Starting phenix.real_space_refine
on Tue May 13 01:26:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j91_36084/05_2025/8j91_36084.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j91_36084/05_2025/8j91_36084.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j91_36084/05_2025/8j91_36084.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j91_36084/05_2025/8j91_36084.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j91_36084/05_2025/8j91_36084.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j91_36084/05_2025/8j91_36084.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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     226      5.49       5
     S      10      5.16       5
     C    5557      2.51       5
     N    1843      2.21       5
     O    2308      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9944
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 598
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 2, 'TRANS': 71}
    Chain: "B"
      Number of atoms: 665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 665
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 688
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 3, 'TRANS': 87}
    Chain: "D"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 716
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
    Chain: "E"
      Number of atoms: 612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 612
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "F"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 694
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
    Chain: "H"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 716
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
    Chain: "I"
      Number of atoms: 2301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 2301
          Classifications: {'DNA': 113}
          Link IDs: {'rna3p': 112}
    Chain: "J"
      Number of atoms: 2332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 2332
          Classifications: {'DNA': 113}
          Link IDs: {'rna3p': 112}
  Time building chain proxies: 5.53, per 1000 atoms: 0.56
  Number of scatterers: 9944
  At special positions: 0
  Unit cell: (119.78, 118.72, 101.76, 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      10     16.00
     P     226     15.00
     O    2308      8.00
     N    1843      7.00
     C    5557      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.24
  Conformation dependent library (CDL) restraints added in 609.3 milliseconds
  

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1264

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 10 sheets defined
      75.2% alpha, 2.9% beta
      79 base pairs and 200 stacking pairs defined.
    Time for finding SS restraints: 4.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.868A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.605A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.894A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.537A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 23
      removed outlier: 3.776A  pdb=" N   ALA C  22 " --> pdb=" O   ARG C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 48 through 53
    Processing helix  chain 'C' and resid 57 through 74
    Processing helix  chain 'C' and resid 80 through 91
    Processing helix  chain 'C' and resid 91 through 99
      removed outlier: 3.538A  pdb=" N   LYS C  96 " --> pdb=" O   GLU C  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 63 through 74
      removed outlier: 3.724A  pdb=" N   GLN D  72 " --> pdb=" O   LYS D  68 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL D  73 " --> pdb=" O   VAL D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 108
      removed outlier: 3.649A  pdb=" N   LEU D 105 " --> pdb=" O   GLU D 101 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   TYR D 108 " --> pdb=" O   LYS D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 127
    Processing helix  chain 'D' and resid 128 through 149
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.676A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.902A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.656A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 23
      removed outlier: 3.539A  pdb=" N   ALA G  22 " --> pdb=" O   ARG G  18 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 27 through 38
    Processing helix  chain 'G' and resid 48 through 74
      removed outlier: 3.893A  pdb=" N   ALA G  54 " --> pdb=" O   VAL G  50 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLU G  57 " --> pdb=" O   ALA G  53 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 88
      removed outlier: 3.778A  pdb=" N   ILE G  84 " --> pdb=" O   VAL G  80 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLN G  85 " --> pdb=" O   PRO G  81 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 99
    Processing helix  chain 'H' and resid 62 through 74
    Processing helix  chain 'H' and resid 80 through 109
    Processing helix  chain 'H' and resid 115 through 127
    Processing helix  chain 'H' and resid 128 through 149
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.075A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44
      removed outlier: 7.468A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103
      removed outlier: 6.788A  pdb=" N   THR C 102 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.073A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44
      removed outlier: 7.291A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H 114 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79

    367 hydrogen bonds defined for protein.
    1089 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      198 hydrogen bonds
      396 hydrogen bond angles
      0 basepair planarities
      79 basepair parallelities
      200 stacking parallelities
  Total time for adding SS restraints: 3.28

  Time building geometry restraints manager: 2.67 seconds

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

  Histogram of bond lengths:
        1.06 -     1.21: 4
        1.21 -     1.36: 2977
        1.36 -     1.51: 4403
        1.51 -     1.66: 3171
        1.66 -     1.81: 18
  Bond restraints: 10573
  Sorted by residual:
  bond pdb=" C6   DG I -52 "
       pdb=" O6   DG I -52 "
    ideal  model  delta    sigma   weight residual
    1.239  1.065  0.174 2.00e-02 2.50e+03 7.59e+01
  bond pdb=" C4   DC J  52 "
       pdb=" N4   DC J  52 "
    ideal  model  delta    sigma   weight residual
    1.337  1.187  0.150 2.00e-02 2.50e+03 5.59e+01
  bond pdb=" C1'  DA I  24 "
       pdb=" N9   DA I  24 "
    ideal  model  delta    sigma   weight residual
    1.460  1.363  0.097 2.00e-02 2.50e+03 2.34e+01
  bond pdb=" CA  ALA E  96 "
       pdb=" CB  ALA E  96 "
    ideal  model  delta    sigma   weight residual
    1.528  1.462  0.066 1.59e-02 3.96e+03 1.72e+01
  bond pdb=" O3'  DC J  24 "
       pdb=" P    DT J  25 "
    ideal  model  delta    sigma   weight residual
    1.607  1.546  0.061 1.50e-02 4.44e+03 1.66e+01
  ... (remaining 10568 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.26: 15191
        6.26 -    12.53: 43
       12.53 -    18.79: 3
       18.79 -    25.05: 1
       25.05 -    31.31: 4
  Bond angle restraints: 15242
  Sorted by residual:
  angle pdb=" O3'  DA I  24 "
        pdb=" P    DG I  25 "
        pdb=" O5'  DG I  25 "
      ideal   model   delta    sigma   weight residual
     104.00  131.03  -27.03 1.50e+00 4.44e-01 3.25e+02
  angle pdb=" O3'  DA I  24 "
        pdb=" P    DG I  25 "
        pdb=" OP2  DG I  25 "
      ideal   model   delta    sigma   weight residual
     108.00   76.69   31.31 3.00e+00 1.11e-01 1.09e+02
  angle pdb=" OP2  DG I  25 "
        pdb=" P    DG I  25 "
        pdb=" O5'  DG I  25 "
      ideal   model   delta    sigma   weight residual
     108.00   78.64   29.36 3.00e+00 1.11e-01 9.58e+01
  angle pdb=" O3'  DC J  24 "
        pdb=" C3'  DC J  24 "
        pdb=" C2'  DC J  24 "
      ideal   model   delta    sigma   weight residual
     111.50   96.95   14.55 1.50e+00 4.44e-01 9.41e+01
  angle pdb=" O3'  DT J  54 "
        pdb=" C3'  DT J  54 "
        pdb=" C2'  DT J  54 "
      ideal   model   delta    sigma   weight residual
     111.50  125.27  -13.77 1.50e+00 4.44e-01 8.42e+01
  ... (remaining 15237 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.97: 4661
       32.97 -    65.95: 1057
       65.95 -    98.92: 34
       98.92 -   131.89: 2
      131.89 -   164.86: 2
  Dihedral angle restraints: 5756
    sinusoidal: 3800
      harmonic: 1956
  Sorted by residual:
  dihedral pdb=" C4'  DA I  24 "
           pdb=" C3'  DA I  24 "
           pdb=" O3'  DA I  24 "
           pdb=" P    DG I  25 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   55.14  164.86     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   58.65  161.35     1      3.50e+01 8.16e-04 1.53e+01
  dihedral pdb=" CA  ASP C 100 "
           pdb=" CB  ASP C 100 "
           pdb=" CG  ASP C 100 "
           pdb=" OD1 ASP C 100 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.66   58.66     1      2.00e+01 2.50e-03 1.15e+01
  ... (remaining 5753 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.128: 1652
       0.128 -    0.257: 84
       0.257 -    0.385: 9
       0.385 -    0.514: 3
       0.514 -    0.642: 1
  Chirality restraints: 1749
  Sorted by residual:
  chirality pdb=" C3'  DA I  24 "
            pdb=" C4'  DA I  24 "
            pdb=" O3'  DA I  24 "
            pdb=" C2'  DA I  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -3.30    0.64 2.00e-01 2.50e+01 1.03e+01
  chirality pdb=" P    DT J  25 "
            pdb=" OP1  DT J  25 "
            pdb=" OP2  DT J  25 "
            pdb=" O5'  DT J  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -1.86    0.48 2.00e-01 2.50e+01 5.77e+00
  chirality pdb=" C3'  DT J -17 "
            pdb=" C4'  DT J -17 "
            pdb=" O3'  DT J -17 "
            pdb=" C2'  DT J -17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.22   -0.44 2.00e-01 2.50e+01 4.87e+00
  ... (remaining 1746 not shown)

  Planarity restraints: 1143
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J  57 "   -0.174 2.00e-02 2.50e+03   9.24e-02 2.56e+02
        pdb=" N9   DG J  57 "   -0.023 2.00e-02 2.50e+03
        pdb=" C8   DG J  57 "    0.163 2.00e-02 2.50e+03
        pdb=" N7   DG J  57 "    0.123 2.00e-02 2.50e+03
        pdb=" C5   DG J  57 "   -0.034 2.00e-02 2.50e+03
        pdb=" C6   DG J  57 "   -0.072 2.00e-02 2.50e+03
        pdb=" O6   DG J  57 "   -0.107 2.00e-02 2.50e+03
        pdb=" N1   DG J  57 "   -0.021 2.00e-02 2.50e+03
        pdb=" C2   DG J  57 "    0.031 2.00e-02 2.50e+03
        pdb=" N2   DG J  57 "    0.101 2.00e-02 2.50e+03
        pdb=" N3   DG J  57 "    0.024 2.00e-02 2.50e+03
        pdb=" C4   DG J  57 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  -5 "   -0.211 2.00e-02 2.50e+03   9.46e-02 2.46e+02
        pdb=" N9   DA I  -5 "    0.028 2.00e-02 2.50e+03
        pdb=" C8   DA I  -5 "    0.102 2.00e-02 2.50e+03
        pdb=" N7   DA I  -5 "    0.092 2.00e-02 2.50e+03
        pdb=" C5   DA I  -5 "    0.010 2.00e-02 2.50e+03
        pdb=" C6   DA I  -5 "   -0.051 2.00e-02 2.50e+03
        pdb=" N6   DA I  -5 "   -0.143 2.00e-02 2.50e+03
        pdb=" N1   DA I  -5 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I  -5 "    0.081 2.00e-02 2.50e+03
        pdb=" N3   DA I  -5 "    0.060 2.00e-02 2.50e+03
        pdb=" C4   DA I  -5 "    0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J -21 "   -0.144 2.00e-02 2.50e+03   8.09e-02 1.96e+02
        pdb=" N9   DG J -21 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8   DG J -21 "    0.136 2.00e-02 2.50e+03
        pdb=" N7   DG J -21 "    0.119 2.00e-02 2.50e+03
        pdb=" C5   DG J -21 "   -0.023 2.00e-02 2.50e+03
        pdb=" C6   DG J -21 "   -0.060 2.00e-02 2.50e+03
        pdb=" O6   DG J -21 "   -0.095 2.00e-02 2.50e+03
        pdb=" N1   DG J -21 "   -0.028 2.00e-02 2.50e+03
        pdb=" C2   DG J -21 "    0.035 2.00e-02 2.50e+03
        pdb=" N2   DG J -21 "    0.095 2.00e-02 2.50e+03
        pdb=" N3   DG J -21 "    0.011 2.00e-02 2.50e+03
        pdb=" C4   DG J -21 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 1140 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 225
        2.68 -     3.23: 8262
        3.23 -     3.79: 17170
        3.79 -     4.34: 23603
        4.34 -     4.90: 34329
  Nonbonded interactions: 83589
  Sorted by model distance:
  nonbonded pdb=" C2'  DA I  24 "
            pdb=" OP1  DG I  25 "
     model   vdw
     2.122 3.440
  nonbonded pdb=" C4'  DA I  24 "
            pdb=" OP1  DG I  25 "
     model   vdw
     2.163 3.470
  nonbonded pdb=" O   LEU G  86 "
            pdb=" ND2 ASN G  90 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" C3'  DA I  24 "
            pdb=" OP1  DG I  25 "
     model   vdw
     2.229 2.776
  nonbonded pdb=" NZ  LYS G  36 "
            pdb=" OP2  DA I  39 "
     model   vdw
     2.297 3.120
  ... (remaining 83584 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 61 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 16 through 106)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

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:             0.410
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.370
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  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:11.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
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      :  0.011   0.174  10573  Z= 0.538
  Angle     :  1.552  31.314  15242  Z= 0.964
  Chirality :  0.069   0.642   1749
  Planarity :  0.015   0.095   1143
  Dihedral  : 26.616 164.864   4492
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.54 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.31), residues: 662
  helix:  1.58 (0.23), residues: 488
  sheet:  None (None), residues: 0
  loop : -0.77 (0.40), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.014   0.002   PHE G  26 
 TYR   0.017   0.002   TYR D  65 
 ARG   0.006   0.001   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18380 (  565)
  hydrogen bonds       : angle       5.31683 ( 1485)
  covalent geometry    : bond        0.01088 (10573)
  covalent geometry    : angle       1.55243 (15242)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 133
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
REVERT: B   79 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7852 (mmtm)
REVERT: D   84 MET cc_start: 0.7773 (mmp) cc_final: 0.7542 (mmt)
REVERT: H  110 LYS cc_start: 0.8022 (mppt) cc_final: 0.7799 (mmtp)
REVERT: H  141 LYS cc_start: 0.8351 (ttpp) cc_final: 0.8140 (ttmm)
  outliers start: 1
  outliers final: 0
  residues processed: 134
  average time/residue: 1.8527
  time to fit residues: 259.7415
Evaluate side-chains
  77 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 22 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 113 HIS
B  27 GLN
C  74 ASN
** D  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
F  93 GLN
G  85 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.182236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.132357 restraints weight = 10582.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 1.32
r_work: 0.3189 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.097  10573  Z= 0.177
  Angle     :  0.777  37.825  15242  Z= 0.392
  Chirality :  0.039   0.585   1749
  Planarity :  0.005   0.046   1143
  Dihedral  : 30.382 161.266   3192
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 10.23 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.26 (0.32), residues: 662
  helix:  2.12 (0.23), residues: 498
  sheet:  None (None), residues: 0
  loop : -0.42 (0.42), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.015   0.002   TYR F  51 
 ARG   0.008   0.001   ARG C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04643 (  565)
  hydrogen bonds       : angle       3.10296 ( 1485)
  covalent geometry    : bond        0.00389 (10573)
  covalent geometry    : angle       0.77669 (15242)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.875 
Fit side-chains
REVERT: A  129 ARG cc_start: 0.8370 (ttt180) cc_final: 0.8142 (ttt90)
REVERT: B   79 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8184 (mmtm)
REVERT: C   36 LYS cc_start: 0.8124 (mttt) cc_final: 0.7746 (mttp)
REVERT: C   73 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6718 (t0)
REVERT: C   89 ARG cc_start: 0.6819 (mmt90) cc_final: 0.6550 (mmt90)
REVERT: H   65 TYR cc_start: 0.8735 (m-80) cc_final: 0.8356 (m-80)
REVERT: H   93 ASP cc_start: 0.8398 (t70) cc_final: 0.7925 (t70)
REVERT: H  141 LYS cc_start: 0.8542 (ttpp) cc_final: 0.8340 (ttmm)
  outliers start: 10
  outliers final: 2
  residues processed: 101
  average time/residue: 1.6155
  time to fit residues: 171.9216
Evaluate side-chains
  89 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 86
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain H residue   64 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 23 optimal weight:    0.4980
   chunk 79 optimal weight:    5.9990
   chunk 73 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0770
   chunk 47 optimal weight:    9.9990
   chunk 48 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.9144

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

Flipped N/Q/H residues before XYZ refinement:
C  74 ASN
F  25 ASN
F  93 GLN
G  74 ASN
G  85 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.176987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.128283 restraints weight = 10660.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.24
r_work: 0.3097 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10573  Z= 0.214
  Angle     :  0.608  10.109  15242  Z= 0.352
  Chirality :  0.038   0.159   1749
  Planarity :  0.005   0.045   1143
  Dihedral  : 30.641 172.277   3192
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 11.49 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.32), residues: 662
  helix:  1.97 (0.23), residues: 502
  sheet:  None (None), residues: 0
  loop : -0.39 (0.42), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 113 
 PHE   0.010   0.002   PHE A 104 
 TYR   0.018   0.002   TYR F  51 
 ARG   0.006   0.001   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05355 (  565)
  hydrogen bonds       : angle       3.16041 ( 1485)
  covalent geometry    : bond        0.00496 (10573)
  covalent geometry    : angle       0.60785 (15242)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.694 
Fit side-chains
REVERT: A   76 GLN cc_start: 0.8225 (tt0) cc_final: 0.7793 (pt0)
REVERT: B   79 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8277 (mmtp)
REVERT: C   36 LYS cc_start: 0.8143 (mttt) cc_final: 0.7716 (mttp)
REVERT: C   73 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6723 (t0)
REVERT: C   89 ARG cc_start: 0.6921 (mmt90) cc_final: 0.6677 (mmt90)
REVERT: C  103 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8424 (mm)
REVERT: D  147 THR cc_start: 0.7904 (m) cc_final: 0.7589 (m)
REVERT: G   78 ARG cc_start: 0.7658 (ttp80) cc_final: 0.7291 (ttt180)
REVERT: G   80 VAL cc_start: 0.8610 (m) cc_final: 0.8375 (m)
REVERT: H   65 TYR cc_start: 0.8754 (m-80) cc_final: 0.8419 (m-80)
REVERT: H   93 ASP cc_start: 0.8525 (t70) cc_final: 0.8120 (t70)
  outliers start: 17
  outliers final: 6
  residues processed: 106
  average time/residue: 1.6727
  time to fit residues: 186.3445
Evaluate side-chains
  101 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain H residue   64 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 80 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
F  93 GLN
G  74 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.177441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.125901 restraints weight = 10539.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 1.25
r_work: 0.3109 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10573  Z= 0.167
  Angle     :  0.564   9.537  15242  Z= 0.335
  Chirality :  0.035   0.183   1749
  Planarity :  0.005   0.049   1143
  Dihedral  : 30.575 163.428   3192
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.00 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.31), residues: 662
  helix:  2.17 (0.23), residues: 502
  sheet:  None (None), residues: 0
  loop : -0.33 (0.42), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.015   0.002   TYR F  51 
 ARG   0.007   0.001   ARG F  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04697 (  565)
  hydrogen bonds       : angle       3.08874 ( 1485)
  covalent geometry    : bond        0.00371 (10573)
  covalent geometry    : angle       0.56431 (15242)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8159 (tt0) cc_final: 0.7705 (pt0)
REVERT: B   79 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8226 (mmtp)
REVERT: C   36 LYS cc_start: 0.8121 (mttt) cc_final: 0.7708 (mttp)
REVERT: C   73 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6701 (t0)
REVERT: C   74 ASN cc_start: 0.6814 (m110) cc_final: 0.6534 (t0)
REVERT: D  147 THR cc_start: 0.7862 (m) cc_final: 0.7557 (m)
REVERT: H   65 TYR cc_start: 0.8709 (m-80) cc_final: 0.8415 (m-80)
REVERT: H   93 ASP cc_start: 0.8452 (t70) cc_final: 0.8039 (t70)
  outliers start: 16
  outliers final: 8
  residues processed: 102
  average time/residue: 1.5693
  time to fit residues: 168.7976
Evaluate side-chains
  99 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain D residue   64 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain H residue   64 ILE
Chi-restraints excluded: chain H residue   84 MET
Chi-restraints excluded: chain H residue  126 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   chunk 84 optimal weight:    5.9990
   chunk 75 optimal weight:   10.0000
   chunk 74 optimal weight:    6.9990
   chunk 71 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
E  68 GLN
G  74 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.171876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.120775 restraints weight = 10448.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 1.29
r_work: 0.3008 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.3704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.065  10573  Z= 0.353
  Angle     :  0.731  12.048  15242  Z= 0.414
  Chirality :  0.045   0.245   1749
  Planarity :  0.007   0.087   1143
  Dihedral  : 31.301 162.509   3192
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 15.44 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.31), residues: 662
  helix:  1.49 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -0.69 (0.42), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS A 113 
 PHE   0.013   0.003   PHE H  95 
 TYR   0.014   0.003   TYR F  51 
 ARG   0.008   0.001   ARG E 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07063 (  565)
  hydrogen bonds       : angle       3.43395 ( 1485)
  covalent geometry    : bond        0.00840 (10573)
  covalent geometry    : angle       0.73134 (15242)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8158 (tt0) cc_final: 0.7747 (pt0)
REVERT: B   79 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8278 (mmtp)
REVERT: C   25 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7588 (mp10)
REVERT: C   36 LYS cc_start: 0.8138 (mttt) cc_final: 0.7762 (mttp)
REVERT: C   73 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6682 (t0)
REVERT: C  103 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8802 (mm)
REVERT: D  108 TYR cc_start: 0.7366 (m-10) cc_final: 0.6853 (t80)
REVERT: G   57 GLU cc_start: 0.8669 (tt0) cc_final: 0.8377 (tt0)
REVERT: H   63 LYS cc_start: 0.8366 (mptt) cc_final: 0.7321 (ttpp)
REVERT: H   65 TYR cc_start: 0.8778 (m-80) cc_final: 0.8519 (m-80)
  outliers start: 17
  outliers final: 11
  residues processed: 108
  average time/residue: 1.7627
  time to fit residues: 199.9190
Evaluate side-chains
  102 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  122 LYS
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain H residue   84 MET
Chi-restraints excluded: chain H residue  126 VAL
Chi-restraints excluded: chain H residue  140 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 64 optimal weight:    0.3980
   chunk 11 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 105 ASN
F  75 HIS
G 105 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.177200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.127235 restraints weight = 10468.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.26
r_work: 0.3108 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.3766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10573  Z= 0.163
  Angle     :  0.568   9.714  15242  Z= 0.336
  Chirality :  0.035   0.146   1749
  Planarity :  0.005   0.052   1143
  Dihedral  : 30.851 162.203   3192
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.13 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.25 (0.31), residues: 662
  helix:  2.09 (0.22), residues: 502
  sheet:  None (None), residues: 0
  loop : -0.43 (0.44), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.007   0.001   ARG C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04767 (  565)
  hydrogen bonds       : angle       3.12630 ( 1485)
  covalent geometry    : bond        0.00360 (10573)
  covalent geometry    : angle       0.56754 (15242)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8169 (tt0) cc_final: 0.7722 (pt0)
REVERT: B   79 LYS cc_start: 0.8692 (mtpt) cc_final: 0.8236 (mmtp)
REVERT: C   36 LYS cc_start: 0.8075 (mttt) cc_final: 0.7683 (mttp)
REVERT: C   73 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6847 (t0)
REVERT: C   74 ASN cc_start: 0.6694 (m110) cc_final: 0.6359 (t0)
REVERT: C   78 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7245 (ttm110)
REVERT: D  108 TYR cc_start: 0.7354 (m-10) cc_final: 0.6890 (t80)
REVERT: E   80 THR cc_start: 0.8690 (p) cc_final: 0.8444 (t)
REVERT: F   93 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7776 (mt0)
REVERT: H   65 TYR cc_start: 0.8654 (m-80) cc_final: 0.8247 (m-80)
REVERT: H   93 ASP cc_start: 0.8366 (t70) cc_final: 0.8163 (t70)
REVERT: H  141 LYS cc_start: 0.8461 (ttmm) cc_final: 0.8115 (ttpt)
  outliers start: 13
  outliers final: 5
  residues processed: 98
  average time/residue: 1.6148
  time to fit residues: 166.6812
Evaluate side-chains
  93 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain H residue   64 ILE
Chi-restraints excluded: chain H residue   84 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 74 optimal weight:    7.9990
   chunk 71 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 68 optimal weight:    5.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
G 105 ASN
H  72 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.174180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.124272 restraints weight = 10622.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 1.23
r_work: 0.3055 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10573  Z= 0.225
  Angle     :  0.603  10.082  15242  Z= 0.352
  Chirality :  0.038   0.162   1749
  Planarity :  0.005   0.059   1143
  Dihedral  : 30.873 161.877   3192
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.85 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.31), residues: 662
  helix:  2.07 (0.22), residues: 502
  sheet:  None (None), residues: 0
  loop : -0.56 (0.43), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 113 
 PHE   0.010   0.002   PHE E  67 
 TYR   0.017   0.002   TYR F  51 
 ARG   0.007   0.001   ARG C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05532 (  565)
  hydrogen bonds       : angle       3.17706 ( 1485)
  covalent geometry    : bond        0.00523 (10573)
  covalent geometry    : angle       0.60265 (15242)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8194 (tt0) cc_final: 0.7744 (pt0)
REVERT: B   79 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8218 (mmtp)
REVERT: C   25 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7615 (mp10)
REVERT: C   36 LYS cc_start: 0.8138 (mttt) cc_final: 0.7742 (mttp)
REVERT: C   73 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6658 (t0)
REVERT: C   74 ASN cc_start: 0.6686 (m110) cc_final: 0.6349 (t0)
REVERT: D  108 TYR cc_start: 0.7346 (m-10) cc_final: 0.6904 (t80)
REVERT: G   57 GLU cc_start: 0.8631 (tt0) cc_final: 0.8353 (tt0)
REVERT: H   65 TYR cc_start: 0.8726 (m-80) cc_final: 0.8452 (m-80)
REVERT: H  141 LYS cc_start: 0.8465 (ttmm) cc_final: 0.8077 (ttpp)
  outliers start: 15
  outliers final: 8
  residues processed: 94
  average time/residue: 1.8106
  time to fit residues: 179.0472
Evaluate side-chains
  92 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain D residue   64 ILE
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain H residue   64 ILE
Chi-restraints excluded: chain H residue   84 MET
Chi-restraints excluded: chain H residue  126 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 59 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 64 optimal weight:    0.3980
   chunk 74 optimal weight:    7.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
F  93 GLN
H  72 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.175340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.127198 restraints weight = 10518.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 1.19
r_work: 0.3080 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10573  Z= 0.164
  Angle     :  0.573   9.508  15242  Z= 0.340
  Chirality :  0.036   0.233   1749
  Planarity :  0.005   0.056   1143
  Dihedral  : 30.870 161.673   3192
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 19.03 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.32), residues: 662
  helix:  2.28 (0.22), residues: 502
  sheet:  None (None), residues: 0
  loop : -0.52 (0.44), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.011   0.001   PHE E  67 
 TYR   0.016   0.002   TYR F  51 
 ARG   0.005   0.001   ARG C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04949 (  565)
  hydrogen bonds       : angle       3.15136 ( 1485)
  covalent geometry    : bond        0.00360 (10573)
  covalent geometry    : angle       0.57335 (15242)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8394 (tt0) cc_final: 0.7872 (pt0)
REVERT: B   79 LYS cc_start: 0.8796 (mtpt) cc_final: 0.8290 (mmtp)
REVERT: C   25 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7652 (mp10)
REVERT: C   36 LYS cc_start: 0.8155 (mttt) cc_final: 0.7758 (mttp)
REVERT: C   73 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6749 (t0)
REVERT: C   74 ASN cc_start: 0.6711 (m110) cc_final: 0.6359 (t0)
REVERT: D  108 TYR cc_start: 0.7645 (m-10) cc_final: 0.7026 (t80)
REVERT: H   65 TYR cc_start: 0.8772 (m-80) cc_final: 0.8472 (m-80)
REVERT: H  141 LYS cc_start: 0.8424 (ttmm) cc_final: 0.8038 (ttpp)
  outliers start: 12
  outliers final: 5
  residues processed: 88
  average time/residue: 1.6795
  time to fit residues: 155.5642
Evaluate side-chains
  88 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain H residue   64 ILE
Chi-restraints excluded: chain H residue   84 MET
Chi-restraints excluded: chain H residue  126 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 32 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0370
   chunk 69 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 65 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    2.1864

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

Flipped N/Q/H residues before XYZ refinement:
H  72 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.174051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.124767 restraints weight = 10467.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.24
r_work: 0.3052 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10573  Z= 0.225
  Angle     :  0.604  10.010  15242  Z= 0.352
  Chirality :  0.038   0.206   1749
  Planarity :  0.005   0.056   1143
  Dihedral  : 30.879 162.226   3192
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 19.75 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.32), residues: 662
  helix:  2.16 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -0.60 (0.44), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 113 
 PHE   0.010   0.002   PHE E  67 
 TYR   0.017   0.002   TYR B  88 
 ARG   0.008   0.001   ARG C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05563 (  565)
  hydrogen bonds       : angle       3.18338 ( 1485)
  covalent geometry    : bond        0.00524 (10573)
  covalent geometry    : angle       0.60402 (15242)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8257 (tt0) cc_final: 0.7806 (pt0)
REVERT: B   79 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8192 (mmtp)
REVERT: C   25 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7600 (mp10)
REVERT: C   36 LYS cc_start: 0.8102 (mttt) cc_final: 0.7699 (mttp)
REVERT: C   73 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6635 (t0)
REVERT: C   74 ASN cc_start: 0.6626 (m110) cc_final: 0.6283 (t0)
REVERT: C   78 ARG cc_start: 0.7622 (mmm-85) cc_final: 0.7408 (ttm110)
REVERT: D  108 TYR cc_start: 0.7487 (m-10) cc_final: 0.6906 (t80)
REVERT: G   57 GLU cc_start: 0.8644 (tt0) cc_final: 0.8361 (tt0)
REVERT: H   65 TYR cc_start: 0.8736 (m-80) cc_final: 0.8478 (m-80)
REVERT: H  141 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8041 (ttpp)
  outliers start: 8
  outliers final: 5
  residues processed: 88
  average time/residue: 1.8001
  time to fit residues: 166.3297
Evaluate side-chains
  88 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain H residue   64 ILE
Chi-restraints excluded: chain H residue  126 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 78 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
F  93 GLN
H  72 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.175156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.126126 restraints weight = 10497.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.23
r_work: 0.3070 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10573  Z= 0.166
  Angle     :  0.582   9.436  15242  Z= 0.344
  Chirality :  0.036   0.236   1749
  Planarity :  0.005   0.058   1143
  Dihedral  : 30.863 161.975   3192
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 20.11 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.55 (0.32), residues: 662
  helix:  2.35 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -0.54 (0.45), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.011   0.001   PHE E  67 
 TYR   0.023   0.002   TYR B  88 
 ARG   0.008   0.001   ARG C  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04985 (  565)
  hydrogen bonds       : angle       3.16078 ( 1485)
  covalent geometry    : bond        0.00363 (10573)
  covalent geometry    : angle       0.58198 (15242)

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

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

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1324 Ramachandran restraints generated.
    662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8254 (tt0) cc_final: 0.7797 (pt0)
REVERT: B   79 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8188 (mmtp)
REVERT: C   25 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7603 (mp10)
REVERT: C   36 LYS cc_start: 0.8094 (mttt) cc_final: 0.7693 (mttp)
REVERT: C   73 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6627 (t0)
REVERT: C   74 ASN cc_start: 0.6594 (m110) cc_final: 0.6297 (t160)
REVERT: C   78 ARG cc_start: 0.7637 (mmm-85) cc_final: 0.7378 (ttm110)
REVERT: D  108 TYR cc_start: 0.7469 (m-10) cc_final: 0.6908 (t80)
REVERT: H   65 TYR cc_start: 0.8716 (m-80) cc_final: 0.8440 (m-80)
REVERT: H  141 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8038 (ttpp)
  outliers start: 9
  outliers final: 6
  residues processed: 85
  average time/residue: 1.7107
  time to fit residues: 152.7655
Evaluate side-chains
  85 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   77 ARG
Chi-restraints excluded: chain H residue   64 ILE
Chi-restraints excluded: chain H residue  126 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 81 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0670
   chunk 51 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 55 optimal weight:    6.9990
   chunk 63 optimal weight:    0.3980
   chunk 72 optimal weight:    5.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
F  93 GLN
H  72 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.175734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.126838 restraints weight = 10512.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 1.23
r_work: 0.3064 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.3964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10573  Z= 0.157
  Angle     :  0.566   9.537  15242  Z= 0.336
  Chirality :  0.035   0.214   1749
  Planarity :  0.004   0.057   1143
  Dihedral  : 30.825 162.249   3192
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 20.29 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.70 (0.32), residues: 662
  helix:  2.45 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -0.47 (0.45), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.017   0.002   TYR H 108 
 ARG   0.005   0.001   ARG C  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04760 (  565)
  hydrogen bonds       : angle       3.11422 ( 1485)
  covalent geometry    : bond        0.00336 (10573)
  covalent geometry    : angle       0.56606 (15242)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5952.86 seconds
wall clock time: 103 minutes 3.43 seconds (6183.43 seconds total)