Starting phenix.real_space_refine
on Fri Aug 22 15:55:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cpe_16780/08_2025/8cpe_16780.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cpe_16780/08_2025/8cpe_16780.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cpe_16780/08_2025/8cpe_16780.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cpe_16780/08_2025/8cpe_16780.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cpe_16780/08_2025/8cpe_16780.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cpe_16780/08_2025/8cpe_16780.cif"
  }
  resolution = 4.0
  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=   0.002
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
     S      15      5.16       5
     C    1795      2.51       5
     N     470      2.21       5
     O     625      1.98       5
     H    2615      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5520
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 1104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1104
          Classifications: {'peptide': 77}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1104
          Classifications: {'peptide': 77}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1104
          Classifications: {'peptide': 77}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1104
          Classifications: {'peptide': 77}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1104
          Classifications: {'peptide': 77}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
          Chain breaks: 1
  Time building chain proxies: 1.30, per 1000 atoms: 0.24
  Number of scatterers: 5520
  At special positions: 0
  Unit cell: (81.5308, 64.7779, 44.6744, 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      15     16.00
     O     625      8.00
     N     470      7.00
     C    1795      6.00
     H    2615      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  91 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 138.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  700

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 9 sheets defined
      0.0% alpha, 50.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5
      removed outlier: 6.335A  pdb=" N   MET A   3 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   MET C   3 " --> pdb=" O   LEU D   4 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   MET D   3 " --> pdb=" O   LEU E   4 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12
      removed outlier: 6.578A  pdb=" N   VAL A  10 " --> pdb=" O   SER B  11 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL C  10 " --> pdb=" O   SER D  11 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   VAL D  10 " --> pdb=" O   SER E  11 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 19 through 21
      removed outlier: 6.186A  pdb=" N   THR A  19 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   THR C  19 " --> pdb=" O   ILE D  20 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   THR D  19 " --> pdb=" O   ILE E  20 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 27 through 29
      removed outlier: 6.423A  pdb=" N   ALA A  27 " --> pdb=" O   SER B  28 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   SER C  28 " --> pdb=" O   ILE B  29 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 32 through 34
      removed outlier: 6.556A  pdb=" N   TYR C  33 " --> pdb=" O   VAL B  34 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 67 through 74
      removed outlier: 6.172A  pdb=" N   ILE A  67 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   SER B  70 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
      removed outlier: 5.378A  pdb=" N   SER A  69 " --> pdb=" O   SER B  70 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ASN B  72 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   SER A  71 " --> pdb=" O   ASN B  72 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   ALA B  74 " --> pdb=" O   SER A  71 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   SER A  73 " --> pdb=" O   ALA B  74 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   SER B  71 " --> pdb=" O   SER C  70 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   ILE C  67 " --> pdb=" O   ASP D  68 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   SER D  70 " --> pdb=" O   ILE C  67 " (cutoff:3.500A)
      removed outlier: 5.328A  pdb=" N   SER C  69 " --> pdb=" O   SER D  70 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   ASN D  72 " --> pdb=" O   SER C  69 " (cutoff:3.500A)
      removed outlier: 6.000A  pdb=" N   SER C  71 " --> pdb=" O   ASN D  72 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   ALA D  74 " --> pdb=" O   SER C  71 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   SER C  73 " --> pdb=" O   ALA D  74 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   ILE D  67 " --> pdb=" O   ASP E  68 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   SER E  70 " --> pdb=" O   ILE D  67 " (cutoff:3.500A)
      removed outlier: 5.384A  pdb=" N   SER D  69 " --> pdb=" O   SER E  70 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ASN E  72 " --> pdb=" O   SER D  69 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   SER D  71 " --> pdb=" O   ASN E  72 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   ALA E  74 " --> pdb=" O   SER D  71 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   SER D  73 " --> pdb=" O   ALA E  74 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 77 through 78
      removed outlier: 6.645A  pdb=" N   THR C  77 " --> pdb=" O   ILE B  78 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 81 through 99
      removed outlier: 3.625A  pdb=" N   ASP A  85 " --> pdb=" O   GLU B  84 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   LYS C  82 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
      removed outlier: 8.520A  pdb=" N   ASP B  85 " --> pdb=" O   LYS C  82 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   GLU C  84 " --> pdb=" O   ASP B  85 " (cutoff:3.500A)
      removed outlier: 8.507A  pdb=" N   ALA B  87 " --> pdb=" O   GLU C  84 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   GLU C  86 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   TYR B  89 " --> pdb=" O   GLU C  86 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   ASP C  88 " --> pdb=" O   TYR B  89 " (cutoff:3.500A)
      removed outlier: 8.298A  pdb=" N   CYS B  91 " --> pdb=" O   ASP C  88 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   TYR C  90 " --> pdb=" O   CYS B  91 " (cutoff:3.500A)
      removed outlier: 8.302A  pdb=" N   SER B  93 " --> pdb=" O   TYR C  90 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   GLN C  92 " --> pdb=" O   SER B  93 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   ASP B  95 " --> pdb=" O   GLN C  92 " (cutoff:3.500A)
      removed outlier: 5.851A  pdb=" N   TYR C  94 " --> pdb=" O   ASP B  95 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   ASN B  97 " --> pdb=" O   TYR C  94 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   GLY C  96 " --> pdb=" O   ASN B  97 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   HIS B  99 " --> pdb=" O   GLY C  96 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   ASN C  98 " --> pdb=" O   HIS B  99 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASP C  85 " --> pdb=" O   GLU D  84 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ASP D  85 " --> pdb=" O   GLU E  84 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 102 through 104
      removed outlier: 6.483A  pdb=" N   GLY C 103 " --> pdb=" O   GLY B 104 " (cutoff:3.500A)

    83 hydrogen bonds defined for protein.
    249 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: 1.19

  Time building geometry restraints manager: 0.67 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 2615
        1.03 -     1.23: 5
        1.23 -     1.42: 1375
        1.42 -     1.62: 1575
        1.62 -     1.82: 20
  Bond restraints: 5590
  Sorted by residual:
  bond pdb=" CA  GLY E 104 "
       pdb=" C   GLY E 104 "
    ideal  model  delta    sigma   weight residual
    1.520  1.513  0.007 7.30e-03 1.88e+04 8.68e-01
  bond pdb=" CA  GLY B 104 "
       pdb=" C   GLY B 104 "
    ideal  model  delta    sigma   weight residual
    1.520  1.514  0.006 7.30e-03 1.88e+04 7.76e-01
  bond pdb=" CA  GLY D 104 "
       pdb=" C   GLY D 104 "
    ideal  model  delta    sigma   weight residual
    1.520  1.514  0.006 7.30e-03 1.88e+04 7.19e-01
  bond pdb=" CG  TYR B  33 "
       pdb=" CD1 TYR B  33 "
    ideal  model  delta    sigma   weight residual
    1.389  1.375  0.014 2.10e-02 2.27e+03 4.26e-01
  bond pdb=" CA  THR B  17 "
       pdb=" HA  THR B  17 "
    ideal  model  delta    sigma   weight residual
    0.970  0.958  0.012 2.00e-02 2.50e+03 3.54e-01
  ... (remaining 5585 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 9595
        1.63 -     3.25: 278
        3.25 -     4.88: 47
        4.88 -     6.51: 0
        6.51 -     8.14: 15
  Bond angle restraints: 9935
  Sorted by residual:
  angle pdb=" N   ASN E  97 "
        pdb=" CA  ASN E  97 "
        pdb=" C   ASN E  97 "
      ideal   model   delta    sigma   weight residual
     107.62  100.11    7.51 1.97e+00 2.58e-01 1.45e+01
  angle pdb=" N   ASN A  97 "
        pdb=" CA  ASN A  97 "
        pdb=" C   ASN A  97 "
      ideal   model   delta    sigma   weight residual
     107.62  100.18    7.44 1.97e+00 2.58e-01 1.43e+01
  angle pdb=" N   ASN B  97 "
        pdb=" CA  ASN B  97 "
        pdb=" C   ASN B  97 "
      ideal   model   delta    sigma   weight residual
     107.62  100.24    7.38 1.97e+00 2.58e-01 1.40e+01
  angle pdb=" N   ASN D  97 "
        pdb=" CA  ASN D  97 "
        pdb=" C   ASN D  97 "
      ideal   model   delta    sigma   weight residual
     107.62  100.25    7.37 1.97e+00 2.58e-01 1.40e+01
  angle pdb=" N   ASN C  97 "
        pdb=" CA  ASN C  97 "
        pdb=" C   ASN C  97 "
      ideal   model   delta    sigma   weight residual
     107.62  100.27    7.35 1.97e+00 2.58e-01 1.39e+01
  ... (remaining 9930 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.51: 2400
       13.51 -    27.01: 205
       27.01 -    40.52: 75
       40.52 -    54.02: 32
       54.02 -    67.53: 28
  Dihedral angle restraints: 2740
    sinusoidal: 1385
      harmonic: 1355
  Sorted by residual:
  dihedral pdb=" CA  GLY D  15 "
           pdb=" C   GLY D  15 "
           pdb=" N   LYS D  16 "
           pdb=" CA  LYS D  16 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.05   28.95     0      5.00e+00 4.00e-02 3.35e+01
  dihedral pdb=" CA  GLY E  15 "
           pdb=" C   GLY E  15 "
           pdb=" N   LYS E  16 "
           pdb=" CA  LYS E  16 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.07   28.93     0      5.00e+00 4.00e-02 3.35e+01
  dihedral pdb=" CA  GLY B  15 "
           pdb=" C   GLY B  15 "
           pdb=" N   LYS B  16 "
           pdb=" CA  LYS B  16 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.12   28.88     0      5.00e+00 4.00e-02 3.34e+01
  ... (remaining 2737 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 202
       0.032 -    0.063: 110
       0.063 -    0.095: 72
       0.095 -    0.127: 32
       0.127 -    0.158: 19
  Chirality restraints: 435
  Sorted by residual:
  chirality pdb=" CA  ILE B  20 "
            pdb=" N   ILE B  20 "
            pdb=" C   ILE B  20 "
            pdb=" CB  ILE B  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.28e-01
  chirality pdb=" CA  ILE E  20 "
            pdb=" N   ILE E  20 "
            pdb=" C   ILE E  20 "
            pdb=" CB  ILE E  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.92e-01
  chirality pdb=" CA  ILE D  20 "
            pdb=" N   ILE D  20 "
            pdb=" C   ILE D  20 "
            pdb=" CB  ILE D  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.86e-01
  ... (remaining 432 not shown)

  Planarity restraints: 880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 102 "   -0.001 2.00e-02 2.50e+03   2.22e-02 1.48e+01
        pdb=" CG  PHE C 102 "   -0.056 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 102 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 102 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 102 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 102 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 102 "   -0.008 2.00e-02 2.50e+03
        pdb=" HD1 PHE C 102 "    0.034 2.00e-02 2.50e+03
        pdb=" HD2 PHE C 102 "    0.031 2.00e-02 2.50e+03
        pdb=" HE1 PHE C 102 "   -0.017 2.00e-02 2.50e+03
        pdb=" HE2 PHE C 102 "    0.004 2.00e-02 2.50e+03
        pdb=" HZ  PHE C 102 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 102 "   -0.001 2.00e-02 2.50e+03   2.22e-02 1.48e+01
        pdb=" CG  PHE B 102 "   -0.056 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 102 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 102 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 102 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 102 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 102 "   -0.009 2.00e-02 2.50e+03
        pdb=" HD1 PHE B 102 "    0.033 2.00e-02 2.50e+03
        pdb=" HD2 PHE B 102 "    0.031 2.00e-02 2.50e+03
        pdb=" HE1 PHE B 102 "   -0.017 2.00e-02 2.50e+03
        pdb=" HE2 PHE B 102 "    0.003 2.00e-02 2.50e+03
        pdb=" HZ  PHE B 102 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 102 "    0.000 2.00e-02 2.50e+03   2.21e-02 1.47e+01
        pdb=" CG  PHE A 102 "   -0.055 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 102 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 102 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 102 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 102 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 102 "   -0.010 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 102 "    0.033 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 102 "    0.031 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 102 "   -0.018 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 102 "    0.004 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 102 "    0.009 2.00e-02 2.50e+03
  ... (remaining 877 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 144
        2.11 -     2.73: 9149
        2.73 -     3.35: 13555
        3.35 -     3.98: 18395
        3.98 -     4.60: 27655
  Nonbonded interactions: 68898
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A   1 "
            pdb=" HG  SER B  26 "
     model   vdw
     1.485 2.450
  nonbonded pdb=" HG  SER C  26 "
            pdb=" OD1 ASN B   1 "
     model   vdw
     1.493 2.450
  nonbonded pdb=" OD1 ASN C   1 "
            pdb=" HG  SER D  26 "
     model   vdw
     1.500 2.450
  nonbonded pdb=" OD1 ASN D   1 "
            pdb=" HG  SER E  26 "
     model   vdw
     1.501 2.450
  nonbonded pdb=" OE1 GLN B  92 "
            pdb=" HH  TYR B  94 "
     model   vdw
     1.526 2.450
  ... (remaining 68893 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'E'
}

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:             1.370
  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:             0.030
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.380
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
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      :  0.002   0.019   2980  Z= 0.124
  Angle     :  0.934   8.136   4050  Z= 0.532
  Chirality :  0.059   0.158    435
  Planarity :  0.005   0.023    515
  Dihedral  : 12.165  49.684    990
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.80 (0.28), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.21), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.047   0.007   TYR D  33 
 PHE   0.044   0.010   PHE C 102 
 TRP   0.016   0.006   TRP A  36 
 HIS   0.014   0.004   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 2975)
  covalent geometry    : angle       0.93213 ( 4040)
  SS BOND              : bond        0.00416 (    5)
  SS BOND              : angle       1.48476 (   10)
  hydrogen bonds       : bond        0.19503 (   83)
  hydrogen bonds       : angle      10.33466 (  249)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.155 
Fit side-chains
REVERT: D   35 GLN cc_start: 0.7436 (pt0) cc_final: 0.7187 (pm20)
REVERT: E   68 ASP cc_start: 0.7589 (t0) cc_final: 0.7320 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0614
  time to fit residues: 5.0651
Evaluate side-chains
  25 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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 = 0.3990 r_free = 0.3990 target = 0.093231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.083547 restraints weight = 21218.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.086468 restraints weight = 8676.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.088125 restraints weight = 4439.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.089355 restraints weight = 2704.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.090182 restraints weight = 1843.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2980  Z= 0.198
  Angle     :  0.610   4.397   4050  Z= 0.342
  Chirality :  0.049   0.130    435
  Planarity :  0.004   0.025    515
  Dihedral  :  7.893  24.518    400
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.61 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.62 (0.29), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.22), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.002   TYR D  33 
 PHE   0.010   0.002   PHE E   2 
 TRP   0.007   0.001   TRP B  36 
 HIS   0.004   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 2975)
  covalent geometry    : angle       0.60803 ( 4040)
  SS BOND              : bond        0.01016 (    5)
  SS BOND              : angle       1.05326 (   10)
  hydrogen bonds       : bond        0.03931 (   83)
  hydrogen bonds       : angle       7.31818 (  249)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.123 
Fit side-chains
  outliers start: 5
  outliers final: 1
  residues processed: 32
  average time/residue: 0.0525
  time to fit residues: 2.4898
Evaluate side-chains
  24 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   17 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
D  35 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.090230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.079632 restraints weight = 21115.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.082478 restraints weight = 8249.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.084430 restraints weight = 4274.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.085605 restraints weight = 2622.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.086481 restraints weight = 1845.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.4272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2980  Z= 0.172
  Angle     :  0.592   4.658   4050  Z= 0.330
  Chirality :  0.049   0.141    435
  Planarity :  0.004   0.030    515
  Dihedral  :  7.513  22.071    400
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.36 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.93 (0.28), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.99 (0.22), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.001   TYR A  89 
 PHE   0.016   0.002   PHE B 102 
 TRP   0.004   0.001   TRP D 100 
 HIS   0.003   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 2975)
  covalent geometry    : angle       0.59274 ( 4040)
  SS BOND              : bond        0.00762 (    5)
  SS BOND              : angle       0.41005 (   10)
  hydrogen bonds       : bond        0.03790 (   83)
  hydrogen bonds       : angle       6.65618 (  249)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.098 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 31
  average time/residue: 0.0578
  time to fit residues: 2.5483
Evaluate side-chains
  28 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   35 GLN
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain B residue  102 PHE
Chi-restraints excluded: chain D residue   28 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 24 optimal weight:    0.4980
   chunk 7 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
B  32 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.088985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.078145 restraints weight = 21163.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.080970 restraints weight = 8432.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.082901 restraints weight = 4440.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.084098 restraints weight = 2757.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.085020 restraints weight = 1953.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.4854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2980  Z= 0.166
  Angle     :  0.587   4.986   4050  Z= 0.321
  Chirality :  0.048   0.129    435
  Planarity :  0.004   0.032    515
  Dihedral  :  7.171  21.914    400
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.97 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.08 (0.27), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.21), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR A  89 
 PHE   0.010   0.002   PHE B 102 
 TRP   0.003   0.001   TRP C 100 
 HIS   0.002   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 2975)
  covalent geometry    : angle       0.58704 ( 4040)
  SS BOND              : bond        0.00774 (    5)
  SS BOND              : angle       0.58296 (   10)
  hydrogen bonds       : bond        0.03208 (   83)
  hydrogen bonds       : angle       6.43636 (  249)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 25
  time to evaluate  : 0.099 
Fit side-chains
  outliers start: 10
  outliers final: 5
  residues processed: 31
  average time/residue: 0.0594
  time to fit residues: 2.6775
Evaluate side-chains
  28 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain B residue   32 HIS
Chi-restraints excluded: chain B residue   35 GLN
Chi-restraints excluded: chain B residue  102 PHE
Chi-restraints excluded: chain D residue   28 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B  32 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.087499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.076698 restraints weight = 22088.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.079308 restraints weight = 9172.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.081100 restraints weight = 5003.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.082201 restraints weight = 3213.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.083138 restraints weight = 2345.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.5212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2980  Z= 0.155
  Angle     :  0.573   5.504   4050  Z= 0.316
  Chirality :  0.048   0.127    435
  Planarity :  0.004   0.032    515
  Dihedral  :  7.043  21.417    400
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.58 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.14 (0.28), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.15 (0.21), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR A  89 
 PHE   0.010   0.002   PHE B 102 
 TRP   0.002   0.001   TRP D 100 
 HIS   0.005   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 2975)
  covalent geometry    : angle       0.57373 ( 4040)
  SS BOND              : bond        0.00660 (    5)
  SS BOND              : angle       0.46036 (   10)
  hydrogen bonds       : bond        0.03030 (   83)
  hydrogen bonds       : angle       6.31825 (  249)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 26
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 7
  residues processed: 30
  average time/residue: 0.0666
  time to fit residues: 2.8384
Evaluate side-chains
  31 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   35 GLN
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain B residue   32 HIS
Chi-restraints excluded: chain B residue   35 GLN
Chi-restraints excluded: chain B residue  102 PHE
Chi-restraints excluded: chain D residue   28 SER
Chi-restraints excluded: chain D residue   91 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 18 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** B  32 HIS ** 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 = 0.3742 r_free = 0.3742 target = 0.079637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.068322 restraints weight = 20412.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.071236 restraints weight = 8074.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.073126 restraints weight = 4138.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.074438 restraints weight = 2478.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.075341 restraints weight = 1650.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.5453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2980  Z= 0.138
  Angle     :  0.570   5.777   4050  Z= 0.312
  Chirality :  0.047   0.124    435
  Planarity :  0.003   0.031    515
  Dihedral  :  6.789  20.931    400
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.88 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.18 (0.28), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.21), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR A  89 
 PHE   0.009   0.002   PHE B 102 
 TRP   0.002   0.001   TRP E  36 
 HIS   0.003   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 2975)
  covalent geometry    : angle       0.56995 ( 4040)
  SS BOND              : bond        0.00569 (    5)
  SS BOND              : angle       0.48696 (   10)
  hydrogen bonds       : bond        0.02843 (   83)
  hydrogen bonds       : angle       6.15540 (  249)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 25
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 8
  residues processed: 31
  average time/residue: 0.0611
  time to fit residues: 2.8097
Evaluate side-chains
  33 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain B residue   32 HIS
Chi-restraints excluded: chain B residue   35 GLN
Chi-restraints excluded: chain B residue  102 PHE
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   28 SER
Chi-restraints excluded: chain D residue   91 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  32 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.085604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.074910 restraints weight = 21438.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.077463 restraints weight = 9053.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.079247 restraints weight = 4908.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.080506 restraints weight = 3149.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.081362 restraints weight = 2208.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.5621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2980  Z= 0.113
  Angle     :  0.549   5.889   4050  Z= 0.297
  Chirality :  0.047   0.127    435
  Planarity :  0.003   0.028    515
  Dihedral  :  6.504  19.605    400
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 18.48 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.25 (0.28), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.23 (0.21), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.001   TYR B  33 
 PHE   0.008   0.001   PHE B 102 
 TRP   0.003   0.001   TRP C  36 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 2975)
  covalent geometry    : angle       0.54926 ( 4040)
  SS BOND              : bond        0.00565 (    5)
  SS BOND              : angle       0.52180 (   10)
  hydrogen bonds       : bond        0.02591 (   83)
  hydrogen bonds       : angle       5.91593 (  249)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 27
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7214 (tt0)
  outliers start: 8
  outliers final: 8
  residues processed: 32
  average time/residue: 0.0685
  time to fit residues: 3.2117
Evaluate side-chains
  34 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 26
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain B residue   32 HIS
Chi-restraints excluded: chain B residue   35 GLN
Chi-restraints excluded: chain B residue  102 PHE
Chi-restraints excluded: chain D residue   28 SER
Chi-restraints excluded: chain D residue   91 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
B  32 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.079042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.067600 restraints weight = 20247.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.070438 restraints weight = 8165.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.072322 restraints weight = 4243.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.073652 restraints weight = 2559.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.074525 restraints weight = 1717.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.5784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2980  Z= 0.137
  Angle     :  0.562   5.826   4050  Z= 0.305
  Chirality :  0.047   0.131    435
  Planarity :  0.003   0.031    515
  Dihedral  :  6.489  20.035    400
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.04 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.18 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.35 (0.28), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.21), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR B  33 
 PHE   0.008   0.002   PHE B 102 
 TRP   0.004   0.001   TRP B  36 
 HIS   0.003   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 2975)
  covalent geometry    : angle       0.56253 ( 4040)
  SS BOND              : bond        0.00665 (    5)
  SS BOND              : angle       0.36729 (   10)
  hydrogen bonds       : bond        0.02772 (   83)
  hydrogen bonds       : angle       5.93222 (  249)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 27
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7159 (tt0)
REVERT: B   32 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.6910 (m90)
  outliers start: 10
  outliers final: 8
  residues processed: 34
  average time/residue: 0.0668
  time to fit residues: 3.3492
Evaluate side-chains
  35 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 26
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain B residue   32 HIS
Chi-restraints excluded: chain B residue   35 GLN
Chi-restraints excluded: chain B residue  102 PHE
Chi-restraints excluded: chain D residue   28 SER
Chi-restraints excluded: chain D residue   91 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0060
   chunk 13 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
B  32 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.079853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.068376 restraints weight = 19976.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.071258 restraints weight = 7932.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.073194 restraints weight = 4093.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.074541 restraints weight = 2452.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.075438 restraints weight = 1635.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.5920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   2980  Z= 0.099
  Angle     :  0.542   5.803   4050  Z= 0.293
  Chirality :  0.047   0.130    435
  Planarity :  0.003   0.029    515
  Dihedral  :  6.210  19.161    400
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 18.48 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.37 (0.28), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.33 (0.21), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR A  33 
 PHE   0.008   0.001   PHE E 102 
 TRP   0.003   0.001   TRP E  36 
 HIS   0.003   0.001   HIS D  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00193 ( 2975)
  covalent geometry    : angle       0.54240 ( 4040)
  SS BOND              : bond        0.00484 (    5)
  SS BOND              : angle       0.49517 (   10)
  hydrogen bonds       : bond        0.02501 (   83)
  hydrogen bonds       : angle       5.78611 (  249)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7188 (tt0)
  outliers start: 8
  outliers final: 8
  residues processed: 30
  average time/residue: 0.0651
  time to fit residues: 2.8904
Evaluate side-chains
  32 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 24
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain B residue   35 GLN
Chi-restraints excluded: chain B residue  102 PHE
Chi-restraints excluded: chain D residue   28 SER
Chi-restraints excluded: chain D residue   91 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.078940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.067532 restraints weight = 20545.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.070392 restraints weight = 8145.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.072326 restraints weight = 4225.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.073602 restraints weight = 2514.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.074498 restraints weight = 1684.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
moved from start:          0.6074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2980  Z= 0.129
  Angle     :  0.554   5.369   4050  Z= 0.301
  Chirality :  0.047   0.127    435
  Planarity :  0.003   0.031    515
  Dihedral  :  6.229  19.843    400
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.05 %
    Favored  : 87.95 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 18.18 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.52 (0.27), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.21), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.014   0.001   TYR B  33 
 PHE   0.009   0.002   PHE E 102 
 TRP   0.005   0.001   TRP B  36 
 HIS   0.001   0.000   HIS D  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 2975)
  covalent geometry    : angle       0.55407 ( 4040)
  SS BOND              : bond        0.00633 (    5)
  SS BOND              : angle       0.27221 (   10)
  hydrogen bonds       : bond        0.02719 (   83)
  hydrogen bonds       : angle       5.82941 (  249)

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 23
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7357 (tt0)
  outliers start: 9
  outliers final: 8
  residues processed: 29
  average time/residue: 0.0465
  time to fit residues: 2.0979
Evaluate side-chains
  31 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 23
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   91 CYS
Chi-restraints excluded: chain C residue  102 PHE
Chi-restraints excluded: chain A residue   91 CYS
Chi-restraints excluded: chain B residue   35 GLN
Chi-restraints excluded: chain B residue  102 PHE
Chi-restraints excluded: chain D residue   28 SER
Chi-restraints excluded: chain D residue   91 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3730 r_free = 0.3730 target = 0.079677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.068166 restraints weight = 20016.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.071053 restraints weight = 7930.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.073029 restraints weight = 4095.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.074370 restraints weight = 2447.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.075292 restraints weight = 1619.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.6143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2980  Z= 0.100
  Angle     :  0.532   5.837   4050  Z= 0.288
  Chirality :  0.047   0.124    435
  Planarity :  0.003   0.029    515
  Dihedral  :  6.035  18.858    400
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.04 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.79 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.57 (0.27), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.47 (0.21), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR B  33 
 PHE   0.009   0.001   PHE E 102 
 TRP   0.003   0.001   TRP C  36 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00199 ( 2975)
  covalent geometry    : angle       0.53175 ( 4040)
  SS BOND              : bond        0.00482 (    5)
  SS BOND              : angle       0.56599 (   10)
  hydrogen bonds       : bond        0.02375 (   83)
  hydrogen bonds       : angle       5.58758 (  249)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1353.70 seconds
wall clock time: 23 minutes 45.24 seconds (1425.24 seconds total)