Starting phenix.real_space_refine
on Tue Nov 18 06:40:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6fq5_4297/11_2025/6fq5_4297.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6fq5_4297/11_2025/6fq5_4297.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6fq5_4297/11_2025/6fq5_4297.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6fq5_4297/11_2025/6fq5_4297.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6fq5_4297/11_2025/6fq5_4297.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6fq5_4297/11_2025/6fq5_4297.map"
  }
  resolution = 3.8
  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=   0.003 sd=   0.031
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     294      5.49       5
     S      12      5.16       5
     C    6741      2.51       5
     N    2303      2.21       5
     O    2843      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12193
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 678
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 678
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
    Chain: "C"
      Number of atoms: 850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 850
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
    Chain: "D"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 746
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 683
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 683
          Classifications: {'peptide': 85}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 83}
    Chain: "G"
      Number of atoms: 850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 850
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
    Chain: "H"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 746
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Time building chain proxies: 2.77, per 1000 atoms: 0.23
  Number of scatterers: 12193
  At special positions: 0
  Unit cell: (78.4, 120.4, 113.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     P     294     15.00
     O    2843      8.00
     N    2303      7.00
     C    6741      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: 0.82
  Conformation dependent library (CDL) restraints added in 300.3 milliseconds
  

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1454

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      71.8% alpha, 2.8% beta
      146 base pairs and 255 stacking pairs defined.
    Time for finding SS restraints: 1.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 4.214A  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: 3.524A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.561A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.519A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.530A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.457A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.725A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 120
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 4.271A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.566A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.688A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.515A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 4.437A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
      removed outlier: 3.728A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.606A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
      removed outlier: 3.605A  pdb=" N   ALA H 104 " --> pdb=" O   PRO H 100 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER H 120 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.916A  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 42 through 43
      removed outlier: 7.379A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.964A  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 42 through 43
      removed outlier: 7.336A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    403 hydrogen bonds defined for protein.
    1188 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      375 hydrogen bonds
      750 hydrogen bond angles
      0 basepair planarities
      146 basepair parallelities
      255 stacking parallelities
  Total time for adding SS restraints: 2.32

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.21 -     1.32: 1746
        1.32 -     1.44: 4620
        1.44 -     1.56: 6033
        1.56 -     1.68: 587
        1.68 -     1.80: 22
  Bond restraints: 13008
  Sorted by residual:
  bond pdb=" C   ILE C  79 "
       pdb=" N   PRO C  80 "
    ideal  model  delta    sigma   weight residual
    1.334  1.405 -0.071 2.34e-02 1.83e+03 9.30e+00
  bond pdb=" C   ILE G  79 "
       pdb=" N   PRO G  80 "
    ideal  model  delta    sigma   weight residual
    1.334  1.400 -0.066 2.34e-02 1.83e+03 7.92e+00
  bond pdb=" C3'  DG I  20 "
       pdb=" O3'  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.499 -0.077 3.00e-02 1.11e+03 6.57e+00
  bond pdb=" C   LEU E  65 "
       pdb=" N   PRO E  66 "
    ideal  model  delta    sigma   weight residual
    1.334  1.370 -0.036 1.51e-02 4.39e+03 5.70e+00
  bond pdb=" C   LEU A  65 "
       pdb=" N   PRO A  66 "
    ideal  model  delta    sigma   weight residual
    1.334  1.370 -0.036 1.51e-02 4.39e+03 5.69e+00
  ... (remaining 13003 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 18063
        2.38 -     4.76: 678
        4.76 -     7.14: 61
        7.14 -     9.51: 14
        9.51 -    11.89: 6
  Bond angle restraints: 18822
  Sorted by residual:
  angle pdb=" CA  ARG C  88 "
        pdb=" CB  ARG C  88 "
        pdb=" CG  ARG C  88 "
      ideal   model   delta    sigma   weight residual
     114.10  124.18  -10.08 2.00e+00 2.50e-01 2.54e+01
  angle pdb=" C   ARG C  77 "
        pdb=" CA  ARG C  77 "
        pdb=" CB  ARG C  77 "
      ideal   model   delta    sigma   weight residual
     109.72  117.90   -8.18 1.73e+00 3.34e-01 2.24e+01
  angle pdb=" CA  ARG G  88 "
        pdb=" CB  ARG G  88 "
        pdb=" CG  ARG G  88 "
      ideal   model   delta    sigma   weight residual
     114.10  123.51   -9.41 2.00e+00 2.50e-01 2.21e+01
  angle pdb=" N   PRO C  80 "
        pdb=" CA  PRO C  80 "
        pdb=" C   PRO C  80 "
      ideal   model   delta    sigma   weight residual
     112.47  122.09   -9.62 2.06e+00 2.36e-01 2.18e+01
  angle pdb=" N   GLY H 101 "
        pdb=" CA  GLY H 101 "
        pdb=" C   GLY H 101 "
      ideal   model   delta    sigma   weight residual
     113.18  123.65  -10.47 2.37e+00 1.78e-01 1.95e+01
  ... (remaining 18817 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.26: 5478
       34.26 -    68.51: 1560
       68.51 -   102.77: 37
      102.77 -   137.02: 3
      137.02 -   171.28: 3
  Dihedral angle restraints: 7081
    sinusoidal: 4831
      harmonic: 2250
  Sorted by residual:
  dihedral pdb=" C4'  DT I -59 "
           pdb=" C3'  DT I -59 "
           pdb=" O3'  DT I -59 "
           pdb=" P    DC I -58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   48.72  171.28     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DG I  20 "
           pdb=" C3'  DG I  20 "
           pdb=" O3'  DG I  20 "
           pdb=" P    DG I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   54.95  165.05     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" CA  ARG D  27 "
           pdb=" C   ARG D  27 "
           pdb=" N   LYS D  28 "
           pdb=" CA  LYS D  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.24  -18.76     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 7078 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1647
       0.065 -    0.130: 424
       0.130 -    0.194: 63
       0.194 -    0.259: 6
       0.259 -    0.324: 3
  Chirality restraints: 2143
  Sorted by residual:
  chirality pdb=" CA  PRO C  80 "
            pdb=" N   PRO C  80 "
            pdb=" C   PRO C  80 "
            pdb=" CB  PRO C  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.39    0.32 2.00e-01 2.50e+01 2.62e+00
  chirality pdb=" CA  PRO G  80 "
            pdb=" N   PRO G  80 "
            pdb=" C   PRO G  80 "
            pdb=" CB  PRO G  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.43    0.29 2.00e-01 2.50e+01 2.09e+00
  chirality pdb=" CG  LEU B  22 "
            pdb=" CB  LEU B  22 "
            pdb=" CD1 LEU B  22 "
            pdb=" CD2 LEU B  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.31   -0.28 2.00e-01 2.50e+01 2.01e+00
  ... (remaining 2140 not shown)

  Planarity restraints: 1360
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  64 "   -0.021 2.00e-02 2.50e+03   4.25e-02 1.81e+01
        pdb=" C   ASN B  64 "    0.074 2.00e-02 2.50e+03
        pdb=" O   ASN B  64 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   VAL B  65 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D 105 "   -0.019 2.00e-02 2.50e+03   3.85e-02 1.48e+01
        pdb=" C   LYS D 105 "    0.067 2.00e-02 2.50e+03
        pdb=" O   LYS D 105 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   HIS D 106 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR F  72 "   -0.018 2.00e-02 2.50e+03   3.67e-02 1.35e+01
        pdb=" C   TYR F  72 "    0.063 2.00e-02 2.50e+03
        pdb=" O   TYR F  72 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   THR F  73 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 1357 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2276
        2.78 -     3.31: 10754
        3.31 -     3.84: 25082
        3.84 -     4.37: 27703
        4.37 -     4.90: 39345
  Nonbonded interactions: 105160
  Sorted by model distance:
  nonbonded pdb=" O   THR C  16 "
            pdb=" OG  SER C  19 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG1 THR H  29 "
            pdb=" OP1  DT J  30 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   THR G  16 "
            pdb=" OG  SER G  19 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" OH  TYR B  98 "
            pdb=" OD2 ASP H  65 "
     model   vdw
     2.340 3.040
  nonbonded pdb=" OE2 GLU E 133 "
            pdb=" NH2 ARG F  95 "
     model   vdw
     2.341 3.120
  ... (remaining 105155 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' and resid 38 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 18 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
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 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:             0.320
  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:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.980
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.077  13008  Z= 0.370
  Angle     :  1.088  11.893  18822  Z= 0.642
  Chirality :  0.058   0.324   2143
  Planarity :  0.008   0.042   1360
  Dihedral  : 28.680 171.275   5627
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  1.55 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.55 (0.25), residues: 758
  helix: -0.74 (0.18), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.39 (0.36), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  30 
 TYR   0.029   0.004   TYR A  54 
 PHE   0.037   0.005   PHE G  25 
 HIS   0.018   0.003   HIS H  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00808 (13008)
  covalent geometry    : angle       1.08773 (18822)
  hydrogen bonds       : bond        0.13266 (  778)
  hydrogen bonds       : angle       4.99491 ( 1938)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  392 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 390
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 PRO cc_start: 0.6958 (Cg_exo) cc_final: 0.6722 (Cg_endo)
REVERT: A   51 ILE cc_start: 0.9322 (mt) cc_final: 0.9024 (mt)
REVERT: A   56 LYS cc_start: 0.8721 (tttt) cc_final: 0.8485 (tttp)
REVERT: A   58 THR cc_start: 0.7519 (p) cc_final: 0.7269 (t)
REVERT: B   24 ASP cc_start: 0.6823 (m-30) cc_final: 0.6108 (p0)
REVERT: B   59 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8402 (ttpp)
REVERT: B   60 VAL cc_start: 0.9172 (t) cc_final: 0.8795 (t)
REVERT: B   63 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7620 (mt-10)
REVERT: C   84 GLN cc_start: 0.7358 (tp40) cc_final: 0.6998 (tp40)
REVERT: C  113 SER cc_start: 0.9098 (m) cc_final: 0.8848 (p)
REVERT: D   31 LYS cc_start: 0.7934 (mttt) cc_final: 0.7571 (pptt)
REVERT: D   40 LYS cc_start: 0.8872 (mttt) cc_final: 0.8515 (mtpt)
REVERT: D   43 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8764 (mmmt)
REVERT: D   76 ARG cc_start: 0.8594 (mtt90) cc_final: 0.8239 (ttm110)
REVERT: D   80 TYR cc_start: 0.7159 (m-10) cc_final: 0.6910 (m-10)
REVERT: D  106 HIS cc_start: 0.8580 (m-70) cc_final: 0.7411 (m-70)
REVERT: D  109 SER cc_start: 0.9321 (t) cc_final: 0.8810 (p)
REVERT: E   51 ILE cc_start: 0.9352 (mt) cc_final: 0.8927 (mt)
REVERT: E   58 THR cc_start: 0.7748 (p) cc_final: 0.7531 (t)
REVERT: E   67 PHE cc_start: 0.8391 (t80) cc_final: 0.7794 (t80)
REVERT: F   59 LYS cc_start: 0.8703 (tttm) cc_final: 0.8159 (ttpp)
REVERT: F   63 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7458 (mt-10)
REVERT: F   82 THR cc_start: 0.8478 (p) cc_final: 0.8258 (p)
REVERT: F   90 LEU cc_start: 0.9224 (mt) cc_final: 0.8892 (mp)
REVERT: F  100 PHE cc_start: 0.7196 (m-80) cc_final: 0.6353 (m-80)
REVERT: G   84 GLN cc_start: 0.7459 (tp40) cc_final: 0.6755 (tp40)
REVERT: G  113 SER cc_start: 0.8966 (m) cc_final: 0.8643 (p)
REVERT: H   40 LYS cc_start: 0.8837 (mttt) cc_final: 0.8610 (mtpt)
REVERT: H   73 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8521 (mm-30)
REVERT: H   86 ILE cc_start: 0.8867 (mt) cc_final: 0.8610 (tp)
REVERT: H  106 HIS cc_start: 0.9053 (m-70) cc_final: 0.7620 (m170)
REVERT: H  109 SER cc_start: 0.9317 (m) cc_final: 0.8825 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 392
  average time/residue: 0.1470
  time to fit residues: 76.3405
Evaluate side-chains
  217 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
A 108 ASN
A 113 HIS
B  18 HIS
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
C 110 ASN
D 106 HIS
E 108 ASN
E 113 HIS
G  38 ASN
G  73 ASN
G 104 GLN
G 110 ASN
H  44 GLN
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.064740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.055441 restraints weight = 65250.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.056919 restraints weight = 32877.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.057893 restraints weight = 20286.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.058593 restraints weight = 14398.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.059006 restraints weight = 11162.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.3495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  13008  Z= 0.232
  Angle     :  0.699   6.510  18822  Z= 0.413
  Chirality :  0.040   0.233   2143
  Planarity :  0.006   0.068   1360
  Dihedral  : 32.116 166.235   4077
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 19.94 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.29), residues: 758
  helix:  1.51 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.62 (0.38), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  45 
 TYR   0.017   0.003   TYR E  54 
 PHE   0.018   0.002   PHE F  61 
 HIS   0.006   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 (13008)
  covalent geometry    : angle       0.69927 (18822)
  hydrogen bonds       : bond        0.05616 (  778)
  hydrogen bonds       : angle       3.53906 ( 1938)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 249
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.9103 (tttt) cc_final: 0.8855 (tttp)
REVERT: A   65 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7219 (mm)
REVERT: A   85 GLN cc_start: 0.8767 (mt0) cc_final: 0.8564 (pt0)
REVERT: A   93 GLN cc_start: 0.8484 (tp40) cc_final: 0.8040 (tp-100)
REVERT: A  108 ASN cc_start: 0.8085 (t160) cc_final: 0.7646 (p0)
REVERT: A  125 GLN cc_start: 0.8580 (mt0) cc_final: 0.8320 (mt0)
REVERT: B   43 VAL cc_start: 0.8868 (t) cc_final: 0.8666 (p)
REVERT: B   44 LYS cc_start: 0.8697 (ttmt) cc_final: 0.8421 (ttpt)
REVERT: B   59 LYS cc_start: 0.8737 (ttpt) cc_final: 0.7924 (ttpp)
REVERT: B   60 VAL cc_start: 0.9239 (t) cc_final: 0.8677 (p)
REVERT: B   63 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7446 (mt-10)
REVERT: B   71 THR cc_start: 0.8997 (m) cc_final: 0.8796 (p)
REVERT: B   90 LEU cc_start: 0.9223 (mt) cc_final: 0.8905 (mp)
REVERT: C   11 ARG cc_start: 0.4695 (mtt180) cc_final: 0.4462 (ttm170)
REVERT: C  113 SER cc_start: 0.8820 (m) cc_final: 0.8598 (p)
REVERT: D   31 LYS cc_start: 0.7740 (mttt) cc_final: 0.7167 (pptt)
REVERT: D   40 LYS cc_start: 0.9321 (mttt) cc_final: 0.9041 (mtpt)
REVERT: D   73 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8510 (mm-30)
REVERT: D   76 ARG cc_start: 0.8689 (mtt90) cc_final: 0.8203 (ttm110)
REVERT: D   80 TYR cc_start: 0.7272 (m-10) cc_final: 0.6817 (m-80)
REVERT: D  106 HIS cc_start: 0.9002 (m90) cc_final: 0.8784 (m170)
REVERT: E   42 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7742 (ptp-110)
REVERT: E   58 THR cc_start: 0.7876 (p) cc_final: 0.7543 (t)
REVERT: E   93 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7878 (tp40)
REVERT: E  123 ASP cc_start: 0.8622 (m-30) cc_final: 0.8156 (t0)
REVERT: E  125 GLN cc_start: 0.8783 (mt0) cc_final: 0.8550 (mm-40)
REVERT: E  133 GLU cc_start: 0.7144 (mp0) cc_final: 0.6034 (mt-10)
REVERT: F   59 LYS cc_start: 0.8872 (tttm) cc_final: 0.8100 (ttpp)
REVERT: F   60 VAL cc_start: 0.8990 (t) cc_final: 0.8275 (p)
REVERT: F   63 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7728 (mt-10)
REVERT: F   71 THR cc_start: 0.8972 (m) cc_final: 0.8717 (p)
REVERT: F   90 LEU cc_start: 0.9138 (mt) cc_final: 0.8824 (mp)
REVERT: H   40 LYS cc_start: 0.9335 (mttt) cc_final: 0.9081 (mtmt)
REVERT: H   73 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8776 (mm-30)
REVERT: H  106 HIS cc_start: 0.9128 (m-70) cc_final: 0.8016 (m90)
REVERT: H  109 SER cc_start: 0.9511 (m) cc_final: 0.9006 (p)
REVERT: H  110 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8355 (mm-30)
  outliers start: 33
  outliers final: 16
  residues processed: 264
  average time/residue: 0.1049
  time to fit residues: 40.5344
Evaluate side-chains
  216 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 198
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain E residue   42 ARG
Chi-restraints excluded: chain E residue   77 ASP
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   65 ASP
Chi-restraints excluded: chain H residue   77 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 49 optimal weight:    6.9990
   chunk 79 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 98 optimal weight:    7.9990
   chunk 74 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 73 optimal weight:    9.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 110 ASN
D  60 ASN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  85 GLN
G 110 ASN
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.061770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.052811 restraints weight = 68674.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.054232 restraints weight = 34910.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.055170 restraints weight = 21572.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.055818 restraints weight = 15277.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.056295 restraints weight = 11999.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.4773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048  13008  Z= 0.306
  Angle     :  0.726   6.783  18822  Z= 0.429
  Chirality :  0.041   0.161   2143
  Planarity :  0.006   0.050   1360
  Dihedral  : 31.887 169.694   4077
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 20.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  6.65 %
    Allowed  : 21.33 %
    Favored  : 72.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.29), residues: 758
  helix:  1.43 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.64 (0.37), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  45 
 TYR   0.013   0.003   TYR C  57 
 PHE   0.022   0.003   PHE A  67 
 HIS   0.007   0.002   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00661 (13008)
  covalent geometry    : angle       0.72593 (18822)
  hydrogen bonds       : bond        0.06655 (  778)
  hydrogen bonds       : angle       3.74798 ( 1938)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 198
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 LEU cc_start: 0.9437 (tp) cc_final: 0.9085 (mm)
REVERT: B   59 LYS cc_start: 0.8807 (ttpt) cc_final: 0.8089 (ttpp)
REVERT: B   60 VAL cc_start: 0.9076 (t) cc_final: 0.8448 (p)
REVERT: B   63 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7495 (mt-10)
REVERT: C    9 LYS cc_start: 0.6756 (mttt) cc_final: 0.5792 (tmtt)
REVERT: C   11 ARG cc_start: 0.5161 (mtt180) cc_final: 0.4885 (mtt180)
REVERT: C   15 LYS cc_start: 0.6827 (tttt) cc_final: 0.6506 (tttm)
REVERT: C  113 SER cc_start: 0.8713 (m) cc_final: 0.8467 (p)
REVERT: D   31 LYS cc_start: 0.7963 (mttt) cc_final: 0.7421 (pptt)
REVERT: D   40 LYS cc_start: 0.9430 (mttt) cc_final: 0.9063 (mtpt)
REVERT: D   73 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8519 (mm-30)
REVERT: D   76 ARG cc_start: 0.8532 (mtt90) cc_final: 0.7973 (ttm110)
REVERT: D  106 HIS cc_start: 0.9179 (m90) cc_final: 0.8334 (m90)
REVERT: D  110 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8501 (mm-30)
REVERT: E   58 THR cc_start: 0.8110 (p) cc_final: 0.7815 (t)
REVERT: E   67 PHE cc_start: 0.8309 (t80) cc_final: 0.8076 (t80)
REVERT: E   93 GLN cc_start: 0.8102 (tp-100) cc_final: 0.7753 (tp40)
REVERT: E  103 LEU cc_start: 0.9415 (tp) cc_final: 0.9112 (mm)
REVERT: E  123 ASP cc_start: 0.8432 (m-30) cc_final: 0.8099 (m-30)
REVERT: E  125 GLN cc_start: 0.8839 (mt0) cc_final: 0.8372 (mt0)
REVERT: G   84 GLN cc_start: 0.8505 (tp40) cc_final: 0.8245 (tp40)
REVERT: G  113 SER cc_start: 0.8704 (m) cc_final: 0.8452 (p)
REVERT: H   31 LYS cc_start: 0.7805 (tptp) cc_final: 0.7330 (tmmt)
REVERT: H   40 LYS cc_start: 0.9438 (mttt) cc_final: 0.9132 (mtpt)
REVERT: H   73 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8747 (mm-30)
REVERT: H  106 HIS cc_start: 0.9236 (m-70) cc_final: 0.7946 (m90)
REVERT: H  109 SER cc_start: 0.9514 (m) cc_final: 0.9058 (p)
REVERT: H  110 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8438 (mm-30)
  outliers start: 43
  outliers final: 33
  residues processed: 217
  average time/residue: 0.1075
  time to fit residues: 33.9516
Evaluate side-chains
  211 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 178
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   77 ASP
Chi-restraints excluded: chain E residue   81 ASP
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   68 ASP
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   65 ASP
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   77 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 90 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   chunk 93 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 84 optimal weight:    8.9990
   chunk 42 optimal weight:    5.9990
   chunk 89 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
B  18 HIS
C 110 ASN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 110 ASN
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.063514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.054620 restraints weight = 65705.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.056118 restraints weight = 31916.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.057142 restraints weight = 19283.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.057853 restraints weight = 13376.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.058309 restraints weight = 10237.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.5130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13008  Z= 0.198
  Angle     :  0.648   7.497  18822  Z= 0.384
  Chirality :  0.038   0.278   2143
  Planarity :  0.005   0.039   1360
  Dihedral  : 31.608 174.630   4077
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 23.03 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.29), residues: 758
  helix:  1.66 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.46 (0.37), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  45 
 TYR   0.021   0.002   TYR H  37 
 PHE   0.020   0.002   PHE E  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 (13008)
  covalent geometry    : angle       0.64842 (18822)
  hydrogen bonds       : bond        0.04610 (  778)
  hydrogen bonds       : angle       3.39478 ( 1938)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 199
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8707 (tp40) cc_final: 0.8458 (tp40)
REVERT: A  103 LEU cc_start: 0.9516 (tp) cc_final: 0.9082 (mm)
REVERT: B   59 LYS cc_start: 0.8644 (ttpt) cc_final: 0.7733 (ttpp)
REVERT: B   60 VAL cc_start: 0.9089 (t) cc_final: 0.8494 (m)
REVERT: B   63 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7444 (mt-10)
REVERT: B   90 LEU cc_start: 0.9150 (mt) cc_final: 0.8810 (mp)
REVERT: C    9 LYS cc_start: 0.6725 (mttt) cc_final: 0.5597 (tmtt)
REVERT: C   11 ARG cc_start: 0.4885 (mtt180) cc_final: 0.4533 (mtt180)
REVERT: C   15 LYS cc_start: 0.6832 (tttt) cc_final: 0.6487 (tttm)
REVERT: C  113 SER cc_start: 0.8881 (m) cc_final: 0.8606 (p)
REVERT: D   31 LYS cc_start: 0.8095 (mttt) cc_final: 0.7556 (pptt)
REVERT: D   40 LYS cc_start: 0.9344 (mttt) cc_final: 0.8931 (mtpt)
REVERT: D   73 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8638 (mm-30)
REVERT: D   76 ARG cc_start: 0.8388 (mtt90) cc_final: 0.7850 (ttm110)
REVERT: D   80 TYR cc_start: 0.7719 (m-10) cc_final: 0.7499 (m-10)
REVERT: D  106 HIS cc_start: 0.9243 (m90) cc_final: 0.8358 (m90)
REVERT: D  110 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8614 (mm-30)
REVERT: E  103 LEU cc_start: 0.9411 (tp) cc_final: 0.9172 (mm)
REVERT: E  107 THR cc_start: 0.9399 (p) cc_final: 0.9003 (t)
REVERT: E  123 ASP cc_start: 0.8418 (m-30) cc_final: 0.8063 (t70)
REVERT: E  125 GLN cc_start: 0.8801 (mt0) cc_final: 0.8546 (mm-40)
REVERT: G   50 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.8094 (t80)
REVERT: G   56 GLU cc_start: 0.8817 (tt0) cc_final: 0.8383 (mt-10)
REVERT: G   82 HIS cc_start: 0.8968 (m90) cc_final: 0.8638 (m90)
REVERT: G   84 GLN cc_start: 0.8492 (tp40) cc_final: 0.8243 (tp40)
REVERT: H   31 LYS cc_start: 0.7756 (tptp) cc_final: 0.7430 (tmmt)
REVERT: H   40 LYS cc_start: 0.9431 (mttt) cc_final: 0.9161 (mtpt)
REVERT: H  106 HIS cc_start: 0.9280 (m-70) cc_final: 0.7952 (m90)
REVERT: H  109 SER cc_start: 0.9528 (m) cc_final: 0.9070 (p)
REVERT: H  110 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8561 (mm-30)
  outliers start: 30
  outliers final: 17
  residues processed: 216
  average time/residue: 0.1065
  time to fit residues: 33.7240
Evaluate side-chains
  192 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 174
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   50 TYR
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   77 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 79 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 52 optimal weight:    9.9990
   chunk 34 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 60 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 90 optimal weight:   10.0000
   chunk 95 optimal weight:   10.0000
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
C 110 ASN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.063057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.054155 restraints weight = 67178.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.055635 restraints weight = 33691.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.056646 restraints weight = 20622.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.057405 restraints weight = 14408.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.057895 restraints weight = 10963.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.5567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  13008  Z= 0.212
  Angle     :  0.653   8.057  18822  Z= 0.385
  Chirality :  0.038   0.291   2143
  Planarity :  0.005   0.041   1360
  Dihedral  : 31.408 176.380   4077
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 16.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 23.18 %
    Favored  : 72.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.66 (0.29), residues: 758
  helix:  1.73 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.44 (0.38), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  35 
 TYR   0.018   0.002   TYR H  37 
 PHE   0.030   0.002   PHE E  67 
 HIS   0.010   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 (13008)
  covalent geometry    : angle       0.65278 (18822)
  hydrogen bonds       : bond        0.04958 (  778)
  hydrogen bonds       : angle       3.43127 ( 1938)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 193
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 LEU cc_start: 0.9519 (tp) cc_final: 0.9125 (mm)
REVERT: A  125 GLN cc_start: 0.8569 (mt0) cc_final: 0.8213 (mt0)
REVERT: B   59 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8163 (ttpp)
REVERT: B   60 VAL cc_start: 0.9080 (t) cc_final: 0.8441 (m)
REVERT: B   63 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7438 (mt-10)
REVERT: B   90 LEU cc_start: 0.9087 (mt) cc_final: 0.8753 (mp)
REVERT: C    9 LYS cc_start: 0.6685 (mttt) cc_final: 0.5428 (tmtt)
REVERT: C   11 ARG cc_start: 0.5133 (mtt180) cc_final: 0.4710 (mtt180)
REVERT: C   15 LYS cc_start: 0.6823 (tttt) cc_final: 0.6576 (tptp)
REVERT: C  113 SER cc_start: 0.8646 (m) cc_final: 0.8412 (p)
REVERT: D   31 LYS cc_start: 0.8076 (mttt) cc_final: 0.7533 (pptt)
REVERT: D   40 LYS cc_start: 0.9262 (mttt) cc_final: 0.8868 (mtpt)
REVERT: D   90 GLU cc_start: 0.8630 (mp0) cc_final: 0.8153 (mp0)
REVERT: D  110 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8616 (mm-30)
REVERT: E  107 THR cc_start: 0.9409 (p) cc_final: 0.8890 (t)
REVERT: E  122 LYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6772 (ptpp)
REVERT: E  123 ASP cc_start: 0.8264 (m-30) cc_final: 0.8041 (t70)
REVERT: F   59 LYS cc_start: 0.9132 (ttpt) cc_final: 0.8264 (ttpt)
REVERT: F   63 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7953 (mp0)
REVERT: G   41 GLU cc_start: 0.8192 (pt0) cc_final: 0.7583 (pp20)
REVERT: G   50 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8104 (t80)
REVERT: G   82 HIS cc_start: 0.8985 (m90) cc_final: 0.8678 (m90)
REVERT: G   84 GLN cc_start: 0.8475 (tp40) cc_final: 0.8186 (tp40)
REVERT: H   31 LYS cc_start: 0.7806 (tptp) cc_final: 0.7457 (tmmt)
REVERT: H   37 TYR cc_start: 0.9189 (m-80) cc_final: 0.8810 (m-80)
REVERT: H   40 LYS cc_start: 0.9494 (mttt) cc_final: 0.9273 (mtpt)
REVERT: H   97 LEU cc_start: 0.8932 (mt) cc_final: 0.8699 (mt)
REVERT: H  106 HIS cc_start: 0.9287 (m-70) cc_final: 0.8002 (m90)
REVERT: H  109 SER cc_start: 0.9498 (m) cc_final: 0.9057 (p)
REVERT: H  110 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8646 (mm-30)
  outliers start: 30
  outliers final: 19
  residues processed: 211
  average time/residue: 0.1028
  time to fit residues: 32.1912
Evaluate side-chains
  199 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 178
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   50 TYR
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   77 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 63 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 62 optimal weight:    2.9990
   chunk 7 optimal weight:    0.4980
   chunk 23 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   chunk 95 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 88 optimal weight:   10.0000
   chunk 29 optimal weight:    0.4980
   chunk 68 optimal weight:    8.9990
   overall best weight:    2.9986

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
A 108 ASN
C 104 GLN
C 110 ASN
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.063060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.054405 restraints weight = 66127.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.055946 restraints weight = 32133.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.056990 restraints weight = 19071.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.057644 restraints weight = 13021.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.058114 restraints weight = 9987.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.5865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13008  Z= 0.210
  Angle     :  0.645   8.481  18822  Z= 0.382
  Chirality :  0.038   0.238   2143
  Planarity :  0.005   0.044   1360
  Dihedral  : 31.339 178.243   4077
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 22.72 %
    Favored  : 72.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.29), residues: 758
  helix:  1.61 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.52 (0.39), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  23 
 TYR   0.027   0.002   TYR D  80 
 PHE   0.021   0.002   PHE A  67 
 HIS   0.005   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 (13008)
  covalent geometry    : angle       0.64467 (18822)
  hydrogen bonds       : bond        0.04830 (  778)
  hydrogen bonds       : angle       3.41952 ( 1938)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 191
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8198 (pp20) cc_final: 0.7699 (pp20)
REVERT: A   99 TYR cc_start: 0.8704 (t80) cc_final: 0.8468 (t80)
REVERT: A  125 GLN cc_start: 0.8571 (mt0) cc_final: 0.8152 (mt0)
REVERT: B   59 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8088 (ttpp)
REVERT: B   63 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7501 (mt-10)
REVERT: C    9 LYS cc_start: 0.6986 (mttt) cc_final: 0.5573 (tmtt)
REVERT: C   11 ARG cc_start: 0.5117 (mtt180) cc_final: 0.4693 (mtt180)
REVERT: C   15 LYS cc_start: 0.6804 (tttt) cc_final: 0.6567 (tptp)
REVERT: C  113 SER cc_start: 0.8743 (m) cc_final: 0.8469 (p)
REVERT: D   31 LYS cc_start: 0.7835 (mttt) cc_final: 0.7536 (pptt)
REVERT: D   40 LYS cc_start: 0.9281 (mttt) cc_final: 0.8882 (mtpt)
REVERT: D   90 GLU cc_start: 0.8550 (mp0) cc_final: 0.7994 (mp0)
REVERT: D  110 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8592 (mm-30)
REVERT: E   93 GLN cc_start: 0.8618 (tp40) cc_final: 0.8391 (tp40)
REVERT: E  107 THR cc_start: 0.9404 (p) cc_final: 0.8990 (t)
REVERT: E  122 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6062 (ptpp)
REVERT: E  123 ASP cc_start: 0.8302 (m-30) cc_final: 0.7995 (t70)
REVERT: E  125 GLN cc_start: 0.8782 (mt0) cc_final: 0.8405 (mt0)
REVERT: F   19 ARG cc_start: 0.6532 (mtm-85) cc_final: 0.5314 (tpt90)
REVERT: F   59 LYS cc_start: 0.9031 (ttpt) cc_final: 0.7934 (ttmt)
REVERT: F   63 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7902 (mp0)
REVERT: G   50 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.8119 (t80)
REVERT: G   82 HIS cc_start: 0.9007 (m90) cc_final: 0.8647 (m90)
REVERT: G   84 GLN cc_start: 0.8423 (tp40) cc_final: 0.8150 (tp40)
REVERT: H   31 LYS cc_start: 0.7787 (tptp) cc_final: 0.7448 (tmmt)
REVERT: H   37 TYR cc_start: 0.9179 (m-80) cc_final: 0.8792 (m-80)
REVERT: H   40 LYS cc_start: 0.9500 (mttt) cc_final: 0.9257 (mtpt)
REVERT: H   42 LEU cc_start: 0.9169 (tp) cc_final: 0.8925 (pp)
REVERT: H  106 HIS cc_start: 0.9293 (m-70) cc_final: 0.7927 (m170)
REVERT: H  110 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8661 (mm-30)
  outliers start: 34
  outliers final: 21
  residues processed: 209
  average time/residue: 0.1055
  time to fit residues: 32.2497
Evaluate side-chains
  196 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 173
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   50 TYR
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   77 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 99 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 37 optimal weight:   10.0000
   chunk 82 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 70 optimal weight:    8.9990
   chunk 73 optimal weight:    9.9990
   chunk 80 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.061958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.053473 restraints weight = 67326.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.054939 restraints weight = 33205.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.055920 restraints weight = 20161.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.056645 restraints weight = 14036.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.057165 restraints weight = 10504.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.6238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13008  Z= 0.249
  Angle     :  0.676   5.955  18822  Z= 0.400
  Chirality :  0.040   0.267   2143
  Planarity :  0.005   0.060   1360
  Dihedral  : 31.349 179.525   4077
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 18.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 23.96 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.29), residues: 758
  helix:  1.52 (0.21), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.69 (0.38), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  76 
 TYR   0.037   0.003   TYR D  80 
 PHE   0.029   0.002   PHE E  67 
 HIS   0.006   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 (13008)
  covalent geometry    : angle       0.67642 (18822)
  hydrogen bonds       : bond        0.05689 (  778)
  hydrogen bonds       : angle       3.56917 ( 1938)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 182
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7636 (mm-30)
REVERT: A   73 GLU cc_start: 0.8253 (pp20) cc_final: 0.7769 (pp20)
REVERT: B   59 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8028 (ttpp)
REVERT: B   60 VAL cc_start: 0.9071 (t) cc_final: 0.8547 (p)
REVERT: B   63 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7407 (mt-10)
REVERT: B   86 VAL cc_start: 0.9445 (t) cc_final: 0.9238 (t)
REVERT: C    9 LYS cc_start: 0.6767 (mttt) cc_final: 0.5496 (tmtt)
REVERT: C   11 ARG cc_start: 0.5051 (mtt180) cc_final: 0.4683 (mtt180)
REVERT: C   15 LYS cc_start: 0.6798 (tttt) cc_final: 0.6562 (tptp)
REVERT: C  113 SER cc_start: 0.8845 (m) cc_final: 0.8554 (p)
REVERT: D   34 TYR cc_start: 0.7588 (m-80) cc_final: 0.7054 (m-80)
REVERT: D   40 LYS cc_start: 0.9396 (mttt) cc_final: 0.9001 (mtpt)
REVERT: D   73 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8831 (mm-30)
REVERT: D   76 ARG cc_start: 0.8921 (mtm-85) cc_final: 0.8563 (ttm110)
REVERT: D   90 GLU cc_start: 0.8583 (mp0) cc_final: 0.8059 (mp0)
REVERT: D  110 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8643 (mm-30)
REVERT: E   93 GLN cc_start: 0.8667 (tp40) cc_final: 0.8345 (tp40)
REVERT: E  125 GLN cc_start: 0.8758 (mt0) cc_final: 0.8404 (mt0)
REVERT: F   19 ARG cc_start: 0.6612 (mtm-85) cc_final: 0.5431 (tpt170)
REVERT: F   59 LYS cc_start: 0.9060 (ttpt) cc_final: 0.8555 (ttpt)
REVERT: F   63 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7977 (mt-10)
REVERT: G   50 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.8175 (t80)
REVERT: G   84 GLN cc_start: 0.8388 (tp40) cc_final: 0.8007 (tp40)
REVERT: G  113 SER cc_start: 0.8841 (m) cc_final: 0.8544 (p)
REVERT: H   37 TYR cc_start: 0.9131 (m-80) cc_final: 0.8751 (m-80)
REVERT: H   40 LYS cc_start: 0.9506 (mttt) cc_final: 0.9286 (mtpt)
REVERT: H   73 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8859 (mm-30)
REVERT: H  106 HIS cc_start: 0.9151 (m-70) cc_final: 0.8137 (m90)
REVERT: H  110 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8678 (mm-30)
  outliers start: 32
  outliers final: 24
  residues processed: 200
  average time/residue: 0.1045
  time to fit residues: 30.9520
Evaluate side-chains
  190 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 165
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  108 ASN
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   50 TYR
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   77 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 68 optimal weight:    0.9980
   chunk 79 optimal weight:   10.0000
   chunk 4 optimal weight:    0.8980
   chunk 67 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   chunk 92 optimal weight:    7.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.063505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.054591 restraints weight = 66501.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.056083 restraints weight = 33811.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.057067 restraints weight = 20852.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.057742 restraints weight = 14754.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.058122 restraints weight = 11435.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.6390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13008  Z= 0.184
  Angle     :  0.655  13.062  18822  Z= 0.380
  Chirality :  0.038   0.200   2143
  Planarity :  0.004   0.048   1360
  Dihedral  : 31.200 179.093   4077
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 25.04 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.29), residues: 758
  helix:  1.52 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.55 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  76 
 TYR   0.024   0.002   TYR D  80 
 PHE   0.025   0.002   PHE E  67 
 HIS   0.006   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (13008)
  covalent geometry    : angle       0.65475 (18822)
  hydrogen bonds       : bond        0.04319 (  778)
  hydrogen bonds       : angle       3.38808 ( 1938)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 186
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8351 (pp20) cc_final: 0.7831 (pp20)
REVERT: A   99 TYR cc_start: 0.8668 (t80) cc_final: 0.8443 (t80)
REVERT: A  123 ASP cc_start: 0.8595 (m-30) cc_final: 0.7388 (t0)
REVERT: B   59 LYS cc_start: 0.8787 (ttpt) cc_final: 0.8515 (ttpp)
REVERT: C    9 LYS cc_start: 0.6781 (mttt) cc_final: 0.5204 (tmtt)
REVERT: C   11 ARG cc_start: 0.4955 (mtt180) cc_final: 0.3670 (mtt180)
REVERT: C   15 LYS cc_start: 0.6859 (tttt) cc_final: 0.6632 (tptp)
REVERT: C   50 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.8052 (t80)
REVERT: C  113 SER cc_start: 0.8850 (m) cc_final: 0.8578 (p)
REVERT: D   40 LYS cc_start: 0.9299 (mttt) cc_final: 0.8907 (mtpt)
REVERT: D   73 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8774 (mm-30)
REVERT: D   76 ARG cc_start: 0.8984 (mtm-85) cc_final: 0.8616 (ttm110)
REVERT: D   90 GLU cc_start: 0.8552 (mp0) cc_final: 0.7989 (mp0)
REVERT: D  110 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8712 (mm-30)
REVERT: E   50 GLU cc_start: 0.8476 (tp30) cc_final: 0.8159 (tp30)
REVERT: E  122 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6275 (ptpp)
REVERT: E  123 ASP cc_start: 0.8392 (m-30) cc_final: 0.7725 (t0)
REVERT: E  125 GLN cc_start: 0.8755 (mt0) cc_final: 0.8444 (mt0)
REVERT: F   19 ARG cc_start: 0.6635 (mtm-85) cc_final: 0.5253 (tpt170)
REVERT: G   50 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.8111 (t80)
REVERT: H   37 TYR cc_start: 0.9102 (m-80) cc_final: 0.8730 (m-80)
REVERT: H   40 LYS cc_start: 0.9474 (mttt) cc_final: 0.9254 (mtpt)
REVERT: H  106 HIS cc_start: 0.9181 (m-70) cc_final: 0.8195 (m90)
REVERT: H  110 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8648 (mm-30)
  outliers start: 25
  outliers final: 17
  residues processed: 199
  average time/residue: 0.1019
  time to fit residues: 30.2176
Evaluate side-chains
  190 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 170
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   50 TYR
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   50 TYR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   77 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 101 optimal weight:    8.9990
   chunk 45 optimal weight:    0.7980
   chunk 37 optimal weight:   10.0000
   chunk 77 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.063384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.054658 restraints weight = 65668.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.056182 restraints weight = 32534.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.057202 restraints weight = 19679.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.057914 restraints weight = 13574.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.058390 restraints weight = 10353.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.6540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  13008  Z= 0.211
  Angle     :  0.661  10.252  18822  Z= 0.386
  Chirality :  0.039   0.196   2143
  Planarity :  0.005   0.050   1360
  Dihedral  : 31.112 179.249   4077
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 17.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 26.89 %
    Favored  : 69.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.29), residues: 758
  helix:  1.39 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.61 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  76 
 TYR   0.019   0.003   TYR D  37 
 PHE   0.015   0.002   PHE B  61 
 HIS   0.005   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (13008)
  covalent geometry    : angle       0.66087 (18822)
  hydrogen bonds       : bond        0.04954 (  778)
  hydrogen bonds       : angle       3.54287 ( 1938)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 176
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8328 (pp20) cc_final: 0.7871 (pp20)
REVERT: A  123 ASP cc_start: 0.8512 (m-30) cc_final: 0.7475 (t0)
REVERT: B   59 LYS cc_start: 0.8794 (ttpt) cc_final: 0.8539 (ttpp)
REVERT: C    9 LYS cc_start: 0.6696 (mttt) cc_final: 0.5272 (tmtt)
REVERT: C   11 ARG cc_start: 0.4956 (mtt180) cc_final: 0.4278 (ptp90)
REVERT: C   15 LYS cc_start: 0.6859 (tttt) cc_final: 0.6629 (tptp)
REVERT: C   50 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.7956 (t80)
REVERT: C  113 SER cc_start: 0.8839 (m) cc_final: 0.8561 (p)
REVERT: C  118 LYS cc_start: 0.8564 (mttt) cc_final: 0.8102 (tmmt)
REVERT: D   40 LYS cc_start: 0.9338 (mttt) cc_final: 0.8983 (mtpt)
REVERT: D   73 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8728 (mm-30)
REVERT: D   76 ARG cc_start: 0.8878 (mtm-85) cc_final: 0.8508 (ttm110)
REVERT: D   90 GLU cc_start: 0.8495 (mp0) cc_final: 0.7907 (mp0)
REVERT: D  110 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8635 (mm-30)
REVERT: E   50 GLU cc_start: 0.8441 (tp30) cc_final: 0.8117 (tp30)
REVERT: E  122 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6069 (ptpp)
REVERT: E  123 ASP cc_start: 0.8380 (m-30) cc_final: 0.7661 (t0)
REVERT: E  125 GLN cc_start: 0.8759 (mt0) cc_final: 0.8475 (mt0)
REVERT: F   19 ARG cc_start: 0.6676 (mtm-85) cc_final: 0.5925 (ttm110)
REVERT: F   59 LYS cc_start: 0.9155 (ttpt) cc_final: 0.8866 (ttmt)
REVERT: G   50 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.8125 (t80)
REVERT: H   37 TYR cc_start: 0.9105 (m-80) cc_final: 0.8728 (m-80)
REVERT: H   40 LYS cc_start: 0.9484 (mttt) cc_final: 0.9247 (mtpt)
REVERT: H  110 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8592 (mm-30)
  outliers start: 25
  outliers final: 21
  residues processed: 190
  average time/residue: 0.0999
  time to fit residues: 28.2982
Evaluate side-chains
  196 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 172
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  108 ASN
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   50 TYR
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   68 ASP
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   50 TYR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   77 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 37 optimal weight:    9.9990
   chunk 40 optimal weight:    6.9990
   chunk 73 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 64 optimal weight:    0.1980
   chunk 68 optimal weight:    2.9990
   chunk 79 optimal weight:   10.0000
   chunk 22 optimal weight:    0.1980
   chunk 32 optimal weight:    3.9990
   chunk 96 optimal weight:   10.0000
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 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 = 0.3547 r_free = 0.3547 target = 0.065114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.056189 restraints weight = 65783.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.057743 restraints weight = 32809.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.058774 restraints weight = 19942.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.059464 restraints weight = 13855.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.059935 restraints weight = 10672.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.6661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13008  Z= 0.161
  Angle     :  0.637  10.967  18822  Z= 0.369
  Chirality :  0.037   0.202   2143
  Planarity :  0.004   0.053   1360
  Dihedral  : 30.970 179.914   4077
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 29.06 %
    Favored  : 69.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.29), residues: 758
  helix:  1.41 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.48 (0.39), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  76 
 TYR   0.017   0.002   TYR E  99 
 PHE   0.024   0.002   PHE E  67 
 HIS   0.006   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (13008)
  covalent geometry    : angle       0.63696 (18822)
  hydrogen bonds       : bond        0.03912 (  778)
  hydrogen bonds       : angle       3.41702 ( 1938)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 185
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8277 (ttpp)
REVERT: C    9 LYS cc_start: 0.6791 (mttt) cc_final: 0.5150 (tmtt)
REVERT: C   11 ARG cc_start: 0.4411 (mtt180) cc_final: 0.4096 (ptt-90)
REVERT: C  113 SER cc_start: 0.8721 (m) cc_final: 0.8485 (p)
REVERT: C  118 LYS cc_start: 0.8550 (mttt) cc_final: 0.8083 (tmmt)
REVERT: D   40 LYS cc_start: 0.9292 (mttt) cc_final: 0.8946 (mtpt)
REVERT: D   73 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8578 (mm-30)
REVERT: D   76 ARG cc_start: 0.8877 (mtm-85) cc_final: 0.8598 (ttm110)
REVERT: D   90 GLU cc_start: 0.8459 (mp0) cc_final: 0.7934 (mp0)
REVERT: E   50 GLU cc_start: 0.8328 (tp30) cc_final: 0.8127 (tp30)
REVERT: E  122 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6143 (ptpp)
REVERT: E  123 ASP cc_start: 0.8406 (m-30) cc_final: 0.7377 (t0)
REVERT: E  125 GLN cc_start: 0.8854 (mt0) cc_final: 0.8626 (mp10)
REVERT: F   19 ARG cc_start: 0.6620 (mtm-85) cc_final: 0.5870 (ttm110)
REVERT: F   59 LYS cc_start: 0.9124 (ttpt) cc_final: 0.8738 (ttmt)
REVERT: G   50 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.8117 (t80)
REVERT: H   37 TYR cc_start: 0.9113 (m-80) cc_final: 0.8791 (m-80)
REVERT: H   40 LYS cc_start: 0.9469 (mttt) cc_final: 0.9226 (mtpt)
  outliers start: 11
  outliers final: 7
  residues processed: 192
  average time/residue: 0.0984
  time to fit residues: 28.2061
Evaluate side-chains
  179 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 170
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   68 ASP
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   50 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 89 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 30 optimal weight:    7.9990
   chunk 100 optimal weight:   10.0000
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.064772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.055853 restraints weight = 66206.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.057361 restraints weight = 34054.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.058387 restraints weight = 20980.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.059072 restraints weight = 14671.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.059570 restraints weight = 11389.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.6799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13008  Z= 0.176
  Angle     :  0.649  10.583  18822  Z= 0.376
  Chirality :  0.038   0.223   2143
  Planarity :  0.004   0.054   1360
  Dihedral  : 30.879 179.763   4077
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 29.98 %
    Favored  : 67.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.29), residues: 758
  helix:  1.37 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.38 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  45 
 TYR   0.017   0.002   TYR C  57 
 PHE   0.029   0.002   PHE F  61 
 HIS   0.006   0.001   HIS D  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (13008)
  covalent geometry    : angle       0.64939 (18822)
  hydrogen bonds       : bond        0.04347 (  778)
  hydrogen bonds       : angle       3.54201 ( 1938)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1682.92 seconds
wall clock time: 29 minutes 55.90 seconds (1795.90 seconds total)