Starting phenix.real_space_refine
on Wed Sep 17 12:50:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zu0_60477/09_2025/8zu0_60477_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zu0_60477/09_2025/8zu0_60477.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zu0_60477/09_2025/8zu0_60477_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zu0_60477/09_2025/8zu0_60477_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zu0_60477/09_2025/8zu0_60477.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zu0_60477/09_2025/8zu0_60477.map"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      40      5.16       5
     C    5460      2.51       5
     N    1574      2.21       5
     O    1674      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8752
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 554, 4323
          Classifications: {'peptide': 554}
          Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 523}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 4323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 554, 4323
          Classifications: {'peptide': 554}
          Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 523}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.30, per 1000 atoms: 0.26
  Number of scatterers: 8752
  At special positions: 0
  Unit cell: (115.175, 98.175, 88.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     P       4     15.00
     O    1674      8.00
     N    1574      7.00
     C    5460      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 266.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2044

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 12 sheets defined
      44.3% alpha, 14.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 29
    Processing helix  chain 'A' and resid 38 through 42
    Processing helix  chain 'A' and resid 56 through 67
    Processing helix  chain 'A' and resid 69 through 77
    Processing helix  chain 'A' and resid 100 through 114
    Processing helix  chain 'A' and resid 180 through 189
    Processing helix  chain 'A' and resid 232 through 236
      removed outlier: 3.869A  pdb=" N   GLN A 235 " --> pdb=" O   ASN A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 259
    Processing helix  chain 'A' and resid 279 through 287
    Processing helix  chain 'A' and resid 317 through 328
      removed outlier: 3.571A  pdb=" N   MET A 328 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 353
    Processing helix  chain 'A' and resid 369 through 373
    Processing helix  chain 'A' and resid 376 through 396
    Processing helix  chain 'A' and resid 408 through 419
    Processing helix  chain 'A' and resid 440 through 442
      No H-bonds generated for 'chain 'A' and resid 440 through 442'
    Processing helix  chain 'A' and resid 443 through 455
      removed outlier: 5.470A  pdb=" N   GLU A 450 " --> pdb=" O   LEU A 446 " (cutoff:3.500A)
      removed outlier: 5.801A  pdb=" N   ILE A 451 " --> pdb=" O   ARG A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 483
    Processing helix  chain 'A' and resid 490 through 498
      removed outlier: 4.097A  pdb=" N   GLU A 494 " --> pdb=" O   GLU A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 514
    Processing helix  chain 'A' and resid 519 through 526
      removed outlier: 3.625A  pdb=" N   LEU A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 548
    Processing helix  chain 'A' and resid 548 through 567
      removed outlier: 3.896A  pdb=" N   ASN A 565 " --> pdb=" O   LYS A 561 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 15 through 29
      removed outlier: 3.528A  pdb=" N   GLY C  29 " --> pdb=" O   ALA C  25 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 38 through 42
    Processing helix  chain 'C' and resid 56 through 67
    Processing helix  chain 'C' and resid 69 through 77
    Processing helix  chain 'C' and resid 100 through 114
    Processing helix  chain 'C' and resid 180 through 189
    Processing helix  chain 'C' and resid 232 through 236
      removed outlier: 3.868A  pdb=" N   GLN C 235 " --> pdb=" O   ASN C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 248 through 259
    Processing helix  chain 'C' and resid 260 through 262
      No H-bonds generated for 'chain 'C' and resid 260 through 262'
    Processing helix  chain 'C' and resid 279 through 287
    Processing helix  chain 'C' and resid 317 through 328
      removed outlier: 3.570A  pdb=" N   MET C 328 " --> pdb=" O   ILE C 324 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 350 through 353
    Processing helix  chain 'C' and resid 369 through 373
    Processing helix  chain 'C' and resid 376 through 396
      removed outlier: 3.515A  pdb=" N   ALA C 380 " --> pdb=" O   GLY C 376 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 408 through 419
    Processing helix  chain 'C' and resid 440 through 442
      No H-bonds generated for 'chain 'C' and resid 440 through 442'
    Processing helix  chain 'C' and resid 443 through 455
      removed outlier: 5.476A  pdb=" N   GLU C 450 " --> pdb=" O   LEU C 446 " (cutoff:3.500A)
      removed outlier: 5.802A  pdb=" N   ILE C 451 " --> pdb=" O   ARG C 447 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 459 through 483
    Processing helix  chain 'C' and resid 490 through 498
      removed outlier: 4.042A  pdb=" N   GLU C 494 " --> pdb=" O   GLU C 490 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 509 through 514
    Processing helix  chain 'C' and resid 519 through 526
      removed outlier: 3.609A  pdb=" N   LEU C 523 " --> pdb=" O   THR C 519 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 535 through 548
    Processing helix  chain 'C' and resid 548 through 567
      removed outlier: 3.896A  pdb=" N   ASN C 565 " --> pdb=" O   LYS C 561 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 122
      removed outlier: 6.519A  pdb=" N   THR A  32 " --> pdb=" O   MET A 119 " (cutoff:3.500A)
      removed outlier: 7.607A  pdb=" N   PHE A 121 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   LEU A  34 " --> pdb=" O   PHE A 121 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   VAL A   9 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
      removed outlier: 7.662A  pdb=" N   LEU A  35 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE A  11 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ILE A  10 " --> pdb=" O   VAL A 152 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   VAL A 151 " --> pdb=" O   PHE A 366 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 52
      removed outlier: 6.132A  pdb=" N   ALA A  94 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ILE A  83 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ARG A  96 " --> pdb=" O   PHE A  81 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   PHE A  81 " --> pdb=" O   ARG A  96 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   GLN A  98 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 131
      removed outlier: 6.633A  pdb=" N   VAL A 139 " --> pdb=" O   GLU A 126 " (cutoff:3.500A)
      removed outlier: 4.896A  pdb=" N   LEU A 128 " --> pdb=" O   GLY A 137 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   GLY A 137 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   VAL A 130 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   VAL A 135 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 171
      removed outlier: 3.893A  pdb=" N   LYS A 162 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 218
      removed outlier: 3.766A  pdb=" N   ALA A 216 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   PHE A 296 " --> pdb=" O   ASN A 310 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ARG A 338 " --> pdb=" O   ARG A 204 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP A 206 " --> pdb=" O   ILE A 336 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   ILE A 336 " --> pdb=" O   ASP A 206 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 484 through 485
    Processing sheet with id=AA7, first strand: chain 'C' and resid 118 through 122
      removed outlier: 6.502A  pdb=" N   THR C  32 " --> pdb=" O   MET C 119 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   PHE C 121 " --> pdb=" O   THR C  32 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   LEU C  34 " --> pdb=" O   PHE C 121 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   VAL C 151 " --> pdb=" O   PHE C 366 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 50 through 52
      removed outlier: 6.149A  pdb=" N   ALA C  94 " --> pdb=" O   ILE C  83 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   ILE C  83 " --> pdb=" O   ALA C  94 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ARG C  96 " --> pdb=" O   PHE C  81 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   PHE C  81 " --> pdb=" O   ARG C  96 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   GLN C  98 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 131
      removed outlier: 6.630A  pdb=" N   VAL C 139 " --> pdb=" O   GLU C 126 " (cutoff:3.500A)
      removed outlier: 4.885A  pdb=" N   LEU C 128 " --> pdb=" O   GLY C 137 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   GLY C 137 " --> pdb=" O   LEU C 128 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   VAL C 130 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   VAL C 135 " --> pdb=" O   VAL C 130 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 168 through 171
      removed outlier: 3.886A  pdb=" N   LYS C 162 " --> pdb=" O   GLU C 344 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 216 through 218
      removed outlier: 3.771A  pdb=" N   ALA C 216 " --> pdb=" O   ILE C 244 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   PHE C 296 " --> pdb=" O   ASN C 310 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ARG C 338 " --> pdb=" O   ARG C 204 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   ASP C 206 " --> pdb=" O   ILE C 336 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ILE C 336 " --> pdb=" O   ASP C 206 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 484 through 485

    384 hydrogen bonds defined for protein.
    1080 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 1.19 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: 3022
        1.34 -     1.46: 1313
        1.46 -     1.57: 4501
        1.57 -     1.69: 8
        1.69 -     1.81: 74
  Bond restraints: 8918
  Sorted by residual:
  bond pdb=" C4  FAD A 601 "
       pdb=" O4  FAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.211  1.395 -0.184 2.00e-02 2.50e+03 8.48e+01
  bond pdb=" C2  FAD A 601 "
       pdb=" O2  FAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.215  1.398 -0.183 2.00e-02 2.50e+03 8.34e+01
  bond pdb=" C2  FAD C 601 "
       pdb=" O2  FAD C 601 "
    ideal  model  delta    sigma   weight residual
    1.215  1.397 -0.182 2.00e-02 2.50e+03 8.32e+01
  bond pdb=" C4  FAD C 601 "
       pdb=" O4  FAD C 601 "
    ideal  model  delta    sigma   weight residual
    1.211  1.393 -0.182 2.00e-02 2.50e+03 8.31e+01
  bond pdb=" C6A FAD C 601 "
       pdb=" N6A FAD C 601 "
    ideal  model  delta    sigma   weight residual
    1.334  1.449 -0.115 2.00e-02 2.50e+03 3.29e+01
  ... (remaining 8913 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.32: 12046
        4.32 -     8.64: 34
        8.64 -    12.95: 2
       12.95 -    17.27: 0
       17.27 -    21.59: 4
  Bond angle restraints: 12086
  Sorted by residual:
  angle pdb=" O1P FAD C 601 "
        pdb=" P   FAD C 601 "
        pdb=" O2P FAD C 601 "
      ideal   model   delta    sigma   weight residual
     122.50  100.91   21.59 3.00e+00 1.11e-01 5.18e+01
  angle pdb=" O1P FAD A 601 "
        pdb=" P   FAD A 601 "
        pdb=" O2P FAD A 601 "
      ideal   model   delta    sigma   weight residual
     122.50  101.67   20.83 3.00e+00 1.11e-01 4.82e+01
  angle pdb=" O1A FAD C 601 "
        pdb=" PA  FAD C 601 "
        pdb=" O2A FAD C 601 "
      ideal   model   delta    sigma   weight residual
     121.20  101.23   19.97 3.00e+00 1.11e-01 4.43e+01
  angle pdb=" O1A FAD A 601 "
        pdb=" PA  FAD A 601 "
        pdb=" O2A FAD A 601 "
      ideal   model   delta    sigma   weight residual
     121.20  101.29   19.91 3.00e+00 1.11e-01 4.41e+01
  angle pdb=" N   CYS C  47 "
        pdb=" CA  CYS C  47 "
        pdb=" C   CYS C  47 "
      ideal   model   delta    sigma   weight residual
     112.12  116.74   -4.62 1.34e+00 5.57e-01 1.19e+01
  ... (remaining 12081 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.91: 5200
       26.91 -    53.81: 251
       53.81 -    80.72: 34
       80.72 -   107.62: 1
      107.62 -   134.53: 2
  Dihedral angle restraints: 5488
    sinusoidal: 2312
      harmonic: 3176
  Sorted by residual:
  dihedral pdb=" O5' FAD A 601 "
           pdb=" O3P FAD A 601 "
           pdb=" P   FAD A 601 "
           pdb=" PA  FAD A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -61.77   72.76 -134.53     1      3.00e+01 1.11e-03 1.81e+01
  dihedral pdb=" O5' FAD C 601 "
           pdb=" O3P FAD C 601 "
           pdb=" P   FAD C 601 "
           pdb=" PA  FAD C 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -61.77   71.21 -132.98     1      3.00e+01 1.11e-03 1.79e+01
  dihedral pdb=" CA  THR C 375 "
           pdb=" C   THR C 375 "
           pdb=" N   GLY C 376 "
           pdb=" CA  GLY C 376 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.81  -15.19     0      5.00e+00 4.00e-02 9.23e+00
  ... (remaining 5485 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1010
       0.044 -    0.087: 244
       0.087 -    0.131: 69
       0.131 -    0.175: 5
       0.175 -    0.218: 2
  Chirality restraints: 1330
  Sorted by residual:
  chirality pdb=" C3B FAD C 601 "
            pdb=" C2B FAD C 601 "
            pdb=" C4B FAD C 601 "
            pdb=" O3B FAD C 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.72   -2.50   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" C3B FAD A 601 "
            pdb=" C2B FAD A 601 "
            pdb=" C4B FAD A 601 "
            pdb=" O3B FAD A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.72   -2.51   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  CYS C  47 "
            pdb=" N   CYS C  47 "
            pdb=" C   CYS C  47 "
            pdb=" CB  CYS C  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.53e-01
  ... (remaining 1327 not shown)

  Planarity restraints: 1598
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C   3 "    0.022 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO C   4 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO C   4 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C   4 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A   3 "    0.021 5.00e-02 4.00e+02   3.28e-02 1.72e+00
        pdb=" N   PRO A   4 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A   4 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A   4 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 181 "    0.021 5.00e-02 4.00e+02   3.28e-02 1.72e+00
        pdb=" N   PRO C 182 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO C 182 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 182 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1595 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 61
        2.51 -     3.10: 6798
        3.10 -     3.70: 12876
        3.70 -     4.30: 19124
        4.30 -     4.90: 31875
  Nonbonded interactions: 70734
  Sorted by model distance:
  nonbonded pdb=" O2' FAD A 601 "
            pdb=" O4' FAD A 601 "
     model   vdw
     1.907 3.040
  nonbonded pdb=" O2' FAD C 601 "
            pdb=" O4' FAD C 601 "
     model   vdw
     1.913 3.040
  nonbonded pdb=" OG1 THR C 157 "
            pdb=" OG  SER C 184 "
     model   vdw
     1.944 3.040
  nonbonded pdb=" OG1 THR A 157 "
            pdb=" OG  SER A 184 "
     model   vdw
     1.945 3.040
  nonbonded pdb=" N   ILE A  39 "
            pdb=" OE1 GLN A 122 "
     model   vdw
     2.039 3.120
  ... (remaining 70729 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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 individual isotropic
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:             9.530
  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:          0.450
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.540
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
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      :  0.008   0.184   8920  Z= 0.371
  Angle     :  0.776  21.591  12086  Z= 0.354
  Chirality :  0.041   0.218   1330
  Planarity :  0.004   0.034   1598
  Dihedral  : 15.114 134.526   3444
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 37.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.26), residues: 1100
  helix:  1.84 (0.25), residues: 432
  sheet:  0.23 (0.38), residues: 172
  loop :  0.24 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  82 
 TYR   0.014   0.002   TYR A 377 
 PHE   0.015   0.002   PHE C 366 
 TRP   0.014   0.002   TRP C 484 
 HIS   0.011   0.002   HIS C  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00788 ( 8918)
  covalent geometry    : angle       0.77639 (12086)
  hydrogen bonds       : bond        0.17514 (  384)
  hydrogen bonds       : angle       6.18135 ( 1080)
  Misc. bond           : bond        0.00174 (    2)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A   93 ARG cc_start: 0.7179 (ptp90) cc_final: 0.6961 (ptp90)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0940
  time to fit residues: 14.9181
Evaluate side-chains
  101 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    0.0970
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 123 GLN
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 HIS
** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 383 GLN
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 123 GLN
** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 383 GLN
** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.204266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.147720 restraints weight = 9618.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 2.38
r_work: 0.3552 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3395 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8920  Z= 0.139
  Angle     :  0.580   6.608  12086  Z= 0.294
  Chirality :  0.043   0.232   1330
  Planarity :  0.004   0.044   1598
  Dihedral  :  9.706  97.913   1310
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  5.26 %
    Favored  : 94.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.26), residues: 1100
  helix:  1.92 (0.24), residues: 442
  sheet:  0.19 (0.38), residues: 172
  loop :  0.21 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 196 
 TYR   0.016   0.001   TYR C 520 
 PHE   0.013   0.001   PHE A 347 
 TRP   0.003   0.001   TRP A 401 
 HIS   0.007   0.001   HIS C  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8918)
  covalent geometry    : angle       0.58006 (12086)
  hydrogen bonds       : bond        0.04612 (  384)
  hydrogen bonds       : angle       4.70407 ( 1080)
  Misc. bond           : bond        0.00067 (    2)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 114
  time to evaluate  : 0.435 
Fit side-chains
  outliers start: 4
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0901
  time to fit residues: 14.9747
Evaluate side-chains
  106 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 72 optimal weight:    0.0370
   chunk 31 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 94 optimal weight:   30.0000
   chunk 2 optimal weight:    0.9980
   chunk 64 optimal weight:    8.9990
   chunk 86 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    1.4064

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 HIS
** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  37 HIS
** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.199345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.141667 restraints weight = 9658.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 2.40
r_work: 0.3538 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8920  Z= 0.136
  Angle     :  0.544   6.104  12086  Z= 0.276
  Chirality :  0.041   0.186   1330
  Planarity :  0.004   0.046   1598
  Dihedral  :  9.212  94.128   1310
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  8.11 %
    Favored  : 91.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.26), residues: 1100
  helix:  2.07 (0.25), residues: 442
  sheet: -0.09 (0.36), residues: 192
  loop :  0.37 (0.31), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  82 
 TYR   0.013   0.001   TYR A 377 
 PHE   0.011   0.001   PHE C 347 
 TRP   0.004   0.001   TRP C 463 
 HIS   0.005   0.001   HIS C  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8918)
  covalent geometry    : angle       0.54351 (12086)
  hydrogen bonds       : bond        0.04324 (  384)
  hydrogen bonds       : angle       4.55437 ( 1080)
  Misc. bond           : bond        0.00035 (    2)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: A  481 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8355 (mtmm)
REVERT: C  122 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7920 (tp40)
REVERT: C  518 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6624 (ppp)
  outliers start: 6
  outliers final: 0
  residues processed: 107
  average time/residue: 0.0797
  time to fit residues: 12.7673
Evaluate side-chains
  103 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 101
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  122 GLN
Chi-restraints excluded: chain C residue  518 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 107 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0570
   chunk 69 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 88 optimal weight:    0.7980
   chunk 91 optimal weight:    6.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    1.3702

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 HIS
** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 123 GLN
** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.199710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.141793 restraints weight = 9865.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 2.43
r_work: 0.3552 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8920  Z= 0.131
  Angle     :  0.537   5.827  12086  Z= 0.270
  Chirality :  0.042   0.186   1330
  Planarity :  0.004   0.047   1598
  Dihedral  :  8.969  90.473   1310
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  9.65 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.26), residues: 1100
  helix:  2.10 (0.25), residues: 442
  sheet: -0.04 (0.37), residues: 192
  loop :  0.36 (0.31), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  82 
 TYR   0.011   0.001   TYR A 520 
 PHE   0.017   0.001   PHE C 347 
 TRP   0.003   0.001   TRP C 463 
 HIS   0.004   0.001   HIS C  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8918)
  covalent geometry    : angle       0.53654 (12086)
  hydrogen bonds       : bond        0.04107 (  384)
  hydrogen bonds       : angle       4.45975 ( 1080)
  Misc. bond           : bond        0.00045 (    2)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A  481 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8345 (mtmm)
REVERT: A  518 MET cc_start: 0.6962 (ppp) cc_final: 0.6560 (ppp)
REVERT: C  122 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7908 (tp40)
REVERT: C  518 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6758 (ppp)
  outliers start: 10
  outliers final: 5
  residues processed: 108
  average time/residue: 0.0821
  time to fit residues: 13.0843
Evaluate side-chains
  112 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue  122 GLN
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  518 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   chunk 43 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 59 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.195576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.137498 restraints weight = 9942.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 2.42
r_work: 0.3514 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8920  Z= 0.190
  Angle     :  0.587   5.838  12086  Z= 0.298
  Chirality :  0.043   0.167   1330
  Planarity :  0.004   0.049   1598
  Dihedral  :  9.045  89.737   1310
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 11.18 %
    Favored  : 87.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.26), residues: 1100
  helix:  1.89 (0.24), residues: 442
  sheet: -0.13 (0.38), residues: 172
  loop :  0.18 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  82 
 TYR   0.018   0.002   TYR A 377 
 PHE   0.014   0.002   PHE A 347 
 TRP   0.004   0.001   TRP A 463 
 HIS   0.007   0.001   HIS C  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 8918)
  covalent geometry    : angle       0.58719 (12086)
  hydrogen bonds       : bond        0.04749 (  384)
  hydrogen bonds       : angle       4.58650 ( 1080)
  Misc. bond           : bond        0.00108 (    2)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.7703 (mmm) cc_final: 0.7441 (mtp)
REVERT: A  417 LEU cc_start: 0.8181 (mt) cc_final: 0.7960 (mt)
REVERT: A  481 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8359 (mtmm)
REVERT: A  518 MET cc_start: 0.7064 (ppp) cc_final: 0.6583 (ppp)
REVERT: C  122 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7928 (tp40)
REVERT: C  518 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6788 (ppp)
  outliers start: 9
  outliers final: 4
  residues processed: 108
  average time/residue: 0.0850
  time to fit residues: 13.4348
Evaluate side-chains
  109 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue  122 GLN
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  518 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   chunk 109 optimal weight:    0.7980
   chunk 11 optimal weight:    0.4980
   chunk 15 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 96 optimal weight:    9.9990
   chunk 0 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 17 optimal weight:    8.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.197168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.139906 restraints weight = 9788.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 2.37
r_work: 0.3529 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8920  Z= 0.155
  Angle     :  0.558   5.898  12086  Z= 0.281
  Chirality :  0.042   0.159   1330
  Planarity :  0.004   0.048   1598
  Dihedral  :  8.914  90.459   1310
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.51 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.26), residues: 1100
  helix:  1.94 (0.25), residues: 442
  sheet: -0.22 (0.38), residues: 172
  loop :  0.15 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  82 
 TYR   0.013   0.002   TYR A 377 
 PHE   0.010   0.001   PHE A 367 
 TRP   0.003   0.001   TRP C 463 
 HIS   0.006   0.001   HIS C  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 8918)
  covalent geometry    : angle       0.55781 (12086)
  hydrogen bonds       : bond        0.04269 (  384)
  hydrogen bonds       : angle       4.47559 ( 1080)
  Misc. bond           : bond        0.00093 (    2)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A  481 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8245 (mtmm)
REVERT: A  518 MET cc_start: 0.7138 (ppp) cc_final: 0.6846 (ppp)
REVERT: C  122 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.8019 (tp40)
REVERT: C  417 LEU cc_start: 0.8167 (mt) cc_final: 0.7928 (mt)
REVERT: C  481 LYS cc_start: 0.8541 (mtmm) cc_final: 0.8324 (mtmm)
REVERT: C  518 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6793 (ppp)
  outliers start: 13
  outliers final: 7
  residues processed: 115
  average time/residue: 0.0872
  time to fit residues: 14.6371
Evaluate side-chains
  114 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue  122 GLN
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  518 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 81 optimal weight:    4.9990
   chunk 72 optimal weight:    9.9990
   chunk 6 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0060
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.9798

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.198662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.141605 restraints weight = 9890.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 2.40
r_work: 0.3553 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8920  Z= 0.110
  Angle     :  0.521   6.539  12086  Z= 0.260
  Chirality :  0.040   0.157   1330
  Planarity :  0.004   0.049   1598
  Dihedral  :  8.676  92.546   1310
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.84 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.26), residues: 1100
  helix:  2.11 (0.25), residues: 442
  sheet: -0.01 (0.39), residues: 172
  loop :  0.13 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  27 
 TYR   0.012   0.001   TYR A 520 
 PHE   0.006   0.001   PHE A 367 
 TRP   0.003   0.001   TRP C 401 
 HIS   0.003   0.001   HIS C  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8918)
  covalent geometry    : angle       0.52082 (12086)
  hydrogen bonds       : bond        0.03647 (  384)
  hydrogen bonds       : angle       4.29557 ( 1080)
  Misc. bond           : bond        0.00044 (    2)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A  481 LYS cc_start: 0.8620 (mtmm) cc_final: 0.8286 (mtmm)
REVERT: A  518 MET cc_start: 0.7188 (ppp) cc_final: 0.6915 (ppp)
REVERT: C  122 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7899 (tp40)
REVERT: C  316 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6008 (mt)
REVERT: C  417 LEU cc_start: 0.8150 (mt) cc_final: 0.7926 (mt)
REVERT: C  518 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6853 (ppp)
  outliers start: 12
  outliers final: 6
  residues processed: 114
  average time/residue: 0.0967
  time to fit residues: 15.7083
Evaluate side-chains
  116 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue  122 GLN
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  316 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  518 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    9.9990
   chunk 73 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 16 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.198162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.140367 restraints weight = 9859.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 2.46
r_work: 0.3536 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8920  Z= 0.135
  Angle     :  0.541   5.639  12086  Z= 0.272
  Chirality :  0.041   0.150   1330
  Planarity :  0.004   0.048   1598
  Dihedral  :  8.685  95.243   1310
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 12.50 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.26), residues: 1100
  helix:  2.06 (0.25), residues: 442
  sheet: -0.09 (0.39), residues: 172
  loop :  0.11 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 196 
 TYR   0.013   0.001   TYR A 377 
 PHE   0.009   0.001   PHE C 366 
 TRP   0.003   0.001   TRP C 463 
 HIS   0.004   0.001   HIS C  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8918)
  covalent geometry    : angle       0.54119 (12086)
  hydrogen bonds       : bond        0.03983 (  384)
  hydrogen bonds       : angle       4.32041 ( 1080)
  Misc. bond           : bond        0.00078 (    2)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
REVERT: A  196 ARG cc_start: 0.7579 (mtp180) cc_final: 0.7377 (mmm160)
REVERT: A  481 LYS cc_start: 0.8620 (mtmm) cc_final: 0.8307 (mtmm)
REVERT: A  518 MET cc_start: 0.7211 (ppp) cc_final: 0.6935 (ppp)
REVERT: A  548 TYR cc_start: 0.7596 (m-80) cc_final: 0.7319 (m-80)
REVERT: C  122 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7907 (tp40)
REVERT: C  316 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6010 (mt)
REVERT: C  518 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6856 (ppp)
  outliers start: 12
  outliers final: 8
  residues processed: 109
  average time/residue: 0.0922
  time to fit residues: 14.2379
Evaluate side-chains
  113 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue  122 GLN
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  316 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  518 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 97 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 49 optimal weight:   20.0000
   chunk 47 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 17 optimal weight:    8.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.196125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.138295 restraints weight = 9789.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.39
r_work: 0.3495 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8920  Z= 0.189
  Angle     :  0.601   6.778  12086  Z= 0.303
  Chirality :  0.043   0.154   1330
  Planarity :  0.005   0.048   1598
  Dihedral  :  8.949  98.982   1310
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 12.72 %
    Favored  : 85.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.26), residues: 1100
  helix:  1.82 (0.25), residues: 442
  sheet: -0.31 (0.38), residues: 172
  loop :  0.07 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 196 
 TYR   0.016   0.002   TYR A 377 
 PHE   0.013   0.002   PHE A 366 
 TRP   0.005   0.001   TRP C 484 
 HIS   0.006   0.001   HIS C  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 8918)
  covalent geometry    : angle       0.60135 (12086)
  hydrogen bonds       : bond        0.04694 (  384)
  hydrogen bonds       : angle       4.50306 ( 1080)
  Misc. bond           : bond        0.00135 (    2)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.7728 (mmm) cc_final: 0.7474 (mtp)
REVERT: A  316 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6003 (mt)
REVERT: A  481 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8321 (mtmm)
REVERT: A  518 MET cc_start: 0.7168 (ppp) cc_final: 0.6880 (ppp)
REVERT: A  548 TYR cc_start: 0.7690 (m-80) cc_final: 0.7402 (m-80)
REVERT: C  122 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7927 (tp40)
REVERT: C  316 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6034 (mt)
REVERT: C  518 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6816 (ppp)
  outliers start: 12
  outliers final: 7
  residues processed: 110
  average time/residue: 0.0982
  time to fit residues: 15.1235
Evaluate side-chains
  115 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue  122 GLN
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  316 LEU
Chi-restraints excluded: chain C residue  518 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 104 optimal weight:   20.0000
   chunk 10 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 67 optimal weight:    0.5980
   chunk 91 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 94 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.199241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.142150 restraints weight = 9818.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 2.39
r_work: 0.3548 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8920  Z= 0.109
  Angle     :  0.528   6.582  12086  Z= 0.264
  Chirality :  0.040   0.152   1330
  Planarity :  0.004   0.049   1598
  Dihedral  :  8.673  99.318   1310
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 12.61 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.26), residues: 1100
  helix:  2.10 (0.25), residues: 442
  sheet: -0.06 (0.39), residues: 172
  loop :  0.06 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  27 
 TYR   0.012   0.001   TYR A 520 
 PHE   0.008   0.001   PHE A 348 
 TRP   0.004   0.001   TRP C 401 
 HIS   0.003   0.001   HIS C  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8918)
  covalent geometry    : angle       0.52774 (12086)
  hydrogen bonds       : bond        0.03588 (  384)
  hydrogen bonds       : angle       4.24074 ( 1080)
  Misc. bond           : bond        0.00050 (    2)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: A  316 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.5935 (mt)
REVERT: A  481 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8293 (mtmm)
REVERT: A  518 MET cc_start: 0.7202 (ppp) cc_final: 0.6935 (ppp)
REVERT: A  548 TYR cc_start: 0.7609 (m-80) cc_final: 0.7330 (m-80)
REVERT: C  122 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7894 (tp40)
REVERT: C  316 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.5957 (mt)
REVERT: C  518 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6850 (ppp)
  outliers start: 12
  outliers final: 5
  residues processed: 113
  average time/residue: 0.0818
  time to fit residues: 13.4273
Evaluate side-chains
  116 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue  122 GLN
Chi-restraints excluded: chain C residue  316 LEU
Chi-restraints excluded: chain C residue  518 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 59 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 17 optimal weight:    8.9990
   chunk 90 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   chunk 12 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  37 HIS
** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.196745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.139390 restraints weight = 9762.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 2.38
r_work: 0.3509 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8920  Z= 0.165
  Angle     :  0.574   6.411  12086  Z= 0.290
  Chirality :  0.042   0.150   1330
  Planarity :  0.004   0.049   1598
  Dihedral  :  8.777 100.426   1310
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 12.72 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.26), residues: 1100
  helix:  1.93 (0.25), residues: 442
  sheet: -0.16 (0.38), residues: 170
  loop :  0.04 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  82 
 TYR   0.024   0.002   TYR A 520 
 PHE   0.012   0.001   PHE C 366 
 TRP   0.004   0.001   TRP C 463 
 HIS   0.005   0.001   HIS C  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 8918)
  covalent geometry    : angle       0.57398 (12086)
  hydrogen bonds       : bond        0.04363 (  384)
  hydrogen bonds       : angle       4.39406 ( 1080)
  Misc. bond           : bond        0.00112 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3135.82 seconds
wall clock time: 54 minutes 16.32 seconds (3256.32 seconds total)