  PRO C 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.73e-01
  chirality pdb=" CA  PRO B 379 "
            pdb=" N   PRO B 379 "
            pdb=" C   PRO B 379 "
            pdb=" CB  PRO B 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.05e-01
  ... (remaining 1756 not shown)

  Planarity restraints: 1760
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 245 "    0.010 2.00e-02 2.50e+03   2.03e-02 4.12e+00
        pdb=" C   ILE B 245 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ILE B 245 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL B 246 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 244 "   -0.009 2.00e-02 2.50e+03   1.71e-02 2.92e+00
        pdb=" C   GLN B 244 "    0.030 2.00e-02 2.50e+03
        pdb=" O   GLN B 244 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ILE B 245 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 128 "    0.028 5.00e-02 4.00e+02   4.21e-02 2.84e+00
        pdb=" N   PRO B 129 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 129 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 129 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1757 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 618
        2.71 -     3.26: 12742
        3.26 -     3.81: 18665
        3.81 -     4.35: 21741
        4.35 -     4.90: 35412
  Nonbonded interactions: 89178
  Sorted by model distance:
  nonbonded pdb=" O   ILE C  63 "
            pdb=" OG  SER C  67 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" O   ALA C 363 "
            pdb=" OH  TYR C 387 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" O   ALA A 363 "
            pdb=" OH  TYR A 387 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" O   ARG A   7 "
            pdb=" NH1 ARG A   7 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" O   ILE B  63 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.183 3.040
  ... (remaining 89173 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 5 through 117 or resid 129 through 501))
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.010
  Find NCS groups from input model:        0.180
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
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      :  0.005   0.037  10509  Z= 0.250
  Angle     :  0.644   7.765  14297  Z= 0.366
  Chirality :  0.040   0.138   1759
  Planarity :  0.004   0.042   1760
  Dihedral  : 12.536  89.120   3717
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 18.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.00 (0.21), residues: 1359
  helix: -1.02 (0.15), residues: 1020
  sheet: -2.42 (0.59), residues: 57
  loop : -1.49 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 401 
 TYR   0.010   0.001   TYR A 169 
 PHE   0.016   0.001   PHE A 302 
 TRP   0.015   0.001   TRP B 428 
 HIS   0.003   0.001   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 (10508)
  covalent geometry    : angle       0.64448 (14295)
  SS BOND              : bond        0.00246 (    1)
  SS BOND              : angle       0.17377 (    2)
  hydrogen bonds       : bond        0.14878 (  801)
  hydrogen bonds       : angle       6.78133 ( 2367)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 LYS cc_start: 0.9378 (mtmm) cc_final: 0.9009 (mtmm)
REVERT: A  243 LEU cc_start: 0.9719 (tp) cc_final: 0.9503 (tp)
REVERT: A  271 MET cc_start: 0.9288 (mtp) cc_final: 0.9012 (mtm)
REVERT: A  288 MET cc_start: 0.9318 (mtp) cc_final: 0.9080 (mtp)
REVERT: A  321 GLN cc_start: 0.9521 (mm-40) cc_final: 0.9225 (mm110)
REVERT: A  394 ASP cc_start: 0.9031 (p0) cc_final: 0.8710 (p0)
REVERT: A  403 MET cc_start: 0.8974 (tmm) cc_final: 0.8105 (tmm)
REVERT: B   50 ASP cc_start: 0.9078 (m-30) cc_final: 0.8751 (m-30)
REVERT: B  180 LYS cc_start: 0.9560 (mmmm) cc_final: 0.9246 (mmmm)
REVERT: B  271 MET cc_start: 0.9245 (mtp) cc_final: 0.8613 (mpp)
REVERT: B  399 MET cc_start: 0.9225 (ptp) cc_final: 0.8956 (ptp)
REVERT: C   97 MET cc_start: 0.8854 (tpp) cc_final: 0.8373 (tpp)
REVERT: C  219 MET cc_start: 0.9598 (tpp) cc_final: 0.9048 (tpp)
REVERT: C  244 GLN cc_start: 0.9504 (tm-30) cc_final: 0.8940 (tm-30)
REVERT: C  271 MET cc_start: 0.9159 (mtm) cc_final: 0.8485 (mtp)
REVERT: C  295 MET cc_start: 0.9319 (mmm) cc_final: 0.9013 (mmm)
REVERT: C  321 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8845 (mm-40)
REVERT: C  365 MET cc_start: 0.8896 (ptp) cc_final: 0.8677 (ptp)
REVERT: C  403 MET cc_start: 0.9153 (tmm) cc_final: 0.8936 (tmm)
REVERT: D   24 LEU cc_start: 0.9341 (mm) cc_final: 0.9134 (mm)
REVERT: D   40 TRP cc_start: 0.9280 (m100) cc_final: 0.8381 (m100)
REVERT: D   42 ARG cc_start: 0.9255 (ttp-170) cc_final: 0.8991 (ttp80)
REVERT: D   55 ILE cc_start: 0.9258 (tt) cc_final: 0.9002 (tt)
REVERT: D   84 TYR cc_start: 0.9112 (m-10) cc_final: 0.8891 (m-10)
REVERT: D   85 LEU cc_start: 0.9517 (tt) cc_final: 0.9239 (tt)
REVERT: D   99 TYR cc_start: 0.9452 (m-10) cc_final: 0.9212 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0882
  time to fit residues: 18.1267
Evaluate side-chains
  110 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 138 ASN
A 341 GLN
B 116 ASN
B 138 ASN
D  36 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.044087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.034362 restraints weight = 59260.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.035601 restraints weight = 27998.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.036326 restraints weight = 17023.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.036942 restraints weight = 12513.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.037305 restraints weight = 9793.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.1190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10509  Z= 0.199
  Angle     :  0.665   8.266  14297  Z= 0.342
  Chirality :  0.042   0.192   1759
  Planarity :  0.004   0.042   1760
  Dihedral  :  4.506  35.830   1470
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 11.89 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.23), residues: 1359
  helix:  0.30 (0.15), residues: 1053
  sheet: -2.16 (0.65), residues: 53
  loop : -1.00 (0.43), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A   7 
 TYR   0.014   0.001   TYR D 109 
 PHE   0.028   0.001   PHE A 302 
 TRP   0.012   0.001   TRP B 428 
 HIS   0.004   0.001   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (10508)
  covalent geometry    : angle       0.66526 (14295)
  SS BOND              : bond        0.00116 (    1)
  SS BOND              : angle       1.23910 (    2)
  hydrogen bonds       : bond        0.04516 (  801)
  hydrogen bonds       : angle       5.00485 ( 2367)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 132
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9354 (m-30) cc_final: 0.9076 (m-30)
REVERT: A  150 LYS cc_start: 0.9318 (mtmm) cc_final: 0.9015 (mtmm)
REVERT: A  243 LEU cc_start: 0.9663 (tp) cc_final: 0.9429 (tp)
REVERT: A  271 MET cc_start: 0.9310 (mtp) cc_final: 0.9012 (mtm)
REVERT: A  321 GLN cc_start: 0.9596 (mm-40) cc_final: 0.9236 (mm110)
REVERT: A  394 ASP cc_start: 0.8979 (p0) cc_final: 0.8603 (p0)
REVERT: A  403 MET cc_start: 0.8889 (tmm) cc_final: 0.8069 (tmm)
REVERT: B   50 ASP cc_start: 0.9215 (m-30) cc_final: 0.8705 (m-30)
REVERT: B  171 MET cc_start: 0.9015 (mmp) cc_final: 0.8396 (mmm)
REVERT: B  180 LYS cc_start: 0.9580 (mmmm) cc_final: 0.9249 (mmmm)
REVERT: B  399 MET cc_start: 0.9225 (ptp) cc_final: 0.8815 (ptp)
REVERT: C   97 MET cc_start: 0.8950 (tpp) cc_final: 0.8562 (tpp)
REVERT: C  174 ASN cc_start: 0.9337 (p0) cc_final: 0.9102 (p0)
REVERT: C  219 MET cc_start: 0.9614 (tpp) cc_final: 0.9034 (tpp)
REVERT: C  244 GLN cc_start: 0.9591 (tm-30) cc_final: 0.9069 (tm-30)
REVERT: C  271 MET cc_start: 0.8949 (mtm) cc_final: 0.8374 (mtp)
REVERT: C  321 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8890 (mm110)
REVERT: C  365 MET cc_start: 0.9093 (ptp) cc_final: 0.8786 (ptp)
REVERT: C  403 MET cc_start: 0.9075 (tmm) cc_final: 0.8873 (tmm)
REVERT: D   24 LEU cc_start: 0.9472 (mm) cc_final: 0.9058 (mm)
REVERT: D   40 TRP cc_start: 0.9262 (m100) cc_final: 0.8074 (m100)
REVERT: D   55 ILE cc_start: 0.9207 (tt) cc_final: 0.8761 (tt)
REVERT: D   69 LYS cc_start: 0.9354 (mmmt) cc_final: 0.9113 (mmmt)
REVERT: D   84 TYR cc_start: 0.8901 (m-10) cc_final: 0.8632 (m-80)
REVERT: D   85 LEU cc_start: 0.9272 (tt) cc_final: 0.8707 (tt)
REVERT: D   99 TYR cc_start: 0.9491 (m-10) cc_final: 0.9179 (m-10)
  outliers start: 8
  outliers final: 2
  residues processed: 137
  average time/residue: 0.0916
  time to fit residues: 18.7895
Evaluate side-chains
  119 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 117
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  272 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 93 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 107 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 50 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 51 optimal weight:    0.2980
   chunk 130 optimal weight:    7.9990
   overall best weight:    2.6588

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

Flipped N/Q/H residues before XYZ refinement:
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 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 = 0.2922 r_free = 0.2922 target = 0.044426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.034735 restraints weight = 59312.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.035971 restraints weight = 28047.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.036702 restraints weight = 17046.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.037311 restraints weight = 12505.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.037705 restraints weight = 9777.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10509  Z= 0.187
  Angle     :  0.642   9.036  14297  Z= 0.327
  Chirality :  0.042   0.183   1759
  Planarity :  0.004   0.051   1760
  Dihedral  :  4.432  34.929   1470
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.10 %
    Favored  : 84.24 %
  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:  0.53 (0.23), residues: 1359
  helix:  0.85 (0.16), residues: 1045
  sheet: -1.88 (0.66), residues: 53
  loop : -0.85 (0.43), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   7 
 TYR   0.014   0.001   TYR C 387 
 PHE   0.025   0.001   PHE A 302 
 TRP   0.015   0.001   TRP D  51 
 HIS   0.005   0.001   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (10508)
  covalent geometry    : angle       0.64199 (14295)
  SS BOND              : bond        0.00023 (    1)
  SS BOND              : angle       0.66345 (    2)
  hydrogen bonds       : bond        0.04134 (  801)
  hydrogen bonds       : angle       4.75746 ( 2367)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9389 (m-30) cc_final: 0.9025 (m-30)
REVERT: A   97 MET cc_start: 0.9553 (mmm) cc_final: 0.9351 (mmt)
REVERT: A  150 LYS cc_start: 0.9266 (mtmm) cc_final: 0.8989 (mtmm)
REVERT: A  243 LEU cc_start: 0.9628 (tp) cc_final: 0.9390 (tp)
REVERT: A  271 MET cc_start: 0.9319 (mtp) cc_final: 0.8735 (mtt)
REVERT: A  321 GLN cc_start: 0.9578 (mm-40) cc_final: 0.9218 (mm110)
REVERT: A  394 ASP cc_start: 0.8973 (p0) cc_final: 0.8574 (p0)
REVERT: A  403 MET cc_start: 0.8867 (tmm) cc_final: 0.7935 (tmm)
REVERT: B   50 ASP cc_start: 0.9169 (m-30) cc_final: 0.8594 (m-30)
REVERT: B  171 MET cc_start: 0.8955 (mmp) cc_final: 0.8389 (mmm)
REVERT: B  180 LYS cc_start: 0.9574 (mmmm) cc_final: 0.9244 (mmmm)
REVERT: B  271 MET cc_start: 0.9392 (mtp) cc_final: 0.8320 (mtp)
REVERT: B  288 MET cc_start: 0.9283 (mtp) cc_final: 0.9066 (mtp)
REVERT: B  371 GLN cc_start: 0.9279 (pp30) cc_final: 0.9061 (pp30)
REVERT: B  399 MET cc_start: 0.9152 (ptp) cc_final: 0.8949 (ptm)
REVERT: B  403 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8357 (tpp)
REVERT: C   30 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8813 (mm)
REVERT: C   97 MET cc_start: 0.8943 (tpp) cc_final: 0.8525 (tpp)
REVERT: C  174 ASN cc_start: 0.9337 (p0) cc_final: 0.9117 (p0)
REVERT: C  219 MET cc_start: 0.9610 (tpp) cc_final: 0.9056 (ttm)
REVERT: C  244 GLN cc_start: 0.9599 (tm-30) cc_final: 0.9128 (tm-30)
REVERT: C  271 MET cc_start: 0.8948 (mtm) cc_final: 0.8365 (mtp)
REVERT: C  321 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8849 (mm110)
REVERT: C  365 MET cc_start: 0.9057 (ptp) cc_final: 0.8808 (ptp)
REVERT: C  403 MET cc_start: 0.9076 (tmm) cc_final: 0.8865 (tmm)
REVERT: D   24 LEU cc_start: 0.9396 (mm) cc_final: 0.8914 (mm)
REVERT: D   40 TRP cc_start: 0.9153 (m100) cc_final: 0.7844 (m100)
REVERT: D   55 ILE cc_start: 0.9235 (tt) cc_final: 0.8686 (tt)
REVERT: D   72 PHE cc_start: 0.9413 (m-80) cc_final: 0.9097 (m-80)
REVERT: D   85 LEU cc_start: 0.9129 (tt) cc_final: 0.8831 (tt)
REVERT: D   99 TYR cc_start: 0.9466 (m-10) cc_final: 0.9156 (m-10)
REVERT: D  108 TYR cc_start: 0.9373 (m-10) cc_final: 0.9103 (m-10)
  outliers start: 18
  outliers final: 6
  residues processed: 146
  average time/residue: 0.0878
  time to fit residues: 19.4793
Evaluate side-chains
  126 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  288 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 116 optimal weight:    2.9990
   chunk 107 optimal weight:    8.9990
   chunk 45 optimal weight:    0.9980
   chunk 101 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 99 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 334 HIS
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.045313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.035692 restraints weight = 59311.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.036957 restraints weight = 27787.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.037690 restraints weight = 16818.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.038326 restraints weight = 12257.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.038649 restraints weight = 9486.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10509  Z= 0.146
  Angle     :  0.635   9.836  14297  Z= 0.318
  Chirality :  0.041   0.199   1759
  Planarity :  0.004   0.056   1760
  Dihedral  :  4.306  32.837   1470
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 15.85 %
    Favored  : 82.30 %
  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:  0.89 (0.23), residues: 1359
  helix:  1.09 (0.16), residues: 1039
  sheet: -1.51 (0.69), residues: 53
  loop : -0.64 (0.43), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   7 
 TYR   0.013   0.001   TYR C 387 
 PHE   0.023   0.001   PHE A 302 
 TRP   0.010   0.001   TRP D 106 
 HIS   0.002   0.001   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (10508)
  covalent geometry    : angle       0.63457 (14295)
  SS BOND              : bond        0.00061 (    1)
  SS BOND              : angle       0.61046 (    2)
  hydrogen bonds       : bond        0.03832 (  801)
  hydrogen bonds       : angle       4.60605 ( 2367)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9374 (m-30) cc_final: 0.8964 (m-30)
REVERT: A  150 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8947 (mtmm)
REVERT: A  243 LEU cc_start: 0.9622 (tp) cc_final: 0.9398 (tp)
REVERT: A  271 MET cc_start: 0.9314 (mtp) cc_final: 0.8730 (mtt)
REVERT: A  321 GLN cc_start: 0.9594 (mm-40) cc_final: 0.9260 (mm110)
REVERT: A  365 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8524 (ttt)
REVERT: A  394 ASP cc_start: 0.8943 (p0) cc_final: 0.8492 (p0)
REVERT: A  403 MET cc_start: 0.8804 (tmm) cc_final: 0.7866 (tmm)
REVERT: B   50 ASP cc_start: 0.9177 (m-30) cc_final: 0.8584 (m-30)
REVERT: B  171 MET cc_start: 0.8928 (mmp) cc_final: 0.8304 (mmm)
REVERT: B  180 LYS cc_start: 0.9566 (mmmm) cc_final: 0.9235 (mmmm)
REVERT: B  271 MET cc_start: 0.9381 (mtp) cc_final: 0.8841 (mtp)
REVERT: B  288 MET cc_start: 0.9244 (mtp) cc_final: 0.9031 (mtp)
REVERT: B  371 GLN cc_start: 0.9255 (pp30) cc_final: 0.9028 (pp30)
REVERT: B  399 MET cc_start: 0.9134 (ptp) cc_final: 0.8876 (ptm)
REVERT: C   30 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8769 (mm)
REVERT: C   97 MET cc_start: 0.8999 (tpp) cc_final: 0.8558 (tpp)
REVERT: C  174 ASN cc_start: 0.9347 (p0) cc_final: 0.9039 (p0)
REVERT: C  219 MET cc_start: 0.9594 (tpp) cc_final: 0.9065 (ttm)
REVERT: C  244 GLN cc_start: 0.9579 (tm-30) cc_final: 0.9129 (tm-30)
REVERT: C  271 MET cc_start: 0.8935 (mtm) cc_final: 0.8521 (mtt)
REVERT: C  295 MET cc_start: 0.9310 (mmp) cc_final: 0.8963 (mmp)
REVERT: C  321 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8842 (mm110)
REVERT: C  365 MET cc_start: 0.9073 (ptp) cc_final: 0.8842 (ptp)
REVERT: D   24 LEU cc_start: 0.9341 (mm) cc_final: 0.8487 (mm)
REVERT: D   36 GLN cc_start: 0.8631 (mt0) cc_final: 0.8402 (pt0)
REVERT: D   40 TRP cc_start: 0.9110 (m100) cc_final: 0.7781 (m100)
REVERT: D   55 ILE cc_start: 0.9142 (tt) cc_final: 0.8804 (tt)
REVERT: D   69 LYS cc_start: 0.9443 (mmmt) cc_final: 0.8964 (mmmt)
REVERT: D   85 LEU cc_start: 0.9122 (tt) cc_final: 0.8827 (tt)
REVERT: D   99 TYR cc_start: 0.9405 (m-10) cc_final: 0.9044 (m-10)
REVERT: D  108 TYR cc_start: 0.9303 (m-10) cc_final: 0.9004 (m-10)
  outliers start: 20
  outliers final: 7
  residues processed: 149
  average time/residue: 0.0845
  time to fit residues: 19.3007
Evaluate side-chains
  132 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  288 MET
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain D residue   87 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 32 optimal weight:    0.0570
   chunk 72 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 70 optimal weight:    5.9990
   chunk 128 optimal weight:    0.0670
   chunk 82 optimal weight:    2.9990
   chunk 132 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9980
   chunk 107 optimal weight:    9.9990
   chunk 117 optimal weight:   20.0000
   overall best weight:    0.8038

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

Flipped N/Q/H residues before XYZ refinement:
C 134 GLN
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.046605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.036767 restraints weight = 58411.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.038045 restraints weight = 27636.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.038942 restraints weight = 16725.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.039451 restraints weight = 11826.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.039868 restraints weight = 9454.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10509  Z= 0.127
  Angle     :  0.651  10.125  14297  Z= 0.320
  Chirality :  0.041   0.188   1759
  Planarity :  0.004   0.056   1760
  Dihedral  :  4.239  30.109   1470
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 18.06 %
    Favored  : 80.46 %
  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:  1.01 (0.23), residues: 1359
  helix:  1.16 (0.16), residues: 1038
  sheet: -1.28 (0.68), residues: 53
  loop : -0.59 (0.43), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   7 
 TYR   0.010   0.001   TYR C 387 
 PHE   0.018   0.001   PHE A 302 
 TRP   0.011   0.001   TRP D  51 
 HIS   0.001   0.000   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10508)
  covalent geometry    : angle       0.65054 (14295)
  SS BOND              : bond        0.00192 (    1)
  SS BOND              : angle       0.56814 (    2)
  hydrogen bonds       : bond        0.03658 (  801)
  hydrogen bonds       : angle       4.51101 ( 2367)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9386 (m-30) cc_final: 0.8954 (m-30)
REVERT: A   97 MET cc_start: 0.9544 (mmm) cc_final: 0.9302 (mmt)
REVERT: A  271 MET cc_start: 0.9310 (mtp) cc_final: 0.8766 (mtt)
REVERT: A  321 GLN cc_start: 0.9599 (mm-40) cc_final: 0.9258 (mm110)
REVERT: A  365 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8448 (ttt)
REVERT: A  394 ASP cc_start: 0.8843 (p0) cc_final: 0.8397 (p0)
REVERT: B   50 ASP cc_start: 0.9175 (m-30) cc_final: 0.8552 (m-30)
REVERT: B  171 MET cc_start: 0.8861 (mmp) cc_final: 0.8270 (mmm)
REVERT: B  180 LYS cc_start: 0.9555 (mmmm) cc_final: 0.9236 (mmmm)
REVERT: B  219 MET cc_start: 0.9134 (mtp) cc_final: 0.8383 (tpp)
REVERT: B  271 MET cc_start: 0.9342 (mtp) cc_final: 0.8847 (mtp)
REVERT: B  288 MET cc_start: 0.9197 (mtp) cc_final: 0.8992 (mtp)
REVERT: B  368 MET cc_start: 0.9074 (tmm) cc_final: 0.8549 (tmm)
REVERT: B  371 GLN cc_start: 0.9229 (pp30) cc_final: 0.8966 (pp30)
REVERT: B  399 MET cc_start: 0.9058 (ptp) cc_final: 0.8772 (ptm)
REVERT: C   97 MET cc_start: 0.9010 (tpp) cc_final: 0.8554 (tpp)
REVERT: C  174 ASN cc_start: 0.9375 (p0) cc_final: 0.9071 (p0)
REVERT: C  219 MET cc_start: 0.9576 (tpp) cc_final: 0.9071 (tpt)
REVERT: C  244 GLN cc_start: 0.9551 (tm-30) cc_final: 0.9111 (tm-30)
REVERT: C  271 MET cc_start: 0.8896 (mtm) cc_final: 0.7976 (mtm)
REVERT: C  295 MET cc_start: 0.9321 (mmp) cc_final: 0.9083 (mmp)
REVERT: C  321 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8804 (mm110)
REVERT: C  365 MET cc_start: 0.9031 (ptp) cc_final: 0.8757 (ptp)
REVERT: D   24 LEU cc_start: 0.9404 (mm) cc_final: 0.8892 (mm)
REVERT: D   36 GLN cc_start: 0.8603 (mt0) cc_final: 0.8364 (pt0)
REVERT: D   40 TRP cc_start: 0.8923 (m100) cc_final: 0.7966 (m100)
REVERT: D   55 ILE cc_start: 0.9113 (tt) cc_final: 0.8714 (tt)
REVERT: D   69 LYS cc_start: 0.9467 (mmmt) cc_final: 0.9142 (tppt)
REVERT: D   85 LEU cc_start: 0.8961 (tt) cc_final: 0.8662 (tt)
REVERT: D   99 TYR cc_start: 0.9374 (m-10) cc_final: 0.9012 (m-10)
REVERT: D  108 TYR cc_start: 0.9307 (m-10) cc_final: 0.8973 (m-10)
  outliers start: 16
  outliers final: 7
  residues processed: 155
  average time/residue: 0.0775
  time to fit residues: 18.5155
Evaluate side-chains
  136 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 128
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain C residue  423 LEU
Chi-restraints excluded: chain D residue   38 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 83 optimal weight:   10.0000
   chunk 110 optimal weight:    0.6980
   chunk 105 optimal weight:    6.9990
   chunk 63 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 117 optimal weight:    0.6980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.046905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.037139 restraints weight = 59143.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.038410 restraints weight = 27871.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.039283 restraints weight = 17051.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.039778 restraints weight = 11973.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.040257 restraints weight = 9534.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10509  Z= 0.129
  Angle     :  0.658  10.429  14297  Z= 0.321
  Chirality :  0.041   0.182   1759
  Planarity :  0.004   0.055   1760
  Dihedral  :  4.209  33.888   1470
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.71 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.23), residues: 1359
  helix:  1.19 (0.16), residues: 1042
  sheet: -1.13 (0.68), residues: 53
  loop : -0.49 (0.44), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 278 
 TYR   0.019   0.001   TYR D  84 
 PHE   0.014   0.001   PHE A 302 
 TRP   0.007   0.001   TRP D  51 
 HIS   0.001   0.000   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10508)
  covalent geometry    : angle       0.65798 (14295)
  SS BOND              : bond        0.00168 (    1)
  SS BOND              : angle       0.52690 (    2)
  hydrogen bonds       : bond        0.03646 (  801)
  hydrogen bonds       : angle       4.46711 ( 2367)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9385 (m-30) cc_final: 0.8935 (m-30)
REVERT: A  271 MET cc_start: 0.9364 (mtp) cc_final: 0.9085 (mtm)
REVERT: A  321 GLN cc_start: 0.9592 (mm-40) cc_final: 0.9225 (mm110)
REVERT: A  365 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8412 (ttt)
REVERT: A  394 ASP cc_start: 0.8839 (p0) cc_final: 0.8444 (p0)
REVERT: B   50 ASP cc_start: 0.9168 (m-30) cc_final: 0.8554 (m-30)
REVERT: B  167 ILE cc_start: 0.9758 (mt) cc_final: 0.9280 (tt)
REVERT: B  171 MET cc_start: 0.8849 (mmp) cc_final: 0.8283 (mmm)
REVERT: B  180 LYS cc_start: 0.9547 (mmmm) cc_final: 0.9228 (mmmm)
REVERT: B  219 MET cc_start: 0.9137 (mtp) cc_final: 0.8367 (tpp)
REVERT: B  271 MET cc_start: 0.9072 (mtp) cc_final: 0.8461 (mtt)
REVERT: B  368 MET cc_start: 0.9107 (tmm) cc_final: 0.8600 (tmm)
REVERT: B  371 GLN cc_start: 0.9256 (pp30) cc_final: 0.9021 (pp30)
REVERT: B  399 MET cc_start: 0.9085 (ptp) cc_final: 0.8783 (ptm)
REVERT: C   97 MET cc_start: 0.9015 (tpp) cc_final: 0.8777 (tpp)
REVERT: C  174 ASN cc_start: 0.9388 (p0) cc_final: 0.9096 (p0)
REVERT: C  219 MET cc_start: 0.9596 (tpp) cc_final: 0.9023 (tpt)
REVERT: C  244 GLN cc_start: 0.9536 (tm-30) cc_final: 0.9146 (tm-30)
REVERT: C  271 MET cc_start: 0.8860 (mtm) cc_final: 0.7673 (mtp)
REVERT: C  321 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8911 (mm110)
REVERT: C  365 MET cc_start: 0.9021 (ptp) cc_final: 0.8770 (ptp)
REVERT: C  403 MET cc_start: 0.9232 (tpt) cc_final: 0.8675 (tpt)
REVERT: D   24 LEU cc_start: 0.9404 (mm) cc_final: 0.8894 (mm)
REVERT: D   36 GLN cc_start: 0.8537 (mt0) cc_final: 0.8302 (pt0)
REVERT: D   40 TRP cc_start: 0.8869 (m100) cc_final: 0.7809 (m100)
REVERT: D   63 TYR cc_start: 0.8521 (m-80) cc_final: 0.8296 (m-80)
REVERT: D   69 LYS cc_start: 0.9474 (mmmt) cc_final: 0.9131 (tppt)
REVERT: D   85 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8642 (tt)
REVERT: D   99 TYR cc_start: 0.9343 (m-10) cc_final: 0.8968 (m-10)
REVERT: D  108 TYR cc_start: 0.9294 (m-10) cc_final: 0.8940 (m-10)
  outliers start: 23
  outliers final: 10
  residues processed: 162
  average time/residue: 0.0770
  time to fit residues: 19.4342
Evaluate side-chains
  143 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  423 LEU
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain D residue   85 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 113 optimal weight:    0.9990
   chunk 89 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 73 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 120 optimal weight:    4.9990
   chunk 131 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** D  81 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 = 0.3026 r_free = 0.3026 target = 0.047453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.037255 restraints weight = 57953.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.038551 restraints weight = 27564.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.039400 restraints weight = 16903.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.039956 restraints weight = 12095.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.040357 restraints weight = 9675.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10509  Z= 0.126
  Angle     :  0.679  11.151  14297  Z= 0.328
  Chirality :  0.042   0.194   1759
  Planarity :  0.004   0.056   1760
  Dihedral  :  4.108  26.090   1470
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 20.28 %
    Favored  : 77.88 %
  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:  1.16 (0.23), residues: 1359
  helix:  1.23 (0.16), residues: 1042
  sheet: -0.95 (0.72), residues: 48
  loop : -0.47 (0.43), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 278 
 TYR   0.016   0.001   TYR D  84 
 PHE   0.016   0.001   PHE B 302 
 TRP   0.014   0.001   TRP D  51 
 HIS   0.001   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (10508)
  covalent geometry    : angle       0.67909 (14295)
  SS BOND              : bond        0.00205 (    1)
  SS BOND              : angle       0.52135 (    2)
  hydrogen bonds       : bond        0.03592 (  801)
  hydrogen bonds       : angle       4.37539 ( 2367)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9394 (m-30) cc_final: 0.8939 (m-30)
REVERT: A   97 MET cc_start: 0.9583 (mmm) cc_final: 0.9320 (mmt)
REVERT: A  271 MET cc_start: 0.9360 (mtp) cc_final: 0.9140 (mtm)
REVERT: A  321 GLN cc_start: 0.9587 (mm-40) cc_final: 0.9267 (mm110)
REVERT: A  394 ASP cc_start: 0.8798 (p0) cc_final: 0.8404 (p0)
REVERT: A  403 MET cc_start: 0.8768 (tmm) cc_final: 0.8059 (tmm)
REVERT: B   50 ASP cc_start: 0.9169 (m-30) cc_final: 0.8543 (m-30)
REVERT: B  167 ILE cc_start: 0.9745 (mt) cc_final: 0.9274 (tt)
REVERT: B  171 MET cc_start: 0.8858 (mmp) cc_final: 0.8260 (mmm)
REVERT: B  180 LYS cc_start: 0.9546 (mmmm) cc_final: 0.9220 (mmmm)
REVERT: B  219 MET cc_start: 0.9165 (mtp) cc_final: 0.8361 (tpp)
REVERT: B  271 MET cc_start: 0.9094 (mtp) cc_final: 0.8667 (mtm)
REVERT: B  321 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8897 (mm-40)
REVERT: B  368 MET cc_start: 0.9112 (tmm) cc_final: 0.8717 (tmm)
REVERT: B  399 MET cc_start: 0.9065 (ptp) cc_final: 0.8761 (ptm)
REVERT: C   97 MET cc_start: 0.9030 (tpp) cc_final: 0.8776 (tpp)
REVERT: C  174 ASN cc_start: 0.9402 (p0) cc_final: 0.9109 (p0)
REVERT: C  219 MET cc_start: 0.9589 (tpp) cc_final: 0.8995 (tpt)
REVERT: C  244 GLN cc_start: 0.9513 (tm-30) cc_final: 0.9141 (tm-30)
REVERT: C  271 MET cc_start: 0.8925 (mtm) cc_final: 0.7725 (mtp)
REVERT: C  306 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9421 (mm)
REVERT: C  321 GLN cc_start: 0.9233 (mm-40) cc_final: 0.8940 (mm110)
REVERT: C  358 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.7952 (p)
REVERT: C  365 MET cc_start: 0.8990 (ptp) cc_final: 0.8741 (ptp)
REVERT: C  403 MET cc_start: 0.9111 (tpt) cc_final: 0.8873 (tpt)
REVERT: D   24 LEU cc_start: 0.9390 (mm) cc_final: 0.8853 (mm)
REVERT: D   40 TRP cc_start: 0.8800 (m100) cc_final: 0.7737 (m100)
REVERT: D   48 GLU cc_start: 0.9332 (tp30) cc_final: 0.8953 (tp30)
REVERT: D   69 LYS cc_start: 0.9462 (mmmt) cc_final: 0.9155 (tppt)
REVERT: D   85 LEU cc_start: 0.8916 (tt) cc_final: 0.8541 (tt)
REVERT: D   99 TYR cc_start: 0.9352 (m-10) cc_final: 0.9058 (m-10)
REVERT: D  108 TYR cc_start: 0.9302 (m-10) cc_final: 0.8933 (m-80)
REVERT: C  501 ASP cc_start: 0.6752 (m-30) cc_final: 0.6352 (m-30)
  outliers start: 20
  outliers final: 13
  residues processed: 157
  average time/residue: 0.0823
  time to fit residues: 19.7473
Evaluate side-chains
  150 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  358 VAL
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  423 LEU
Chi-restraints excluded: chain D residue   37 PHE
Chi-restraints excluded: chain D residue   38 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 63 optimal weight:    0.1980
   chunk 73 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0040
   chunk 54 optimal weight:    0.6980
   chunk 100 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 96 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 133 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    0.9796

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

Flipped N/Q/H residues before XYZ refinement:
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.047405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.037477 restraints weight = 58307.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.038798 restraints weight = 27746.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.039681 restraints weight = 16880.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.040171 restraints weight = 11889.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.040629 restraints weight = 9537.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10509  Z= 0.131
  Angle     :  0.698  11.797  14297  Z= 0.336
  Chirality :  0.042   0.283   1759
  Planarity :  0.004   0.055   1760
  Dihedral  :  4.125  26.486   1470
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 19.63 %
    Favored  : 78.16 %
  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:  1.18 (0.23), residues: 1359
  helix:  1.26 (0.16), residues: 1038
  sheet: -0.89 (0.72), residues: 48
  loop : -0.53 (0.43), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 187 
 TYR   0.029   0.001   TYR D  63 
 PHE   0.016   0.001   PHE A 302 
 TRP   0.013   0.001   TRP D  51 
 HIS   0.001   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10508)
  covalent geometry    : angle       0.69788 (14295)
  SS BOND              : bond        0.00152 (    1)
  SS BOND              : angle       0.53011 (    2)
  hydrogen bonds       : bond        0.03582 (  801)
  hydrogen bonds       : angle       4.36677 ( 2367)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9389 (m-30) cc_final: 0.8928 (m-30)
REVERT: A   97 MET cc_start: 0.9572 (mmm) cc_final: 0.9328 (mmt)
REVERT: A  271 MET cc_start: 0.9368 (mtp) cc_final: 0.9139 (mtm)
REVERT: A  321 GLN cc_start: 0.9581 (mm-40) cc_final: 0.9253 (mm110)
REVERT: A  394 ASP cc_start: 0.8815 (p0) cc_final: 0.8408 (p0)
REVERT: A  403 MET cc_start: 0.8771 (tmm) cc_final: 0.8104 (tmm)
REVERT: B   50 ASP cc_start: 0.9173 (m-30) cc_final: 0.8541 (m-30)
REVERT: B  128 GLN cc_start: 0.8348 (mp10) cc_final: 0.8088 (mp10)
REVERT: B  171 MET cc_start: 0.8832 (mmp) cc_final: 0.8224 (mmm)
REVERT: B  180 LYS cc_start: 0.9541 (mmmm) cc_final: 0.9230 (mmmm)
REVERT: B  219 MET cc_start: 0.9168 (mtp) cc_final: 0.8391 (tpp)
REVERT: B  271 MET cc_start: 0.9090 (mtp) cc_final: 0.8670 (mtm)
REVERT: B  368 MET cc_start: 0.9086 (tmm) cc_final: 0.8757 (tmm)
REVERT: B  399 MET cc_start: 0.9072 (ptp) cc_final: 0.8754 (ptm)
REVERT: C   97 MET cc_start: 0.9011 (tpp) cc_final: 0.8728 (tpp)
REVERT: C  174 ASN cc_start: 0.9397 (p0) cc_final: 0.9102 (p0)
REVERT: C  219 MET cc_start: 0.9577 (tpp) cc_final: 0.8995 (tpt)
REVERT: C  244 GLN cc_start: 0.9508 (tm-30) cc_final: 0.9143 (tm-30)
REVERT: C  271 MET cc_start: 0.8886 (mtm) cc_final: 0.7692 (mtp)
REVERT: C  306 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9430 (mm)
REVERT: C  321 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8851 (mm110)
REVERT: C  358 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.7782 (p)
REVERT: C  365 MET cc_start: 0.8940 (ptp) cc_final: 0.8723 (ptp)
REVERT: D   24 LEU cc_start: 0.9369 (mm) cc_final: 0.8806 (mm)
REVERT: D   40 TRP cc_start: 0.8858 (m100) cc_final: 0.7944 (m100)
REVERT: D   50 GLU cc_start: 0.9467 (pm20) cc_final: 0.9007 (pm20)
REVERT: D   61 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8603 (pp20)
REVERT: D   69 LYS cc_start: 0.9478 (mmmt) cc_final: 0.9213 (tppt)
REVERT: D   85 LEU cc_start: 0.8910 (tt) cc_final: 0.8576 (tt)
REVERT: D   99 TYR cc_start: 0.9337 (m-10) cc_final: 0.8962 (m-10)
REVERT: D  108 TYR cc_start: 0.9272 (m-10) cc_final: 0.8881 (m-80)
REVERT: C  501 ASP cc_start: 0.6845 (m-30) cc_final: 0.6403 (m-30)
  outliers start: 24
  outliers final: 13
  residues processed: 158
  average time/residue: 0.0799
  time to fit residues: 19.4321
Evaluate side-chains
  152 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  423 LEU
Chi-restraints excluded: chain D residue   37 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 117 optimal weight:    7.9990
   chunk 107 optimal weight:    0.9990
   chunk 32 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 50 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.046484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.036689 restraints weight = 58801.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.037963 restraints weight = 28043.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.038797 restraints weight = 17125.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.039380 restraints weight = 12160.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.039756 restraints weight = 9558.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10509  Z= 0.163
  Angle     :  0.729  13.547  14297  Z= 0.349
  Chirality :  0.044   0.335   1759
  Planarity :  0.004   0.055   1760
  Dihedral  :  4.156  27.257   1470
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 20.28 %
    Favored  : 77.79 %
  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:  1.23 (0.24), residues: 1359
  helix:  1.29 (0.16), residues: 1040
  sheet: -0.75 (0.73), residues: 48
  loop : -0.52 (0.43), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 187 
 TYR   0.011   0.001   TYR D  64 
 PHE   0.015   0.001   PHE A 302 
 TRP   0.024   0.001   TRP D  51 
 HIS   0.001   0.000   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (10508)
  covalent geometry    : angle       0.72856 (14295)
  SS BOND              : bond        0.00207 (    1)
  SS BOND              : angle       0.47647 (    2)
  hydrogen bonds       : bond        0.03672 (  801)
  hydrogen bonds       : angle       4.38030 ( 2367)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9398 (m-30) cc_final: 0.8943 (m-30)
REVERT: A   97 MET cc_start: 0.9568 (mmm) cc_final: 0.9330 (mmt)
REVERT: A  271 MET cc_start: 0.9349 (mtp) cc_final: 0.9138 (mtm)
REVERT: A  321 GLN cc_start: 0.9547 (mm-40) cc_final: 0.9248 (mm110)
REVERT: A  394 ASP cc_start: 0.8851 (p0) cc_final: 0.8447 (p0)
REVERT: A  403 MET cc_start: 0.8788 (tmm) cc_final: 0.8148 (tmm)
REVERT: B   50 ASP cc_start: 0.9192 (m-30) cc_final: 0.8550 (m-30)
REVERT: B  171 MET cc_start: 0.8843 (mmp) cc_final: 0.8237 (mmm)
REVERT: B  180 LYS cc_start: 0.9563 (mmmm) cc_final: 0.9254 (mmmm)
REVERT: B  219 MET cc_start: 0.9220 (mtp) cc_final: 0.8354 (tpp)
REVERT: B  271 MET cc_start: 0.9109 (mtp) cc_final: 0.8685 (mtm)
REVERT: B  321 GLN cc_start: 0.9248 (mm-40) cc_final: 0.8871 (mm-40)
REVERT: B  368 MET cc_start: 0.9053 (tmm) cc_final: 0.8735 (tmm)
REVERT: B  389 MET cc_start: 0.9651 (mtm) cc_final: 0.8996 (mpp)
REVERT: B  399 MET cc_start: 0.9125 (ptp) cc_final: 0.8813 (ptm)
REVERT: C   97 MET cc_start: 0.9031 (tpp) cc_final: 0.8539 (tpp)
REVERT: C  174 ASN cc_start: 0.9394 (p0) cc_final: 0.9098 (p0)
REVERT: C  219 MET cc_start: 0.9585 (tpp) cc_final: 0.8995 (tpt)
REVERT: C  244 GLN cc_start: 0.9523 (tm-30) cc_final: 0.9149 (tm-30)
REVERT: C  271 MET cc_start: 0.8665 (mtm) cc_final: 0.7806 (mtt)
REVERT: C  306 LEU cc_start: 0.9722 (OUTLIER) cc_final: 0.9475 (mm)
REVERT: C  321 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8867 (mm110)
REVERT: C  365 MET cc_start: 0.8939 (ptp) cc_final: 0.8716 (ptp)
REVERT: C  403 MET cc_start: 0.9083 (tpt) cc_final: 0.8303 (tpt)
REVERT: D   24 LEU cc_start: 0.9392 (mm) cc_final: 0.8818 (mm)
REVERT: D   40 TRP cc_start: 0.8922 (m100) cc_final: 0.7881 (m100)
REVERT: D   50 GLU cc_start: 0.9483 (pm20) cc_final: 0.9019 (pm20)
REVERT: D   61 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8757 (pp20)
REVERT: D   69 LYS cc_start: 0.9493 (mmmt) cc_final: 0.9098 (mmmt)
REVERT: D   85 LEU cc_start: 0.8930 (tt) cc_final: 0.8601 (tt)
REVERT: D   99 TYR cc_start: 0.9367 (m-10) cc_final: 0.8994 (m-10)
REVERT: D  108 TYR cc_start: 0.9306 (m-10) cc_final: 0.8868 (m-80)
REVERT: C  501 ASP cc_start: 0.6874 (m-30) cc_final: 0.6426 (m-30)
  outliers start: 21
  outliers final: 17
  residues processed: 150
  average time/residue: 0.0826
  time to fit residues: 19.1182
Evaluate side-chains
  151 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  358 VAL
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  423 LEU
Chi-restraints excluded: chain D residue   36 GLN
Chi-restraints excluded: chain D residue   37 PHE
Chi-restraints excluded: chain D residue   87 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 77 optimal weight:    0.0170
   chunk 15 optimal weight:    0.3980
   chunk 76 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 109 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 89 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 131 optimal weight:    9.9990
   chunk 1 optimal weight:    0.0060
   overall best weight:    0.4434

-------------------------------------------------------------------------------
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 = 0.3041 r_free = 0.3041 target = 0.048077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.038278 restraints weight = 57414.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.039578 restraints weight = 27589.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.040454 restraints weight = 16916.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.041081 restraints weight = 11986.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.041445 restraints weight = 9380.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10509  Z= 0.130
  Angle     :  0.727  11.343  14297  Z= 0.344
  Chirality :  0.043   0.251   1759
  Planarity :  0.004   0.056   1760
  Dihedral  :  4.112  27.740   1470
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 21.01 %
    Favored  : 77.79 %
  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:  1.15 (0.23), residues: 1359
  helix:  1.23 (0.16), residues: 1038
  sheet: -0.67 (0.72), residues: 48
  loop : -0.50 (0.42), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 187 
 TYR   0.032   0.001   TYR D  63 
 PHE   0.015   0.001   PHE A 302 
 TRP   0.020   0.001   TRP D  51 
 HIS   0.001   0.000   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10508)
  covalent geometry    : angle       0.72721 (14295)
  SS BOND              : bond        0.00176 (    1)
  SS BOND              : angle       0.56467 (    2)
  hydrogen bonds       : bond        0.03504 (  801)
  hydrogen bonds       : angle       4.31269 ( 2367)

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

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

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2718 Ramachandran restraints generated.
    1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 150
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9382 (m-30) cc_final: 0.8931 (m-30)
REVERT: A   97 MET cc_start: 0.9543 (mmm) cc_final: 0.9296 (mmt)
REVERT: A  150 LYS cc_start: 0.9348 (mtpp) cc_final: 0.8947 (mtmm)
REVERT: A  244 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8929 (tm-30)
REVERT: A  271 MET cc_start: 0.9368 (mtp) cc_final: 0.8903 (mtt)
REVERT: A  321 GLN cc_start: 0.9552 (mm-40) cc_final: 0.9306 (mm110)
REVERT: A  394 ASP cc_start: 0.8833 (p0) cc_final: 0.8431 (p0)
REVERT: A  403 MET cc_start: 0.8756 (tmm) cc_final: 0.8215 (tmm)
REVERT: B   50 ASP cc_start: 0.9167 (m-30) cc_final: 0.8511 (m-30)
REVERT: B  128 GLN cc_start: 0.8352 (mp10) cc_final: 0.8097 (mp10)
REVERT: B  171 MET cc_start: 0.8773 (mmp) cc_final: 0.8172 (mmm)
REVERT: B  180 LYS cc_start: 0.9552 (mmmm) cc_final: 0.9262 (mmmm)
REVERT: B  219 MET cc_start: 0.9152 (mtp) cc_final: 0.8364 (tpp)
REVERT: B  271 MET cc_start: 0.9054 (mtp) cc_final: 0.8266 (mtm)
REVERT: B  321 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8778 (mm-40)
REVERT: B  368 MET cc_start: 0.9067 (tmm) cc_final: 0.8753 (tmm)
REVERT: B  389 MET cc_start: 0.9618 (mtm) cc_final: 0.8889 (mpp)
REVERT: B  399 MET cc_start: 0.9025 (ptp) cc_final: 0.8672 (ptm)
REVERT: B  403 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8412 (tpp)
REVERT: C   97 MET cc_start: 0.9018 (tpp) cc_final: 0.8731 (tpp)
REVERT: C  174 ASN cc_start: 0.9402 (p0) cc_final: 0.9096 (p0)
REVERT: C  219 MET cc_start: 0.9538 (tpp) cc_final: 0.8936 (tpt)
REVERT: C  244 GLN cc_start: 0.9466 (tm-30) cc_final: 0.9149 (tm-30)
REVERT: C  271 MET cc_start: 0.8620 (mtm) cc_final: 0.7942 (mtt)
REVERT: C  306 LEU cc_start: 0.9708 (OUTLIER) cc_final: 0.9456 (mm)
REVERT: C  321 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8813 (mm110)
REVERT: C  358 VAL cc_start: 0.8459 (t) cc_final: 0.7823 (p)
REVERT: C  365 MET cc_start: 0.8864 (ptp) cc_final: 0.8525 (ptp)
REVERT: C  403 MET cc_start: 0.9055 (tpt) cc_final: 0.8650 (tpt)
REVERT: D   24 LEU cc_start: 0.9377 (mm) cc_final: 0.8815 (mm)
REVERT: D   36 GLN cc_start: 0.8545 (mt0) cc_final: 0.8232 (pt0)
REVERT: D   40 TRP cc_start: 0.8852 (m100) cc_final: 0.7782 (m100)
REVERT: D   50 GLU cc_start: 0.9483 (pm20) cc_final: 0.8992 (pm20)
REVERT: D   69 LYS cc_start: 0.9489 (mmmt) cc_final: 0.9179 (mmmm)
REVERT: D   85 LEU cc_start: 0.8931 (tt) cc_final: 0.8595 (tt)
REVERT: D   99 TYR cc_start: 0.9327 (m-10) cc_final: 0.8939 (m-10)
REVERT: D  108 TYR cc_start: 0.9281 (m-10) cc_final: 0.8884 (m-80)
REVERT: C  501 ASP cc_start: 0.7020 (m-30) cc_final: 0.6567 (m-30)
  outliers start: 13
  outliers final: 10
  residues processed: 161
  average time/residue: 0.0827
  time to fit residues: 20.6201
Evaluate side-chains
  152 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  423 LEU
Chi-restraints excluded: chain D residue   37 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 127 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0970
   chunk 35 optimal weight:    7.9990
   chunk 49 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   overall best weight:    1.3982

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

Flipped N/Q/H residues before XYZ refinement:
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.048518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.038914 restraints weight = 57483.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.040157 restraints weight = 27618.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.041014 restraints weight = 17070.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.041553 restraints weight = 12018.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.041887 restraints weight = 9437.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  10509  Z= 0.143
  Angle     :  0.735  11.397  14297  Z= 0.351
  Chirality :  0.044   0.357   1759
  Planarity :  0.004   0.055   1760
  Dihedral  :  4.084  27.066   1470
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 21.57 %
    Favored  : 77.05 %
  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:  1.23 (0.23), residues: 1359
  helix:  1.27 (0.16), residues: 1037
  sheet: -0.54 (0.75), residues: 46
  loop : -0.47 (0.42), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 187 
 TYR   0.011   0.001   TYR D  64 
 PHE   0.015   0.001   PHE A 302 
 TRP   0.025   0.001   TRP D  51 
 HIS   0.001   0.000   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (10508)
  covalent geometry    : angle       0.73504 (14295)
  SS BOND              : bond        0.00171 (    1)
  SS BOND              : angle       0.53582 (    2)
  hydrogen bonds       : bond        0.03575 (  801)
  hydrogen bonds       : angle       4.33037 ( 2367)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1584.80 seconds
wall clock time: 28 minutes 15.19 seconds (1695.19 seconds total)