Starting phenix.real_space_refine
on Mon Jul 28 12:30:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ngh_12314/07_2025/7ngh_12314.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ngh_12314/07_2025/7ngh_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ngh_12314/07_2025/7ngh_12314.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ngh_12314/07_2025/7ngh_12314.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ngh_12314/07_2025/7ngh_12314.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ngh_12314/07_2025/7ngh_12314.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.97, per 1000 atoms: 0.68
  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: 2.95
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 0.92
  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: 3.67

  Time building geometry restraints manager: 3.40 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 430 or resid 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:             1.150
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     28.130
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.080
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.015   0.001   TRP B 428 
 HIS   0.003   0.001   HIS D  39 
 PHE   0.016   0.001   PHE A 302 
 TYR   0.010   0.001   TYR A 169 
 ARG   0.003   0.000   ARG B 401 

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

*********************** 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  : 1.242 
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: 0.9505 (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: 0.8935 (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: 0.2137
  time to fit residues: 42.9728
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  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 113 optimal weight:    0.9990
   chunk 102 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 69 optimal weight:    0.0020
   chunk 54 optimal weight:    1.9990
   chunk 105 optimal weight:    9.9990
   chunk 40 optimal weight:    8.9990
   chunk 64 optimal weight:    0.7980
   chunk 78 optimal weight:    6.9990
   chunk 122 optimal weight:    0.9980
   overall best weight:    0.7190

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.045586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.035838 restraints weight = 57666.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.037126 restraints weight = 27156.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.037968 restraints weight = 16451.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10509  Z= 0.134
  Angle     :  0.655   8.646  14297  Z= 0.330
  Chirality :  0.041   0.180   1759
  Planarity :  0.004   0.042   1760
  Dihedral  :  4.436  34.456   1470
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 12.07 %
    Favored  : 87.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.23), residues: 1359
  helix:  0.44 (0.16), residues: 1049
  sheet: -2.22 (0.60), residues: 59
  loop : -1.01 (0.43), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  40 
 HIS   0.003   0.001   HIS D  39 
 PHE   0.025   0.001   PHE A 302 
 TYR   0.012   0.001   TYR B 217 
 ARG   0.005   0.000   ARG A   7 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04129 (  801)
  hydrogen bonds       : angle       4.82402 ( 2367)
  SS BOND              : bond        0.00438 (    1)
  SS BOND              : angle       1.11249 (    2)
  covalent geometry    : bond        0.00285 (10508)
  covalent geometry    : angle       0.65474 (14295)

*********************** 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
  153 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 146
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9388 (m-30) cc_final: 0.9094 (m-30)
REVERT: A  150 LYS cc_start: 0.9291 (mtmm) cc_final: 0.8977 (mtmm)
REVERT: A  271 MET cc_start: 0.9315 (mtp) cc_final: 0.8777 (mtt)
REVERT: A  321 GLN cc_start: 0.9631 (mm-40) cc_final: 0.9301 (mm110)
REVERT: A  365 MET cc_start: 0.8833 (ptm) cc_final: 0.8576 (ttt)
REVERT: A  394 ASP cc_start: 0.8958 (p0) cc_final: 0.8547 (p0)
REVERT: B   50 ASP cc_start: 0.9209 (m-30) cc_final: 0.8692 (m-30)
REVERT: B  171 MET cc_start: 0.8969 (mmp) cc_final: 0.8402 (mmm)
REVERT: B  180 LYS cc_start: 0.9566 (mmmm) cc_final: 0.9209 (mmmm)
REVERT: B  219 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8923 (mtm)
REVERT: B  271 MET cc_start: 0.9348 (mtp) cc_final: 0.8770 (mtp)
REVERT: C   97 MET cc_start: 0.8968 (tpp) cc_final: 0.8512 (tpp)
REVERT: C  174 ASN cc_start: 0.9368 (p0) cc_final: 0.9139 (p0)
REVERT: C  219 MET cc_start: 0.9593 (tpp) cc_final: 0.9087 (tpt)
REVERT: C  244 GLN cc_start: 0.9602 (tm-30) cc_final: 0.9130 (tm-30)
REVERT: C  271 MET cc_start: 0.8975 (mtm) cc_final: 0.8395 (mtp)
REVERT: C  321 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8885 (mm110)
REVERT: C  365 MET cc_start: 0.9114 (ptp) cc_final: 0.8798 (ptp)
REVERT: D   24 LEU cc_start: 0.9458 (mm) cc_final: 0.8963 (mm)
REVERT: D   40 TRP cc_start: 0.9223 (m100) cc_final: 0.7922 (m100)
REVERT: D   42 ARG cc_start: 0.9221 (ttp-170) cc_final: 0.8983 (ttp80)
REVERT: D   55 ILE cc_start: 0.9214 (tt) cc_final: 0.8845 (tt)
REVERT: D   56 GLU cc_start: 0.8842 (pt0) cc_final: 0.8338 (pt0)
REVERT: D   69 LYS cc_start: 0.9350 (mmmt) cc_final: 0.8911 (mmmt)
REVERT: D   84 TYR cc_start: 0.8862 (m-10) cc_final: 0.8627 (m-10)
REVERT: D   85 LEU cc_start: 0.9260 (tt) cc_final: 0.8748 (tt)
REVERT: D   99 TYR cc_start: 0.9459 (m-10) cc_final: 0.9193 (m-10)
REVERT: D  108 TYR cc_start: 0.9358 (m-10) cc_final: 0.9073 (m-10)
  outliers start: 7
  outliers final: 1
  residues processed: 152
  average time/residue: 0.1942
  time to fit residues: 43.8179
Evaluate side-chains
  123 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 121
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain B residue  219 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 82 optimal weight:    7.9990
   chunk 54 optimal weight:    0.0370
   chunk 55 optimal weight:    0.9990
   chunk 44 optimal weight:    8.9990
   chunk 34 optimal weight:    5.9990
   chunk 84 optimal weight:    9.9990
   chunk 91 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    1.1862

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

Flipped N/Q/H residues before XYZ refinement:
D  78 ASN
** D  81 ASN ** 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 = 0.2971 r_free = 0.2971 target = 0.045867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.036109 restraints weight = 59289.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.037374 restraints weight = 27812.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.038236 restraints weight = 16788.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.1902

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= 0.133
  Angle     :  0.630  10.146  14297  Z= 0.315
  Chirality :  0.041   0.182   1759
  Planarity :  0.004   0.051   1760
  Dihedral  :  4.294  32.668   1470
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 14.65 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.23), residues: 1359
  helix:  0.91 (0.16), residues: 1041
  sheet: -1.83 (0.62), residues: 59
  loop : -0.77 (0.43), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D  51 
 HIS   0.002   0.001   HIS D  39 
 PHE   0.021   0.001   PHE A 302 
 TYR   0.013   0.001   TYR C 387 
 ARG   0.003   0.000   ARG A   7 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03870 (  801)
  hydrogen bonds       : angle       4.62028 ( 2367)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       0.63539 (    2)
  covalent geometry    : bond        0.00294 (10508)
  covalent geometry    : angle       0.63025 (14295)

*********************** 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
  151 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9404 (m-30) cc_final: 0.9027 (m-30)
REVERT: A   97 MET cc_start: 0.9574 (mmm) cc_final: 0.9367 (mmt)
REVERT: A  150 LYS cc_start: 0.9232 (mtmm) cc_final: 0.8977 (mtmm)
REVERT: A  271 MET cc_start: 0.9318 (mtp) cc_final: 0.9060 (mtm)
REVERT: A  321 GLN cc_start: 0.9605 (mm-40) cc_final: 0.9276 (mm110)
REVERT: A  394 ASP cc_start: 0.8916 (p0) cc_final: 0.8496 (p0)
REVERT: B   50 ASP cc_start: 0.9188 (m-30) cc_final: 0.8607 (m-30)
REVERT: B  171 MET cc_start: 0.8985 (mmp) cc_final: 0.8436 (mmm)
REVERT: B  180 LYS cc_start: 0.9568 (mmmm) cc_final: 0.9223 (mmmm)
REVERT: B  271 MET cc_start: 0.9380 (mtp) cc_final: 0.8847 (mtp)
REVERT: B  288 MET cc_start: 0.9222 (mtp) cc_final: 0.9017 (mtp)
REVERT: B  371 GLN cc_start: 0.9194 (pp30) cc_final: 0.8968 (pp30)
REVERT: B  399 MET cc_start: 0.9129 (ptp) cc_final: 0.8875 (ptm)
REVERT: C   97 MET cc_start: 0.9041 (tpp) cc_final: 0.8818 (tpp)
REVERT: C  174 ASN cc_start: 0.9383 (p0) cc_final: 0.9168 (p0)
REVERT: C  219 MET cc_start: 0.9603 (tpp) cc_final: 0.9131 (tpt)
REVERT: C  244 GLN cc_start: 0.9569 (tm-30) cc_final: 0.9112 (tm-30)
REVERT: C  271 MET cc_start: 0.8879 (mtm) cc_final: 0.7919 (mtt)
REVERT: C  321 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8850 (mm110)
REVERT: C  365 MET cc_start: 0.9020 (ptp) cc_final: 0.8711 (ptp)
REVERT: C  403 MET cc_start: 0.9079 (tmm) cc_final: 0.8815 (tpt)
REVERT: C  406 VAL cc_start: 0.9444 (p) cc_final: 0.9086 (p)
REVERT: D   24 LEU cc_start: 0.9366 (mm) cc_final: 0.8911 (mm)
REVERT: D   40 TRP cc_start: 0.9106 (m100) cc_final: 0.7672 (m100)
REVERT: D   42 ARG cc_start: 0.9249 (ttp-170) cc_final: 0.8692 (ttp80)
REVERT: D   50 GLU cc_start: 0.9494 (pp20) cc_final: 0.9091 (pm20)
REVERT: D   55 ILE cc_start: 0.9189 (tt) cc_final: 0.8857 (tt)
REVERT: D   72 PHE cc_start: 0.9373 (m-80) cc_final: 0.8967 (m-80)
REVERT: D   77 ASP cc_start: 0.9406 (t0) cc_final: 0.9189 (t0)
REVERT: D   85 LEU cc_start: 0.9104 (tt) cc_final: 0.8798 (tt)
REVERT: D   99 TYR cc_start: 0.9404 (m-10) cc_final: 0.9105 (m-10)
REVERT: D  108 TYR cc_start: 0.9314 (m-10) cc_final: 0.9031 (m-10)
  outliers start: 11
  outliers final: 1
  residues processed: 149
  average time/residue: 0.2127
  time to fit residues: 47.6151
Evaluate side-chains
  123 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 1.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 103 optimal weight:    8.9990
   chunk 116 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0970
   chunk 56 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 93 optimal weight:    7.9990
   overall best weight:    2.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 334 HIS
A 341 GLN
D  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.045665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.035685 restraints weight = 58408.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.036955 restraints weight = 27888.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.037798 restraints weight = 17127.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.2014

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= 0.164
  Angle     :  0.644   9.684  14297  Z= 0.322
  Chirality :  0.041   0.242   1759
  Planarity :  0.004   0.055   1760
  Dihedral  :  4.234  32.886   1470
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 15.85 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.23), residues: 1359
  helix:  1.10 (0.16), residues: 1037
  sheet: -1.48 (0.63), residues: 59
  loop : -0.75 (0.43), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 106 
 HIS   0.002   0.001   HIS D  39 
 PHE   0.022   0.001   PHE A 302 
 TYR   0.013   0.001   TYR C 387 
 ARG   0.002   0.000   ARG B 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03815 (  801)
  hydrogen bonds       : angle       4.58244 ( 2367)
  SS BOND              : bond        0.00552 (    1)
  SS BOND              : angle       0.48336 (    2)
  covalent geometry    : bond        0.00367 (10508)
  covalent geometry    : angle       0.64400 (14295)

*********************** 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
  150 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 2.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9427 (m-30) cc_final: 0.8999 (m-30)
REVERT: A  150 LYS cc_start: 0.9223 (mtmm) cc_final: 0.8954 (mtmm)
REVERT: A  271 MET cc_start: 0.9323 (mtp) cc_final: 0.8793 (mtt)
REVERT: A  321 GLN cc_start: 0.9586 (mm-40) cc_final: 0.9234 (mm110)
REVERT: A  394 ASP cc_start: 0.8954 (p0) cc_final: 0.8544 (p0)
REVERT: B   50 ASP cc_start: 0.9211 (m-30) cc_final: 0.8612 (m-30)
REVERT: B  171 MET cc_start: 0.8952 (mmp) cc_final: 0.8304 (mmm)
REVERT: B  180 LYS cc_start: 0.9572 (mmmm) cc_final: 0.9239 (mmmm)
REVERT: B  271 MET cc_start: 0.9399 (mtp) cc_final: 0.8852 (mtp)
REVERT: B  288 MET cc_start: 0.9261 (mtp) cc_final: 0.9058 (mtp)
REVERT: B  371 GLN cc_start: 0.9260 (pp30) cc_final: 0.9054 (pp30)
REVERT: B  399 MET cc_start: 0.9152 (ptp) cc_final: 0.8911 (ptm)
REVERT: C   97 MET cc_start: 0.9051 (tpp) cc_final: 0.8571 (tpp)
REVERT: C  174 ASN cc_start: 0.9393 (p0) cc_final: 0.9074 (p0)
REVERT: C  219 MET cc_start: 0.9648 (tpp) cc_final: 0.9053 (tpt)
REVERT: C  244 GLN cc_start: 0.9585 (tm-30) cc_final: 0.9148 (tm-30)
REVERT: C  271 MET cc_start: 0.8843 (mtm) cc_final: 0.7823 (mtt)
REVERT: C  295 MET cc_start: 0.9434 (mmp) cc_final: 0.9086 (mmp)
REVERT: C  321 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8811 (mm110)
REVERT: C  365 MET cc_start: 0.9048 (ptp) cc_final: 0.8765 (ptp)
REVERT: C  403 MET cc_start: 0.9049 (tmm) cc_final: 0.8786 (tpt)
REVERT: C  406 VAL cc_start: 0.9473 (p) cc_final: 0.9107 (p)
REVERT: D   24 LEU cc_start: 0.9324 (mm) cc_final: 0.8870 (mm)
REVERT: D   40 TRP cc_start: 0.9044 (m100) cc_final: 0.7738 (m100)
REVERT: D   42 ARG cc_start: 0.9290 (ttp-170) cc_final: 0.9001 (ttp80)
REVERT: D   55 ILE cc_start: 0.9204 (tt) cc_final: 0.8974 (tt)
REVERT: D   69 LYS cc_start: 0.9421 (mmmt) cc_final: 0.8951 (mmmt)
REVERT: D   85 LEU cc_start: 0.9037 (tt) cc_final: 0.8777 (tt)
REVERT: D   99 TYR cc_start: 0.9415 (m-10) cc_final: 0.9039 (m-10)
REVERT: D  108 TYR cc_start: 0.9297 (m-10) cc_final: 0.8976 (m-10)
  outliers start: 17
  outliers final: 6
  residues processed: 146
  average time/residue: 0.3083
  time to fit residues: 68.2410
Evaluate side-chains
  130 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 124
  time to evaluate  : 1.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain C residue  288 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 84 optimal weight:    9.9990
   chunk 102 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 10 optimal weight:    8.9990
   chunk 105 optimal weight:    9.9990
   chunk 122 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 129 optimal weight:    6.9990
   chunk 90 optimal weight:    6.9990
   chunk 70 optimal weight:    4.9990
   chunk 119 optimal weight:    6.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
C 134 GLN
D  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.044059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.034161 restraints weight = 58839.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.035396 restraints weight = 27655.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.036220 restraints weight = 16915.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10509  Z= 0.203
  Angle     :  0.663   9.838  14297  Z= 0.335
  Chirality :  0.042   0.184   1759
  Planarity :  0.004   0.056   1760
  Dihedral  :  4.267  32.293   1470
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.96 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.23), residues: 1359
  helix:  1.17 (0.16), residues: 1039
  sheet: -1.10 (0.70), residues: 53
  loop : -0.61 (0.43), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  51 
 HIS   0.003   0.001   HIS D  39 
 PHE   0.020   0.001   PHE A 302 
 TYR   0.012   0.001   TYR C 387 
 ARG   0.002   0.000   ARG A 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03903 (  801)
  hydrogen bonds       : angle       4.61576 ( 2367)
  SS BOND              : bond        0.00210 (    1)
  SS BOND              : angle       0.45428 (    2)
  covalent geometry    : bond        0.00447 (10508)
  covalent geometry    : angle       0.66256 (14295)

*********************** 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
  149 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 2.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9420 (m-30) cc_final: 0.8995 (m-30)
REVERT: A   97 MET cc_start: 0.9597 (mmm) cc_final: 0.9349 (mmt)
REVERT: A  150 LYS cc_start: 0.9212 (mtmm) cc_final: 0.8943 (mtmm)
REVERT: A  271 MET cc_start: 0.9296 (mtp) cc_final: 0.8719 (mtt)
REVERT: A  321 GLN cc_start: 0.9544 (mm-40) cc_final: 0.9210 (mm110)
REVERT: A  394 ASP cc_start: 0.9002 (p0) cc_final: 0.8633 (p0)
REVERT: A  403 MET cc_start: 0.8887 (tmm) cc_final: 0.7919 (tmm)
REVERT: B   50 ASP cc_start: 0.9224 (m-30) cc_final: 0.8612 (m-30)
REVERT: B  171 MET cc_start: 0.8994 (mmp) cc_final: 0.8352 (mmm)
REVERT: B  180 LYS cc_start: 0.9573 (mmmm) cc_final: 0.9249 (mmmm)
REVERT: B  271 MET cc_start: 0.9361 (mtp) cc_final: 0.8290 (mtp)
REVERT: B  399 MET cc_start: 0.9164 (ptp) cc_final: 0.8943 (ptm)
REVERT: B  403 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8325 (tpp)
REVERT: C   97 MET cc_start: 0.9051 (tpp) cc_final: 0.8586 (tpp)
REVERT: C  174 ASN cc_start: 0.9386 (p0) cc_final: 0.9069 (p0)
REVERT: C  219 MET cc_start: 0.9653 (tpp) cc_final: 0.9062 (tpt)
REVERT: C  244 GLN cc_start: 0.9573 (tm-30) cc_final: 0.9129 (tm-30)
REVERT: C  271 MET cc_start: 0.8872 (mtm) cc_final: 0.7797 (mtt)
REVERT: C  295 MET cc_start: 0.9431 (mmp) cc_final: 0.9171 (mmp)
REVERT: C  314 MET cc_start: 0.7981 (mpp) cc_final: 0.7775 (mpp)
REVERT: C  321 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8815 (mm110)
REVERT: C  365 MET cc_start: 0.8989 (ptp) cc_final: 0.8753 (ptp)
REVERT: C  403 MET cc_start: 0.9094 (tmm) cc_final: 0.8799 (tpp)
REVERT: C  406 VAL cc_start: 0.9529 (p) cc_final: 0.9291 (p)
REVERT: D   24 LEU cc_start: 0.9291 (mm) cc_final: 0.8849 (mm)
REVERT: D   36 GLN cc_start: 0.9066 (pt0) cc_final: 0.8846 (pm20)
REVERT: D   40 TRP cc_start: 0.9073 (m100) cc_final: 0.7846 (m100)
REVERT: D   42 ARG cc_start: 0.9311 (ttp-170) cc_final: 0.8968 (ttp80)
REVERT: D   55 ILE cc_start: 0.9208 (tt) cc_final: 0.8935 (tt)
REVERT: D   69 LYS cc_start: 0.9487 (mmmt) cc_final: 0.9236 (tppt)
REVERT: D   85 LEU cc_start: 0.9008 (tt) cc_final: 0.8740 (tt)
REVERT: D   99 TYR cc_start: 0.9416 (m-10) cc_final: 0.9001 (m-10)
REVERT: D  108 TYR cc_start: 0.9268 (m-10) cc_final: 0.8862 (m-80)
  outliers start: 21
  outliers final: 10
  residues processed: 144
  average time/residue: 0.2671
  time to fit residues: 59.5024
Evaluate side-chains
  135 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 3.511 
-------------------------------------------------------------------------------
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 B residue  284 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue  288 MET
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain C residue  423 LEU
Chi-restraints excluded: chain D residue   87 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 51 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 121 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 54 optimal weight:    0.1980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.2988 r_free = 0.2988 target = 0.046519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.036752 restraints weight = 58394.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.038045 restraints weight = 27520.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.038893 restraints weight = 16680.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.2365

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= 0.126
  Angle     :  0.658  10.706  14297  Z= 0.324
  Chirality :  0.041   0.201   1759
  Planarity :  0.004   0.057   1760
  Dihedral  :  4.211  29.478   1470
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 18.16 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.23), residues: 1359
  helix:  1.20 (0.16), residues: 1040
  sheet: -1.01 (0.70), residues: 53
  loop : -0.49 (0.43), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  51 
 HIS   0.001   0.000   HIS A  34 
 PHE   0.024   0.001   PHE A 302 
 TYR   0.009   0.001   TYR C 387 
 ARG   0.002   0.000   ARG A   7 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03712 (  801)
  hydrogen bonds       : angle       4.49733 ( 2367)
  SS BOND              : bond        0.00100 (    1)
  SS BOND              : angle       0.34180 (    2)
  covalent geometry    : bond        0.00275 (10508)
  covalent geometry    : angle       0.65824 (14295)

*********************** 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
  160 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9422 (m-30) cc_final: 0.8984 (m-30)
REVERT: A  271 MET cc_start: 0.9313 (mtp) cc_final: 0.8774 (mtt)
REVERT: A  321 GLN cc_start: 0.9575 (mm-40) cc_final: 0.9258 (mm110)
REVERT: A  394 ASP cc_start: 0.8931 (p0) cc_final: 0.8512 (p0)
REVERT: B   50 ASP cc_start: 0.9200 (m-30) cc_final: 0.8583 (m-30)
REVERT: B  171 MET cc_start: 0.8955 (mmp) cc_final: 0.8338 (mmm)
REVERT: B  180 LYS cc_start: 0.9565 (mmmm) cc_final: 0.9250 (mmmm)
REVERT: B  219 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8432 (tpp)
REVERT: B  271 MET cc_start: 0.9346 (mtp) cc_final: 0.8822 (mtp)
REVERT: B  288 MET cc_start: 0.9207 (mtp) cc_final: 0.8993 (mtp)
REVERT: B  399 MET cc_start: 0.9113 (ptp) cc_final: 0.8840 (ptm)
REVERT: C   97 MET cc_start: 0.9040 (tpp) cc_final: 0.8547 (tpp)
REVERT: C  174 ASN cc_start: 0.9409 (p0) cc_final: 0.9109 (p0)
REVERT: C  219 MET cc_start: 0.9601 (tpp) cc_final: 0.9001 (tpt)
REVERT: C  244 GLN cc_start: 0.9554 (tm-30) cc_final: 0.9124 (tm-30)
REVERT: C  271 MET cc_start: 0.8840 (mtm) cc_final: 0.7933 (mtt)
REVERT: C  295 MET cc_start: 0.9275 (mmp) cc_final: 0.9027 (mmp)
REVERT: C  321 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8797 (mm110)
REVERT: C  365 MET cc_start: 0.8998 (ptp) cc_final: 0.8753 (ptp)
REVERT: D    6 VAL cc_start: 0.9147 (OUTLIER) cc_final: 0.8766 (p)
REVERT: D   24 LEU cc_start: 0.9275 (mm) cc_final: 0.8827 (mm)
REVERT: D   40 TRP cc_start: 0.8981 (m100) cc_final: 0.7645 (m100)
REVERT: D   42 ARG cc_start: 0.9256 (ttp-170) cc_final: 0.9008 (ttp80)
REVERT: D   55 ILE cc_start: 0.9246 (tt) cc_final: 0.8977 (tt)
REVERT: D   69 LYS cc_start: 0.9459 (mmmt) cc_final: 0.9209 (tppt)
REVERT: D   85 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8750 (tt)
REVERT: D   99 TYR cc_start: 0.9379 (m-10) cc_final: 0.8982 (m-10)
REVERT: D  108 TYR cc_start: 0.9264 (m-10) cc_final: 0.8864 (m-80)
  outliers start: 18
  outliers final: 9
  residues processed: 153
  average time/residue: 0.2017
  time to fit residues: 46.2055
Evaluate side-chains
  137 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
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 B residue  219 MET
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain C residue  423 LEU
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue   78 ASN
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue   87 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 86 optimal weight:    3.9990
   chunk 103 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 110 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 81 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0970
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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**
C 313 ASN
D   7 GLN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.047097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.037236 restraints weight = 58974.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.038533 restraints weight = 27804.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.039309 restraints weight = 17027.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10509  Z= 0.128
  Angle     :  0.688  10.881  14297  Z= 0.333
  Chirality :  0.042   0.290   1759
  Planarity :  0.004   0.057   1760
  Dihedral  :  4.197  29.583   1470
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 20.09 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.23), residues: 1359
  helix:  1.18 (0.16), residues: 1043
  sheet: -0.98 (0.70), residues: 53
  loop : -0.48 (0.44), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  51 
 HIS   0.001   0.000   HIS D  39 
 PHE   0.017   0.001   PHE A 302 
 TYR   0.008   0.001   TYR C 387 
 ARG   0.002   0.000   ARG C 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03599 (  801)
  hydrogen bonds       : angle       4.46849 ( 2367)
  SS BOND              : bond        0.00496 (    1)
  SS BOND              : angle       0.44946 (    2)
  covalent geometry    : bond        0.00281 (10508)
  covalent geometry    : angle       0.68768 (14295)

*********************** 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: 18
    poor density    : 145
  time to evaluate  : 1.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9405 (m-30) cc_final: 0.8969 (m-30)
REVERT: A   97 MET cc_start: 0.9602 (mmm) cc_final: 0.9340 (mmt)
REVERT: A  150 LYS cc_start: 0.9466 (mtpp) cc_final: 0.9083 (mtmm)
REVERT: A  196 MET cc_start: 0.9751 (mmp) cc_final: 0.9536 (mmp)
REVERT: A  271 MET cc_start: 0.9363 (mtp) cc_final: 0.9089 (mtm)
REVERT: A  321 GLN cc_start: 0.9579 (mm-40) cc_final: 0.9268 (mm110)
REVERT: A  394 ASP cc_start: 0.8934 (p0) cc_final: 0.8572 (p0)
REVERT: B   50 ASP cc_start: 0.9194 (m-30) cc_final: 0.8567 (m-30)
REVERT: B  171 MET cc_start: 0.8891 (mmp) cc_final: 0.8325 (mmm)
REVERT: B  180 LYS cc_start: 0.9550 (mmmm) cc_final: 0.9241 (mmmm)
REVERT: B  271 MET cc_start: 0.9090 (mtp) cc_final: 0.8032 (mtt)
REVERT: B  321 GLN cc_start: 0.9274 (mm-40) cc_final: 0.8974 (mm-40)
REVERT: B  399 MET cc_start: 0.9096 (ptp) cc_final: 0.8800 (ptm)
REVERT: B  403 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8418 (tpp)
REVERT: C   97 MET cc_start: 0.9019 (tpp) cc_final: 0.8755 (tpp)
REVERT: C  174 ASN cc_start: 0.9417 (p0) cc_final: 0.9125 (p0)
REVERT: C  219 MET cc_start: 0.9589 (tpp) cc_final: 0.8993 (tpt)
REVERT: C  244 GLN cc_start: 0.9532 (tm-30) cc_final: 0.9133 (tm-30)
REVERT: C  271 MET cc_start: 0.8898 (mtm) cc_final: 0.7735 (mtp)
REVERT: C  314 MET cc_start: 0.7963 (mpp) cc_final: 0.7633 (mpp)
REVERT: C  321 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8800 (mm110)
REVERT: C  365 MET cc_start: 0.9019 (ptp) cc_final: 0.8790 (ptp)
REVERT: C  403 MET cc_start: 0.9239 (tpt) cc_final: 0.8707 (tpt)
REVERT: D    6 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8693 (p)
REVERT: D   24 LEU cc_start: 0.9245 (mm) cc_final: 0.8512 (mm)
REVERT: D   40 TRP cc_start: 0.8920 (m100) cc_final: 0.7719 (m100)
REVERT: D   42 ARG cc_start: 0.9247 (ttp-170) cc_final: 0.8626 (ttp80)
REVERT: D   50 GLU cc_start: 0.9468 (pp20) cc_final: 0.9140 (pm20)
REVERT: D   69 LYS cc_start: 0.9457 (mmmt) cc_final: 0.9166 (mmmt)
REVERT: D   85 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8643 (tt)
REVERT: D   99 TYR cc_start: 0.9351 (m-10) cc_final: 0.8955 (m-10)
REVERT: D  108 TYR cc_start: 0.9270 (m-10) cc_final: 0.8961 (m-80)
  outliers start: 18
  outliers final: 8
  residues processed: 158
  average time/residue: 0.1872
  time to fit residues: 44.3063
Evaluate side-chains
  144 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
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 B residue  284 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain C residue  423 LEU
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue   78 ASN
Chi-restraints excluded: chain D residue   85 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 130 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 119 optimal weight:    5.9990
   chunk 133 optimal weight:    7.9990
   chunk 2 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 106 optimal weight:    8.9990
   chunk 63 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0030
   overall best weight:    0.9794

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

Flipped N/Q/H residues before XYZ refinement:
D   7 GLN
D  36 GLN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.047199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.037405 restraints weight = 58281.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.038699 restraints weight = 27574.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.039600 restraints weight = 16655.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.2812

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= 0.133
  Angle     :  0.714  11.375  14297  Z= 0.344
  Chirality :  0.043   0.270   1759
  Planarity :  0.004   0.056   1760
  Dihedral  :  4.172  28.397   1470
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 20.37 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.23), residues: 1359
  helix:  1.20 (0.16), residues: 1041
  sheet: -1.10 (0.65), residues: 59
  loop : -0.49 (0.44), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  51 
 HIS   0.001   0.000   HIS A  34 
 PHE   0.015   0.001   PHE B 302 
 TYR   0.010   0.001   TYR B 217 
 ARG   0.002   0.000   ARG B 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03644 (  801)
  hydrogen bonds       : angle       4.45278 ( 2367)
  SS BOND              : bond        0.00094 (    1)
  SS BOND              : angle       0.60598 (    2)
  covalent geometry    : bond        0.00300 (10508)
  covalent geometry    : angle       0.71382 (14295)

*********************** 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
  156 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 1.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9406 (m-30) cc_final: 0.8957 (m-30)
REVERT: A   97 MET cc_start: 0.9600 (mmm) cc_final: 0.9343 (mmt)
REVERT: A  271 MET cc_start: 0.9381 (mtp) cc_final: 0.9143 (mtm)
REVERT: A  321 GLN cc_start: 0.9563 (mm-40) cc_final: 0.9241 (mm110)
REVERT: A  394 ASP cc_start: 0.8913 (p0) cc_final: 0.8516 (p0)
REVERT: A  403 MET cc_start: 0.8773 (tmm) cc_final: 0.8057 (tmm)
REVERT: B   50 ASP cc_start: 0.9201 (m-30) cc_final: 0.8562 (m-30)
REVERT: B  171 MET cc_start: 0.8918 (mmp) cc_final: 0.8333 (mmm)
REVERT: B  180 LYS cc_start: 0.9555 (mmmm) cc_final: 0.9249 (mmmm)
REVERT: B  219 MET cc_start: 0.8870 (ttp) cc_final: 0.8233 (tmm)
REVERT: B  368 MET cc_start: 0.9053 (tmm) cc_final: 0.8790 (tmm)
REVERT: B  399 MET cc_start: 0.9099 (ptp) cc_final: 0.8820 (ptm)
REVERT: B  403 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8382 (tpp)
REVERT: C   97 MET cc_start: 0.9035 (tpp) cc_final: 0.8764 (tpp)
REVERT: C  174 ASN cc_start: 0.9431 (p0) cc_final: 0.9136 (p0)
REVERT: C  219 MET cc_start: 0.9569 (tpp) cc_final: 0.8960 (tpt)
REVERT: C  244 GLN cc_start: 0.9518 (tm-30) cc_final: 0.9131 (tm-30)
REVERT: C  271 MET cc_start: 0.8876 (mtm) cc_final: 0.7933 (mtt)
REVERT: C  306 LEU cc_start: 0.9697 (OUTLIER) cc_final: 0.9421 (mm)
REVERT: C  314 MET cc_start: 0.8024 (mpp) cc_final: 0.7816 (mpp)
REVERT: C  389 MET cc_start: 0.9495 (ptm) cc_final: 0.9117 (ppp)
REVERT: C  403 MET cc_start: 0.9198 (tpt) cc_final: 0.8767 (tpt)
REVERT: D   24 LEU cc_start: 0.9318 (mm) cc_final: 0.8840 (mm)
REVERT: D   40 TRP cc_start: 0.8877 (m100) cc_final: 0.7666 (m100)
REVERT: D   50 GLU cc_start: 0.9445 (pp20) cc_final: 0.9018 (pm20)
REVERT: D   69 LYS cc_start: 0.9468 (mmmt) cc_final: 0.9184 (tppt)
REVERT: D   85 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8656 (tt)
REVERT: D   99 TYR cc_start: 0.9341 (m-10) cc_final: 0.8947 (m-10)
REVERT: D  108 TYR cc_start: 0.9261 (m-10) cc_final: 0.8925 (m-80)
  outliers start: 21
  outliers final: 12
  residues processed: 150
  average time/residue: 0.2505
  time to fit residues: 56.9241
Evaluate side-chains
  143 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 1.349 
-------------------------------------------------------------------------------
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 B residue  284 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    7 GLN
Chi-restraints excluded: chain D residue   37 PHE
Chi-restraints excluded: chain D residue   78 ASN
Chi-restraints excluded: chain D residue   85 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 52 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0060
   chunk 81 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 122 optimal weight:    4.9990
   chunk 54 optimal weight:    0.5980
   chunk 78 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0020
   overall best weight:    0.4004

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

Flipped N/Q/H residues before XYZ refinement:
D   7 GLN
** D  81 ASN ** 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 = 0.3031 r_free = 0.3031 target = 0.047877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.038058 restraints weight = 58030.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.039399 restraints weight = 27523.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.040280 restraints weight = 16654.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10509  Z= 0.132
  Angle     :  0.724  11.923  14297  Z= 0.347
  Chirality :  0.043   0.252   1759
  Planarity :  0.004   0.056   1760
  Dihedral  :  4.201  26.370   1470
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 21.11 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.23), residues: 1359
  helix:  1.17 (0.16), residues: 1044
  sheet: -0.90 (0.70), residues: 54
  loop : -0.37 (0.44), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D  51 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.015   0.001   PHE B 302 
 TYR   0.018   0.001   TYR D  84 
 ARG   0.002   0.000   ARG B 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03550 (  801)
  hydrogen bonds       : angle       4.41808 ( 2367)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.59058 (    2)
  covalent geometry    : bond        0.00286 (10508)
  covalent geometry    : angle       0.72395 (14295)

*********************** 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
  162 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9406 (m-30) cc_final: 0.8962 (m-30)
REVERT: A   97 MET cc_start: 0.9592 (mmm) cc_final: 0.9363 (mmt)
REVERT: A  244 GLN cc_start: 0.9270 (tm-30) cc_final: 0.9006 (tm-30)
REVERT: A  271 MET cc_start: 0.9384 (mtp) cc_final: 0.9165 (mtm)
REVERT: A  321 GLN cc_start: 0.9573 (mm-40) cc_final: 0.9287 (mm110)
REVERT: A  394 ASP cc_start: 0.8901 (p0) cc_final: 0.8555 (p0)
REVERT: A  403 MET cc_start: 0.8779 (tmm) cc_final: 0.8191 (tmm)
REVERT: B   50 ASP cc_start: 0.9194 (m-30) cc_final: 0.8554 (m-30)
REVERT: B  128 GLN cc_start: 0.8399 (mp10) cc_final: 0.8144 (mp10)
REVERT: B  167 ILE cc_start: 0.9756 (mt) cc_final: 0.9284 (tt)
REVERT: B  171 MET cc_start: 0.8887 (mmp) cc_final: 0.8327 (mmm)
REVERT: B  180 LYS cc_start: 0.9548 (mmmm) cc_final: 0.9225 (mmmm)
REVERT: B  219 MET cc_start: 0.8824 (ttp) cc_final: 0.8271 (tmm)
REVERT: B  321 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8842 (mm-40)
REVERT: B  368 MET cc_start: 0.9015 (tmm) cc_final: 0.8600 (tmm)
REVERT: B  371 GLN cc_start: 0.9107 (pp30) cc_final: 0.8835 (pp30)
REVERT: B  389 MET cc_start: 0.9688 (mtm) cc_final: 0.9004 (mpp)
REVERT: B  399 MET cc_start: 0.9095 (ptp) cc_final: 0.8773 (ptm)
REVERT: B  403 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8385 (tpp)
REVERT: C   61 MET cc_start: 0.8078 (mtp) cc_final: 0.7795 (mtp)
REVERT: C   97 MET cc_start: 0.9042 (tpp) cc_final: 0.8778 (tpp)
REVERT: C  174 ASN cc_start: 0.9428 (p0) cc_final: 0.9133 (p0)
REVERT: C  219 MET cc_start: 0.9555 (tpp) cc_final: 0.8955 (tpt)
REVERT: C  244 GLN cc_start: 0.9501 (tm-30) cc_final: 0.9152 (tm-30)
REVERT: C  271 MET cc_start: 0.8856 (mtm) cc_final: 0.7909 (mtt)
REVERT: C  306 LEU cc_start: 0.9703 (OUTLIER) cc_final: 0.9461 (mm)
REVERT: C  389 MET cc_start: 0.9498 (ptm) cc_final: 0.9122 (ppp)
REVERT: C  403 MET cc_start: 0.9161 (tpt) cc_final: 0.8867 (tpt)
REVERT: D   24 LEU cc_start: 0.9312 (mm) cc_final: 0.8845 (mm)
REVERT: D   40 TRP cc_start: 0.8862 (m100) cc_final: 0.7730 (m100)
REVERT: D   50 GLU cc_start: 0.9417 (pp20) cc_final: 0.8980 (pm20)
REVERT: D   69 LYS cc_start: 0.9470 (mmmt) cc_final: 0.9193 (tppt)
REVERT: D   85 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8606 (tt)
REVERT: D   99 TYR cc_start: 0.9329 (m-10) cc_final: 0.8952 (m-10)
REVERT: D  108 TYR cc_start: 0.9252 (m-10) cc_final: 0.8951 (m-10)
  outliers start: 19
  outliers final: 11
  residues processed: 157
  average time/residue: 0.1935
  time to fit residues: 45.3650
Evaluate side-chains
  149 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
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 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    7 GLN
Chi-restraints excluded: chain D residue   37 PHE
Chi-restraints excluded: chain D residue   85 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 34 optimal weight:    0.1980
   chunk 62 optimal weight:    1.9990
   chunk 129 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 98 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 110 optimal weight:    0.0980
   chunk 111 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
D  78 ASN
** D  81 ASN ** 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 = 0.3044 r_free = 0.3044 target = 0.048249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.037982 restraints weight = 57635.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.039285 restraints weight = 27781.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.040157 restraints weight = 17112.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10509  Z= 0.135
  Angle     :  0.757  13.223  14297  Z= 0.360
  Chirality :  0.043   0.243   1759
  Planarity :  0.004   0.056   1760
  Dihedral  :  4.194  27.162   1470
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 21.84 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.23), residues: 1359
  helix:  1.20 (0.16), residues: 1038
  sheet: -0.75 (0.70), residues: 54
  loop : -0.47 (0.43), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP D  51 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.023   0.001   PHE A 302 
 TYR   0.014   0.001   TYR C 387 
 ARG   0.017   0.000   ARG B 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03625 (  801)
  hydrogen bonds       : angle       4.40665 ( 2367)
  SS BOND              : bond        0.00122 (    1)
  SS BOND              : angle       0.53239 (    2)
  covalent geometry    : bond        0.00299 (10508)
  covalent geometry    : angle       0.75699 (14295)

********************** 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
  156 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 1.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.9404 (m-30) cc_final: 0.8954 (m-30)
REVERT: A   97 MET cc_start: 0.9553 (mmm) cc_final: 0.9330 (mmt)
REVERT: A  271 MET cc_start: 0.9395 (mtp) cc_final: 0.9126 (mtm)
REVERT: A  321 GLN cc_start: 0.9572 (mm-40) cc_final: 0.9292 (mm110)
REVERT: A  394 ASP cc_start: 0.8899 (p0) cc_final: 0.8543 (p0)
REVERT: B   50 ASP cc_start: 0.9181 (m-30) cc_final: 0.8528 (m-30)
REVERT: B  128 GLN cc_start: 0.8393 (mp10) cc_final: 0.8135 (mp10)
REVERT: B  171 MET cc_start: 0.8890 (mmp) cc_final: 0.8282 (mmm)
REVERT: B  180 LYS cc_start: 0.9578 (mmmm) cc_final: 0.9260 (mmmm)
REVERT: B  219 MET cc_start: 0.8829 (ttp) cc_final: 0.8350 (tmm)
REVERT: B  271 MET cc_start: 0.9054 (mtp) cc_final: 0.8220 (mtm)
REVERT: B  368 MET cc_start: 0.9033 (tmm) cc_final: 0.8609 (tmm)
REVERT: B  371 GLN cc_start: 0.9142 (pp30) cc_final: 0.8876 (pp30)
REVERT: B  389 MET cc_start: 0.9650 (mtm) cc_final: 0.8971 (mpp)
REVERT: B  399 MET cc_start: 0.9096 (ptp) cc_final: 0.8755 (ptm)
REVERT: B  403 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8350 (tpp)
REVERT: C   61 MET cc_start: 0.8170 (mtp) cc_final: 0.7941 (mtp)
REVERT: C   97 MET cc_start: 0.9057 (tpp) cc_final: 0.8768 (tpp)
REVERT: C  174 ASN cc_start: 0.9435 (p0) cc_final: 0.9141 (p0)
REVERT: C  219 MET cc_start: 0.9562 (tpp) cc_final: 0.8965 (tpt)
REVERT: C  244 GLN cc_start: 0.9495 (tm-30) cc_final: 0.9190 (tm-30)
REVERT: C  271 MET cc_start: 0.8886 (mtm) cc_final: 0.7853 (mtt)
REVERT: C  306 LEU cc_start: 0.9703 (OUTLIER) cc_final: 0.9450 (mm)
REVERT: C  403 MET cc_start: 0.9152 (tpt) cc_final: 0.8869 (tpt)
REVERT: D   24 LEU cc_start: 0.9299 (mm) cc_final: 0.8814 (mm)
REVERT: D   40 TRP cc_start: 0.8793 (m100) cc_final: 0.7590 (m100)
REVERT: D   50 GLU cc_start: 0.9392 (pp20) cc_final: 0.8977 (pm20)
REVERT: D   69 LYS cc_start: 0.9472 (mmmt) cc_final: 0.9149 (tppt)
REVERT: D   71 ARG cc_start: 0.8534 (mtp-110) cc_final: 0.7840 (ttp80)
REVERT: D   85 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8542 (tt)
REVERT: D   99 TYR cc_start: 0.9324 (m-10) cc_final: 0.8966 (m-10)
REVERT: D  108 TYR cc_start: 0.9223 (m-10) cc_final: 0.8880 (m-10)
  outliers start: 17
  outliers final: 10
  residues processed: 151
  average time/residue: 0.2755
  time to fit residues: 62.5496
Evaluate side-chains
  144 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
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 B residue  284 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
Chi-restraints excluded: chain D residue   85 LEU
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 86 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   chunk 102 optimal weight:    3.9990
   chunk 114 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   chunk 113 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9980
   chunk 125 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0870
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  78 ASN
** D  81 ASN ** 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 = 0.3046 r_free = 0.3046 target = 0.048401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.038522 restraints weight = 57504.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.039847 restraints weight = 27638.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.040727 restraints weight = 16919.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10509  Z= 0.132
  Angle     :  0.746  12.419  14297  Z= 0.356
  Chirality :  0.044   0.236   1759
  Planarity :  0.004   0.055   1760
  Dihedral  :  4.168  26.268   1470
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 22.21 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.23), residues: 1359
  helix:  1.17 (0.16), residues: 1042
  sheet:  0.07 (0.77), residues: 46
  loop : -0.49 (0.42), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP D  51 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.024   0.001   PHE A 302 
 TYR   0.019   0.001   TYR D  84 
 ARG   0.015   0.000   ARG B 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03581 (  801)
  hydrogen bonds       : angle       4.38013 ( 2367)
  SS BOND              : bond        0.00100 (    1)
  SS BOND              : angle       0.54660 (    2)
  covalent geometry    : bond        0.00297 (10508)
  covalent geometry    : angle       0.74559 (14295)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3578.13 seconds
wall clock time: 65 minutes 44.17 seconds (3944.17 seconds total)