Starting phenix.real_space_refine
on Wed Jul 30 00:50:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6fq5_4297/07_2025/6fq5_4297.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6fq5_4297/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6fq5_4297/07_2025/6fq5_4297.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6fq5_4297/07_2025/6fq5_4297.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6fq5_4297/07_2025/6fq5_4297.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6fq5_4297/07_2025/6fq5_4297.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.16, per 1000 atoms: 0.59
  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: 2.79
  Conformation dependent library (CDL) restraints added in 956.3 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: 5.76
  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: 4.47

  Time building geometry restraints manager: 3.38 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:             0.210
  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:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     33.020
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.030
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (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
 HIS   0.018   0.003   HIS H  46 
 PHE   0.037   0.005   PHE G  25 
 TYR   0.029   0.004   TYR A  54 
 ARG   0.004   0.001   ARG H  30 

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

*********************** 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  : 0.932 
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: 0.9023 (mt)
REVERT: A   56 LYS cc_start: 0.8721 (tttt) cc_final: 0.8483 (tttp)
REVERT: A   58 THR cc_start: 0.7519 (p) cc_final: 0.7243 (t)
REVERT: B   24 ASP cc_start: 0.6823 (m-30) cc_final: 0.6023 (p0)
REVERT: B   59 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8404 (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: 0.7621 (mt-10)
REVERT: C   84 GLN cc_start: 0.7358 (tp40) cc_final: 0.7001 (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: 0.8516 (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: 0.6911 (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: 0.8809 (p)
REVERT: E   51 ILE cc_start: 0.9352 (mt) cc_final: 0.8928 (mt)
REVERT: E   58 THR cc_start: 0.7748 (p) cc_final: 0.7533 (t)
REVERT: E   67 PHE cc_start: 0.8391 (t80) cc_final: 0.7800 (t80)
REVERT: F   59 LYS cc_start: 0.8703 (tttm) cc_final: 0.8160 (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: 0.8265 (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: 0.6343 (m-80)
REVERT: G   84 GLN cc_start: 0.7459 (tp40) cc_final: 0.6757 (tp40)
REVERT: G  113 SER cc_start: 0.8966 (m) cc_final: 0.8642 (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: 0.8609 (tp)
REVERT: H  106 HIS cc_start: 0.9053 (m-70) cc_final: 0.7622 (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: 0.3091
  time to fit residues: 160.2196
Evaluate side-chains
  216 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 77 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 48 optimal weight:    9.9990
   chunk 59 optimal weight:    0.8980
   chunk 92 optimal weight:    7.9990
   overall best weight:    2.7186

-------------------------------------------------------------------------------
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
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**
H 106 HIS

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.065306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.055912 restraints weight = 64170.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.057418 restraints weight = 32377.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.058431 restraints weight = 20025.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.3355

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= 0.215
  Angle     :  0.689   6.571  18822  Z= 0.407
  Chirality :  0.039   0.244   2143
  Planarity :  0.006   0.066   1360
  Dihedral  : 32.107 166.158   4077
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 19.94 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.29), residues: 758
  helix:  1.49 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.66 (0.39), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS B  75 
 PHE   0.019   0.002   PHE F  61 
 TYR   0.019   0.002   TYR E  54 
 ARG   0.007   0.001   ARG B  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05272 (  778)
  hydrogen bonds       : angle       3.48756 ( 1938)
  covalent geometry    : bond        0.00466 (13008)
  covalent geometry    : angle       0.68922 (18822)

*********************** 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
  284 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 254
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.8686 (mt0) cc_final: 0.8485 (pt0)
REVERT: A   93 GLN cc_start: 0.8465 (tp40) cc_final: 0.7894 (tp-100)
REVERT: A  125 GLN cc_start: 0.8542 (mt0) cc_final: 0.8325 (mt0)
REVERT: B   59 LYS cc_start: 0.8723 (ttpt) cc_final: 0.7993 (ttpp)
REVERT: B   60 VAL cc_start: 0.9252 (t) cc_final: 0.8716 (p)
REVERT: B   63 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7549 (mt-10)
REVERT: B   90 LEU cc_start: 0.9219 (mt) cc_final: 0.8895 (mp)
REVERT: C   84 GLN cc_start: 0.8379 (tp40) cc_final: 0.8103 (tp40)
REVERT: C  113 SER cc_start: 0.8829 (m) cc_final: 0.8617 (p)
REVERT: D   31 LYS cc_start: 0.7730 (mttt) cc_final: 0.7161 (pptt)
REVERT: D   40 LYS cc_start: 0.9327 (mttt) cc_final: 0.9008 (mtpt)
REVERT: D   73 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8557 (mm-30)
REVERT: D   76 ARG cc_start: 0.8791 (mtt90) cc_final: 0.8294 (ttm110)
REVERT: D   80 TYR cc_start: 0.7266 (m-10) cc_final: 0.6879 (m-80)
REVERT: D  106 HIS cc_start: 0.8952 (m90) cc_final: 0.8322 (m170)
REVERT: D  109 SER cc_start: 0.9148 (t) cc_final: 0.8925 (p)
REVERT: D  110 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8245 (mm-30)
REVERT: E   58 THR cc_start: 0.7852 (p) cc_final: 0.7527 (t)
REVERT: E   78 PHE cc_start: 0.8259 (m-80) cc_final: 0.8023 (m-80)
REVERT: E  123 ASP cc_start: 0.8659 (m-30) cc_final: 0.8212 (t0)
REVERT: E  125 GLN cc_start: 0.8797 (mt0) cc_final: 0.8536 (mm-40)
REVERT: E  133 GLU cc_start: 0.7002 (mp0) cc_final: 0.6175 (mt-10)
REVERT: F   59 LYS cc_start: 0.8863 (tttm) cc_final: 0.8220 (ttpp)
REVERT: F   60 VAL cc_start: 0.9020 (t) cc_final: 0.8341 (p)
REVERT: F   63 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7735 (mt-10)
REVERT: F   71 THR cc_start: 0.8951 (m) cc_final: 0.8684 (p)
REVERT: F   90 LEU cc_start: 0.9171 (mt) cc_final: 0.8894 (mp)
REVERT: H   40 LYS cc_start: 0.9318 (mttt) cc_final: 0.9071 (mtmt)
REVERT: H   73 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8916 (mm-30)
REVERT: H  106 HIS cc_start: 0.9018 (m90) cc_final: 0.8422 (m90)
REVERT: H  109 SER cc_start: 0.9509 (m) cc_final: 0.9036 (t)
REVERT: H  110 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8091 (mm-30)
  outliers start: 30
  outliers final: 14
  residues processed: 266
  average time/residue: 0.2203
  time to fit residues: 84.7422
Evaluate side-chains
  212 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 198
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain B residue   46 ILE
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   42 LEU
Chi-restraints excluded: chain D residue   64 ASN
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   49 VAL
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 56 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   chunk 80 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 63 optimal weight:    3.9990
   chunk 15 optimal weight:    8.9990
   chunk 87 optimal weight:   10.0000
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
C 110 ASN
E  68 GLN
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 = 0.3520 r_free = 0.3520 target = 0.064234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.055110 restraints weight = 64774.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.056594 restraints weight = 32248.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.057595 restraints weight = 19696.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.4364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  13008  Z= 0.222
  Angle     :  0.662   6.892  18822  Z= 0.391
  Chirality :  0.038   0.151   2143
  Planarity :  0.005   0.047   1360
  Dihedral  : 31.699 167.825   4077
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 19.94 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.29), residues: 758
  helix:  1.64 (0.21), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.52 (0.38), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.018   0.002   PHE F  61 
 TYR   0.024   0.002   TYR H  80 
 ARG   0.005   0.001   ARG B  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05208 (  778)
  hydrogen bonds       : angle       3.43161 ( 1938)
  covalent geometry    : bond        0.00487 (13008)
  covalent geometry    : angle       0.66243 (18822)

*********************** 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
  242 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 211
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLN cc_start: 0.8590 (mt0) cc_final: 0.8184 (mt0)
REVERT: B   59 LYS cc_start: 0.8718 (ttpt) cc_final: 0.7878 (ttpp)
REVERT: B   60 VAL cc_start: 0.9148 (t) cc_final: 0.8512 (p)
REVERT: B   63 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7437 (mt-10)
REVERT: B   90 LEU cc_start: 0.9133 (mt) cc_final: 0.8805 (mp)
REVERT: C   15 LYS cc_start: 0.6790 (tttt) cc_final: 0.6501 (tttm)
REVERT: C   84 GLN cc_start: 0.8500 (tp40) cc_final: 0.7942 (tp40)
REVERT: C  113 SER cc_start: 0.8985 (m) cc_final: 0.8711 (p)
REVERT: D   31 LYS cc_start: 0.7711 (mttt) cc_final: 0.7065 (pptt)
REVERT: D   40 LYS cc_start: 0.9362 (mttt) cc_final: 0.9033 (mtpt)
REVERT: D   73 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8520 (mm-30)
REVERT: D   76 ARG cc_start: 0.8584 (mtt90) cc_final: 0.8085 (ttm110)
REVERT: D   80 TYR cc_start: 0.7463 (m-10) cc_final: 0.6047 (m-10)
REVERT: D  106 HIS cc_start: 0.9111 (m90) cc_final: 0.8239 (m90)
REVERT: D  109 SER cc_start: 0.9259 (t) cc_final: 0.8850 (p)
REVERT: D  110 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8098 (mm-30)
REVERT: E   58 THR cc_start: 0.8043 (p) cc_final: 0.7768 (t)
REVERT: E   93 GLN cc_start: 0.8315 (tp40) cc_final: 0.7963 (tp40)
REVERT: E  103 LEU cc_start: 0.9403 (tp) cc_final: 0.9080 (mm)
REVERT: E  123 ASP cc_start: 0.8409 (m-30) cc_final: 0.8089 (t70)
REVERT: F   59 LYS cc_start: 0.8843 (tttm) cc_final: 0.8635 (ttpp)
REVERT: F   60 VAL cc_start: 0.8866 (t) cc_final: 0.8597 (p)
REVERT: F   63 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8101 (mt-10)
REVERT: F   90 LEU cc_start: 0.8973 (mt) cc_final: 0.8678 (mp)
REVERT: G   84 GLN cc_start: 0.8485 (tp40) cc_final: 0.8281 (tp40)
REVERT: H   31 LYS cc_start: 0.7866 (tptp) cc_final: 0.7393 (tmmt)
REVERT: H   40 LYS cc_start: 0.9443 (mttt) cc_final: 0.9211 (mtmt)
REVERT: H   73 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8710 (mm-30)
REVERT: H   98 LEU cc_start: 0.9200 (tt) cc_final: 0.8984 (tt)
REVERT: H  106 HIS cc_start: 0.9144 (m90) cc_final: 0.7934 (m170)
REVERT: H  109 SER cc_start: 0.9550 (m) cc_final: 0.9162 (p)
REVERT: H  110 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8442 (mm-30)
  outliers start: 31
  outliers final: 20
  residues processed: 225
  average time/residue: 0.2092
  time to fit residues: 68.8867
Evaluate side-chains
  209 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 189
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
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   46 ILE
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   51 ILE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain E residue   46 VAL
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 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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0040
   chunk 40 optimal weight:    7.9990
   chunk 100 optimal weight:   10.0000
   chunk 97 optimal weight:    8.9990
   chunk 92 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 20 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    2.2000

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  18 HIS
C 110 ASN
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
E 125 GLN
G 110 ASN
** H  46 HIS ** 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 = 0.3536 r_free = 0.3536 target = 0.064984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.056060 restraints weight = 65105.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.057522 restraints weight = 32582.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.058532 restraints weight = 20045.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.4884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13008  Z= 0.189
  Angle     :  0.628   7.765  18822  Z= 0.371
  Chirality :  0.037   0.284   2143
  Planarity :  0.005   0.038   1360
  Dihedral  : 31.486 171.703   4077
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 23.03 %
    Favored  : 72.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.29), residues: 758
  helix:  1.73 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.36 (0.38), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.024   0.002   PHE A  67 
 TYR   0.029   0.003   TYR B  88 
 ARG   0.006   0.000   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04380 (  778)
  hydrogen bonds       : angle       3.30377 ( 1938)
  covalent geometry    : bond        0.00414 (13008)
  covalent geometry    : angle       0.62765 (18822)

*********************** 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
  236 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 208
  time to evaluate  : 0.905 
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: A   93 GLN cc_start: 0.8677 (tp40) cc_final: 0.8369 (tp40)
REVERT: A  107 THR cc_start: 0.9182 (m) cc_final: 0.8944 (p)
REVERT: B   59 LYS cc_start: 0.8725 (ttpt) cc_final: 0.7927 (ttpp)
REVERT: B   60 VAL cc_start: 0.9177 (t) cc_final: 0.8571 (p)
REVERT: B   63 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7488 (mt-10)
REVERT: C   15 LYS cc_start: 0.6744 (tttt) cc_final: 0.6542 (tptp)
REVERT: C   84 GLN cc_start: 0.8438 (tp40) cc_final: 0.7884 (tp40)
REVERT: C  113 SER cc_start: 0.8919 (m) cc_final: 0.8655 (p)
REVERT: D   31 LYS cc_start: 0.7879 (mttt) cc_final: 0.7305 (pptt)
REVERT: D   40 LYS cc_start: 0.9287 (mttt) cc_final: 0.8873 (mtpt)
REVERT: D   73 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8547 (mm-30)
REVERT: D   76 ARG cc_start: 0.8517 (mtt90) cc_final: 0.8012 (ttm110)
REVERT: D  106 HIS cc_start: 0.9198 (m90) cc_final: 0.8203 (m90)
REVERT: D  110 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8421 (mm-30)
REVERT: E   58 THR cc_start: 0.8112 (p) cc_final: 0.7789 (t)
REVERT: E   67 PHE cc_start: 0.8570 (t80) cc_final: 0.8229 (t80)
REVERT: E  103 LEU cc_start: 0.9383 (tp) cc_final: 0.9113 (mm)
REVERT: E  122 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6376 (ptpp)
REVERT: E  123 ASP cc_start: 0.8389 (m-30) cc_final: 0.8088 (t70)
REVERT: F   90 LEU cc_start: 0.9071 (mt) cc_final: 0.8831 (mp)
REVERT: G   82 HIS cc_start: 0.8935 (m90) cc_final: 0.8653 (m90)
REVERT: G   84 GLN cc_start: 0.8485 (tp40) cc_final: 0.8232 (tp40)
REVERT: H   40 LYS cc_start: 0.9428 (mttt) cc_final: 0.9137 (mtmt)
REVERT: H   80 TYR cc_start: 0.7718 (m-10) cc_final: 0.6927 (m-80)
REVERT: H  106 HIS cc_start: 0.9214 (m90) cc_final: 0.7955 (m170)
REVERT: H  110 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8526 (mm-30)
  outliers start: 28
  outliers final: 14
  residues processed: 223
  average time/residue: 0.2263
  time to fit residues: 72.6769
Evaluate side-chains
  196 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 181
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   81 VAL
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   64 ASN
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   87 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 G residue   16 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain H residue   51 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 51 optimal weight:    6.9990
   chunk 44 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0060
   chunk 75 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 99 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 14 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    2.8600

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
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**
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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.063999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.055232 restraints weight = 66614.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.056675 restraints weight = 33657.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.057668 restraints weight = 20822.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.5386

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= 0.208
  Angle     :  0.637   8.098  18822  Z= 0.377
  Chirality :  0.037   0.243   2143
  Planarity :  0.005   0.075   1360
  Dihedral  : 31.342 175.569   4077
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 22.10 %
    Favored  : 72.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.29), residues: 758
  helix:  1.70 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.37 (0.38), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.017   0.002   PHE E  67 
 TYR   0.022   0.003   TYR D  80 
 ARG   0.007   0.000   ARG E 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04810 (  778)
  hydrogen bonds       : angle       3.37112 ( 1938)
  covalent geometry    : bond        0.00455 (13008)
  covalent geometry    : angle       0.63742 (18822)

*********************** 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
  227 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 195
  time to evaluate  : 0.886 
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: A   73 GLU cc_start: 0.8153 (pp20) cc_final: 0.7746 (pp20)
REVERT: A   99 TYR cc_start: 0.8604 (t80) cc_final: 0.8369 (t80)
REVERT: A  125 GLN cc_start: 0.8686 (mt0) cc_final: 0.8267 (mt0)
REVERT: B   59 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8493 (ttpp)
REVERT: C    9 LYS cc_start: 0.6621 (mttt) cc_final: 0.5420 (tmtt)
REVERT: C   11 ARG cc_start: 0.5141 (mtt180) cc_final: 0.4729 (mtt180)
REVERT: C   15 LYS cc_start: 0.6842 (tttt) cc_final: 0.6620 (tptp)
REVERT: C   41 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8013 (pp20)
REVERT: C  113 SER cc_start: 0.8853 (m) cc_final: 0.8564 (p)
REVERT: D   31 LYS cc_start: 0.7820 (mttt) cc_final: 0.7275 (pptt)
REVERT: D   40 LYS cc_start: 0.9250 (mttt) cc_final: 0.8845 (mtpt)
REVERT: D   73 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8851 (mm-30)
REVERT: D   90 GLU cc_start: 0.8606 (mp0) cc_final: 0.8072 (mp0)
REVERT: D  106 HIS cc_start: 0.9231 (m90) cc_final: 0.8372 (m90)
REVERT: D  110 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8650 (mm-30)
REVERT: E   67 PHE cc_start: 0.8615 (t80) cc_final: 0.8343 (t80)
REVERT: E   93 GLN cc_start: 0.8492 (tp40) cc_final: 0.8065 (tp40)
REVERT: E  123 ASP cc_start: 0.8365 (m-30) cc_final: 0.8079 (t70)
REVERT: G   50 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.8103 (t80)
REVERT: G   82 HIS cc_start: 0.8934 (m90) cc_final: 0.8666 (m90)
REVERT: G   84 GLN cc_start: 0.8542 (tp40) cc_final: 0.8283 (tp40)
REVERT: H   37 TYR cc_start: 0.9286 (m-80) cc_final: 0.8930 (m-80)
REVERT: H   40 LYS cc_start: 0.9433 (mttt) cc_final: 0.9137 (mtpt)
REVERT: H  106 HIS cc_start: 0.9170 (m90) cc_final: 0.8226 (m90)
REVERT: H  110 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8611 (mm-30)
  outliers start: 32
  outliers final: 22
  residues processed: 214
  average time/residue: 0.2102
  time to fit residues: 66.4892
Evaluate side-chains
  195 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 171
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
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   43 VAL
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   41 GLU
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   64 ASN
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   80 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   46 ILE
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   78 ILE
Chi-restraints excluded: chain H residue   51 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 75 optimal weight:   10.0000
   chunk 89 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 7 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 44 optimal weight:   20.0000
   chunk 85 optimal weight:   10.0000
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
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**
** 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 = 0.3544 r_free = 0.3544 target = 0.065415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.056273 restraints weight = 65468.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.057829 restraints weight = 32946.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.058893 restraints weight = 20125.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.5679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13008  Z= 0.170
  Angle     :  0.627  10.584  18822  Z= 0.367
  Chirality :  0.036   0.170   2143
  Planarity :  0.005   0.042   1360
  Dihedral  : 31.186 177.515   4077
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 13.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 23.65 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.29), residues: 758
  helix:  1.72 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.29 (0.38), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.021   0.002   PHE A  67 
 TYR   0.032   0.002   TYR E  99 
 ARG   0.004   0.000   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04065 (  778)
  hydrogen bonds       : angle       3.27939 ( 1938)
  covalent geometry    : bond        0.00372 (13008)
  covalent geometry    : angle       0.62698 (18822)

*********************** 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
  218 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 192
  time to evaluate  : 1.034 
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: A   50 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7512 (mm-30)
REVERT: A   73 GLU cc_start: 0.8209 (pp20) cc_final: 0.7782 (pp20)
REVERT: B   44 LYS cc_start: 0.8432 (ttmt) cc_final: 0.7857 (ttmm)
REVERT: B   59 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8514 (ttpp)
REVERT: C    9 LYS cc_start: 0.6252 (mttt) cc_final: 0.5023 (tmtt)
REVERT: C   11 ARG cc_start: 0.4943 (mtt180) cc_final: 0.4530 (mtt180)
REVERT: C  113 SER cc_start: 0.8803 (m) cc_final: 0.8538 (p)
REVERT: D   31 LYS cc_start: 0.7812 (mttt) cc_final: 0.7203 (pptt)
REVERT: D   40 LYS cc_start: 0.9245 (mttt) cc_final: 0.8837 (mtpt)
REVERT: D   90 GLU cc_start: 0.8599 (mp0) cc_final: 0.8055 (mp0)
REVERT: D  110 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8654 (mm-30)
REVERT: E   67 PHE cc_start: 0.8690 (t80) cc_final: 0.8321 (t80)
REVERT: E   93 GLN cc_start: 0.8457 (tp40) cc_final: 0.8073 (tp40)
REVERT: E  122 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6389 (ptpp)
REVERT: E  123 ASP cc_start: 0.8350 (m-30) cc_final: 0.7934 (t70)
REVERT: E  124 ILE cc_start: 0.9346 (tp) cc_final: 0.9097 (tp)
REVERT: F   19 ARG cc_start: 0.6318 (mtm-85) cc_final: 0.5239 (tpt90)
REVERT: G   50 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.8087 (t80)
REVERT: G   82 HIS cc_start: 0.8868 (m90) cc_final: 0.8631 (m90)
REVERT: G   84 GLN cc_start: 0.8521 (tp40) cc_final: 0.8274 (tp40)
REVERT: H   37 TYR cc_start: 0.9227 (m-80) cc_final: 0.8845 (m-80)
REVERT: H   40 LYS cc_start: 0.9465 (mttt) cc_final: 0.9196 (mtpt)
REVERT: H  106 HIS cc_start: 0.9197 (m90) cc_final: 0.8377 (m90)
REVERT: H  110 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8545 (mm-30)
  outliers start: 26
  outliers final: 18
  residues processed: 205
  average time/residue: 0.2261
  time to fit residues: 67.3146
Evaluate side-chains
  195 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 175
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 ASN
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   64 ASN
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   46 ILE
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
Chi-restraints excluded: chain H residue   86 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 93 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 80 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 64 optimal weight:    8.9990
   chunk 101 optimal weight:   10.0000
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
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 ** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.062489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.054044 restraints weight = 68406.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.055481 restraints weight = 34371.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.056475 restraints weight = 21018.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.5973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  13008  Z= 0.267
  Angle     :  0.699   9.062  18822  Z= 0.409
  Chirality :  0.040   0.263   2143
  Planarity :  0.006   0.044   1360
  Dihedral  : 31.247 179.457   4077
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 19.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 23.80 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.29), residues: 758
  helix:  1.51 (0.21), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.35 (0.38), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS F  75 
 PHE   0.018   0.002   PHE E  67 
 TYR   0.052   0.004   TYR D  80 
 ARG   0.005   0.001   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05950 (  778)
  hydrogen bonds       : angle       3.60851 ( 1938)
  covalent geometry    : bond        0.00588 (13008)
  covalent geometry    : angle       0.69928 (18822)

*********************** 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
  218 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 185
  time to evaluate  : 1.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8222 (pp20) cc_final: 0.7772 (pp20)
REVERT: B   59 LYS cc_start: 0.8838 (ttpt) cc_final: 0.8570 (ttpp)
REVERT: C    9 LYS cc_start: 0.6998 (mttt) cc_final: 0.5600 (tmtt)
REVERT: C   11 ARG cc_start: 0.5332 (mtt180) cc_final: 0.4405 (mtt180)
REVERT: C  113 SER cc_start: 0.8767 (m) cc_final: 0.8504 (p)
REVERT: D   31 LYS cc_start: 0.7866 (mttt) cc_final: 0.7415 (pptt)
REVERT: D   34 TYR cc_start: 0.7645 (m-80) cc_final: 0.7382 (m-80)
REVERT: D   40 LYS cc_start: 0.9347 (mttt) cc_final: 0.8967 (mtpt)
REVERT: D   86 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8032 (tp)
REVERT: D   90 GLU cc_start: 0.8660 (mp0) cc_final: 0.8075 (mp0)
REVERT: D  110 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8592 (mm-30)
REVERT: E   67 PHE cc_start: 0.8649 (t80) cc_final: 0.8276 (t80)
REVERT: E   93 GLN cc_start: 0.8559 (tp40) cc_final: 0.8359 (tp40)
REVERT: E  122 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6352 (ptpp)
REVERT: E  123 ASP cc_start: 0.8364 (m-30) cc_final: 0.7836 (t70)
REVERT: E  133 GLU cc_start: 0.8542 (mp0) cc_final: 0.8300 (mp0)
REVERT: F   19 ARG cc_start: 0.6529 (mtm-85) cc_final: 0.5301 (tpt170)
REVERT: F   63 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8221 (mt-10)
REVERT: G   50 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.8119 (t80)
REVERT: G   84 GLN cc_start: 0.8562 (tp40) cc_final: 0.8340 (tp40)
REVERT: G  113 SER cc_start: 0.8812 (m) cc_final: 0.8459 (p)
REVERT: H   31 LYS cc_start: 0.7773 (tptp) cc_final: 0.7426 (tmmt)
REVERT: H   37 TYR cc_start: 0.9250 (m-80) cc_final: 0.8917 (m-80)
REVERT: H   40 LYS cc_start: 0.9524 (mttt) cc_final: 0.9292 (mtpt)
REVERT: H  110 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8652 (mm-30)
  outliers start: 33
  outliers final: 22
  residues processed: 203
  average time/residue: 0.2260
  time to fit residues: 67.3949
Evaluate side-chains
  205 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 180
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
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   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 D residue   28 LYS
Chi-restraints excluded: chain D residue   64 ASN
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   80 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   78 ILE
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 85 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   chunk 87 optimal weight:   10.0000
   chunk 72 optimal weight:    0.1980
   chunk 82 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
A 125 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 ** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.064657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.056156 restraints weight = 65646.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.057726 restraints weight = 32032.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.058787 restraints weight = 18979.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.6135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13008  Z= 0.177
  Angle     :  0.656  12.980  18822  Z= 0.379
  Chirality :  0.037   0.193   2143
  Planarity :  0.005   0.047   1360
  Dihedral  : 31.122 179.686   4077
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 27.20 %
    Favored  : 68.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.29), residues: 758
  helix:  1.55 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.39 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.026   0.002   PHE B  61 
 TYR   0.038   0.002   TYR D  80 
 ARG   0.004   0.000   ARG B  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04216 (  778)
  hydrogen bonds       : angle       3.40721 ( 1938)
  covalent geometry    : bond        0.00390 (13008)
  covalent geometry    : angle       0.65588 (18822)

*********************** 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
  218 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 192
  time to evaluate  : 0.878 
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: symmetry clash
REVERT: A   50 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7738 (mm-30)
REVERT: A   73 GLU cc_start: 0.8360 (pp20) cc_final: 0.7927 (pp20)
REVERT: B   59 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8441 (ttpp)
REVERT: B   84 MET cc_start: 0.7544 (mmm) cc_final: 0.6904 (tmm)
REVERT: C    9 LYS cc_start: 0.6778 (mttt) cc_final: 0.5437 (tmtt)
REVERT: C   11 ARG cc_start: 0.5096 (mtt180) cc_final: 0.4780 (mtt180)
REVERT: C  113 SER cc_start: 0.8876 (m) cc_final: 0.8606 (p)
REVERT: D   31 LYS cc_start: 0.7705 (mttt) cc_final: 0.7198 (pptt)
REVERT: D   37 TYR cc_start: 0.8830 (m-80) cc_final: 0.8490 (m-80)
REVERT: D   40 LYS cc_start: 0.9318 (mttt) cc_final: 0.8922 (mtpt)
REVERT: D  110 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8594 (mm-30)
REVERT: E   67 PHE cc_start: 0.8674 (t80) cc_final: 0.8291 (t80)
REVERT: E   93 GLN cc_start: 0.8541 (tp40) cc_final: 0.8103 (tp40)
REVERT: E  122 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6451 (ptpp)
REVERT: E  123 ASP cc_start: 0.8313 (m-30) cc_final: 0.7821 (t70)
REVERT: F   19 ARG cc_start: 0.6551 (mtm-85) cc_final: 0.5324 (tpt90)
REVERT: F   63 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8101 (mt-10)
REVERT: G   50 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.8166 (t80)
REVERT: G   84 GLN cc_start: 0.8539 (tp40) cc_final: 0.8306 (tp40)
REVERT: H   31 LYS cc_start: 0.7724 (tptp) cc_final: 0.7405 (tmmt)
REVERT: H   37 TYR cc_start: 0.9204 (m-80) cc_final: 0.8850 (m-80)
REVERT: H   40 LYS cc_start: 0.9489 (mttt) cc_final: 0.9256 (mtpt)
REVERT: H   90 GLU cc_start: 0.8404 (mp0) cc_final: 0.7922 (mp0)
REVERT: H  106 HIS cc_start: 0.9200 (m90) cc_final: 0.8449 (m90)
REVERT: H  110 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8673 (mm-30)
  outliers start: 26
  outliers final: 20
  residues processed: 207
  average time/residue: 0.2140
  time to fit residues: 64.9248
Evaluate side-chains
  193 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 171
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  108 ASN
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue   64 ASN
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain E residue  124 ILE
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   78 ILE
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   77 LEU
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 20 optimal weight:    9.9990
   chunk 101 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 90 optimal weight:   10.0000
   chunk 94 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9980
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
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 ** 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 = 0.3493 r_free = 0.3493 target = 0.062530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.053868 restraints weight = 68351.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.055379 restraints weight = 34591.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.056390 restraints weight = 21046.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.6335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  13008  Z= 0.252
  Angle     :  0.702  11.253  18822  Z= 0.407
  Chirality :  0.040   0.243   2143
  Planarity :  0.005   0.048   1360
  Dihedral  : 31.106 179.049   4077
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 19.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 26.58 %
    Favored  : 68.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.29), residues: 758
  helix:  1.34 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.46 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS F  75 
 PHE   0.015   0.002   PHE E  67 
 TYR   0.026   0.003   TYR E  99 
 ARG   0.004   0.001   ARG F  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05672 (  778)
  hydrogen bonds       : angle       3.66341 ( 1938)
  covalent geometry    : bond        0.00555 (13008)
  covalent geometry    : angle       0.70172 (18822)

*********************** 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
  208 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 178
  time to evaluate  : 0.991 
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: A   50 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7743 (mm-30)
REVERT: A   73 GLU cc_start: 0.8448 (pp20) cc_final: 0.8031 (pp20)
REVERT: B   59 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8551 (ttpp)
REVERT: C    9 LYS cc_start: 0.6946 (mttt) cc_final: 0.5512 (tmtt)
REVERT: C  113 SER cc_start: 0.8784 (m) cc_final: 0.8513 (p)
REVERT: D   31 LYS cc_start: 0.7745 (mttt) cc_final: 0.7248 (pptt)
REVERT: D   40 LYS cc_start: 0.9354 (mttt) cc_final: 0.8970 (mtpt)
REVERT: D   76 ARG cc_start: 0.8746 (mtm-85) cc_final: 0.8362 (ttm110)
REVERT: D  110 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8648 (mm-30)
REVERT: E   67 PHE cc_start: 0.8657 (t80) cc_final: 0.8272 (t80)
REVERT: E  107 THR cc_start: 0.9340 (p) cc_final: 0.8982 (t)
REVERT: E  122 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6263 (ptpp)
REVERT: E  123 ASP cc_start: 0.8259 (m-30) cc_final: 0.7753 (t70)
REVERT: E  133 GLU cc_start: 0.8427 (mp0) cc_final: 0.7056 (mt-10)
REVERT: F   19 ARG cc_start: 0.6618 (mtm-85) cc_final: 0.5395 (tpt170)
REVERT: G   50 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.8101 (t80)
REVERT: G   84 GLN cc_start: 0.8498 (tp40) cc_final: 0.8280 (tp40)
REVERT: H   31 LYS cc_start: 0.7726 (tptp) cc_final: 0.7441 (tmmt)
REVERT: H   37 TYR cc_start: 0.9189 (m-80) cc_final: 0.8816 (m-80)
REVERT: H   40 LYS cc_start: 0.9523 (mttt) cc_final: 0.9299 (mtpt)
REVERT: H  110 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8659 (mm-30)
  outliers start: 30
  outliers final: 22
  residues processed: 195
  average time/residue: 0.2111
  time to fit residues: 60.7322
Evaluate side-chains
  193 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 169
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  106 ASP
Chi-restraints excluded: chain B residue   68 ASP
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  108 LEU
Chi-restraints excluded: chain D residue   28 LYS
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   64 ASN
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  112 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain E residue  124 ILE
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   78 ILE
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 90 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    9.9990
   chunk 97 optimal weight:    7.9990
   chunk 63 optimal weight:    8.9990
   chunk 57 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
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 ** 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 = 0.3482 r_free = 0.3482 target = 0.061794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.052970 restraints weight = 67001.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.054381 restraints weight = 33560.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.055346 restraints weight = 20571.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.6694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.060  13008  Z= 0.368
  Angle     :  0.804   9.868  18822  Z= 0.463
  Chirality :  0.046   0.265   2143
  Planarity :  0.006   0.046   1360
  Dihedral  : 31.578 178.883   4077
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 24.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 26.12 %
    Favored  : 68.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.28), residues: 758
  helix:  0.82 (0.21), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.96 (0.39), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS F  75 
 PHE   0.031   0.003   PHE A  67 
 TYR   0.035   0.004   TYR E  99 
 ARG   0.011   0.001   ARG C  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07714 (  778)
  hydrogen bonds       : angle       4.14151 ( 1938)
  covalent geometry    : bond        0.00806 (13008)
  covalent geometry    : angle       0.80362 (18822)

********************** 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
  222 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 189
  time to evaluate  : 0.964 
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   50 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7685 (mm-30)
REVERT: A   73 GLU cc_start: 0.8355 (pp20) cc_final: 0.7959 (pp20)
REVERT: A   93 GLN cc_start: 0.8711 (tp40) cc_final: 0.8463 (tp40)
REVERT: B   59 LYS cc_start: 0.8826 (ttpt) cc_final: 0.8546 (ttpp)
REVERT: C    9 LYS cc_start: 0.6929 (mttt) cc_final: 0.5446 (tmtt)
REVERT: C  113 SER cc_start: 0.8964 (m) cc_final: 0.8701 (p)
REVERT: C  118 LYS cc_start: 0.8672 (mttt) cc_final: 0.8173 (ttpt)
REVERT: D   40 LYS cc_start: 0.9433 (mttt) cc_final: 0.9088 (mtpt)
REVERT: D   76 ARG cc_start: 0.8808 (mtm-85) cc_final: 0.8467 (ttm110)
REVERT: D  110 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8655 (mm-30)
REVERT: E   67 PHE cc_start: 0.8613 (t80) cc_final: 0.8305 (t80)
REVERT: E   93 GLN cc_start: 0.8652 (tp40) cc_final: 0.8110 (tp40)
REVERT: E  107 THR cc_start: 0.9312 (p) cc_final: 0.8671 (t)
REVERT: E  123 ASP cc_start: 0.8303 (m-30) cc_final: 0.7713 (t70)
REVERT: F   19 ARG cc_start: 0.6679 (mtm-85) cc_final: 0.5528 (tpt170)
REVERT: F   54 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8838 (p)
REVERT: G   50 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8196 (t80)
REVERT: G  113 SER cc_start: 0.8897 (m) cc_final: 0.8531 (p)
REVERT: H   40 LYS cc_start: 0.9477 (mttt) cc_final: 0.9265 (mtpt)
REVERT: H   56 MET cc_start: 0.8499 (ptp) cc_final: 0.8147 (pmm)
REVERT: H  110 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8749 (mm-30)
  outliers start: 33
  outliers final: 25
  residues processed: 210
  average time/residue: 0.2302
  time to fit residues: 70.5150
Evaluate side-chains
  199 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 172
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
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   22 LEU
Chi-restraints excluded: chain B residue   23 ARG
Chi-restraints excluded: chain B residue   68 ASP
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 D residue   28 LYS
Chi-restraints excluded: chain D residue   51 ILE
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   80 THR
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain F residue   54 THR
Chi-restraints excluded: chain F residue   68 ASP
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   86 ILE
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 93 optimal weight:   10.0000
   chunk 36 optimal weight:    0.8980
   chunk 41 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 52 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 85 optimal weight:    7.9990
   chunk 55 optimal weight:    0.0770
   chunk 77 optimal weight:    6.9990
   chunk 88 optimal weight:   10.0000
   overall best weight:    3.5944

-------------------------------------------------------------------------------
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  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**
** 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 = 0.3485 r_free = 0.3485 target = 0.062403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.053692 restraints weight = 65957.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.055195 restraints weight = 32744.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.056217 restraints weight = 19790.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.6781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  13008  Z= 0.241
  Angle     :  0.733  12.914  18822  Z= 0.419
  Chirality :  0.041   0.233   2143
  Planarity :  0.005   0.046   1360
  Dihedral  : 31.444 179.539   4077
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 19.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 26.58 %
    Favored  : 68.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.29), residues: 758
  helix:  0.95 (0.21), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.76 (0.39), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS F  75 
 PHE   0.020   0.002   PHE E  67 
 TYR   0.031   0.003   TYR E  99 
 ARG   0.006   0.001   ARG H  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05521 (  778)
  hydrogen bonds       : angle       3.80303 ( 1938)
  covalent geometry    : bond        0.00533 (13008)
  covalent geometry    : angle       0.73300 (18822)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3261.88 seconds
wall clock time: 57 minutes 34.60 seconds (3454.60 seconds total)