Starting phenix.real_space_refine
on Wed Mar  4 06:46:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v90_31806/03_2026/7v90_31806.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v90_31806/03_2026/7v90_31806.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v90_31806/03_2026/7v90_31806.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v90_31806/03_2026/7v90_31806.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v90_31806/03_2026/7v90_31806.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v90_31806/03_2026/7v90_31806.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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     288      5.49       5
     S      14      5.16       5
     C    6737      2.51       5
     N    2288      2.21       5
     O    2821      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12148
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 824
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 783
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "E"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 825
          Classifications: {'peptide': 100}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 773
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "I"
      Number of atoms: 3067
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 3067
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2872
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.57, per 1000 atoms: 0.21
  Number of scatterers: 12148
  At special positions: 0
  Unit cell: (115.83, 113.256, 124.41, 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      14     16.00
     P     288     15.00
     O    2821      8.00
     N    2288      7.00
     C    6737      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 409.3 milliseconds
  

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1458

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 7 sheets defined
      69.4% alpha, 2.3% beta
      123 base pairs and 249 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 64 through 75
      removed outlier: 3.633A  pdb=" N   ALA A  75 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.575A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 126
      removed outlier: 3.977A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLN A 125 " --> pdb=" O   PRO A 121 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A 126 " --> pdb=" O   LYS A 122 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 120 through 126'
    Processing helix  chain 'A' and resid 126 through 131
      removed outlier: 3.568A  pdb=" N   ARG A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 27
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.796A  pdb=" N   GLY B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 76
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.794A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY B  94 " --> pdb=" O   LEU B  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.467A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 95
      removed outlier: 4.057A  pdb=" N   ASN C  94 " --> pdb=" O   ASP C  90 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 90 through 95'
    Processing helix  chain 'D' and resid 35 through 46
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.699A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 121
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.566A  pdb=" N   ARG E  52 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.667A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.745A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.644A  pdb=" N   ILE F  34 " --> pdb=" O   THR F  30 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 50 through 76
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.680A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (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 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 34 through 46
      removed outlier: 3.597A  pdb=" N   LYS H  40 " --> pdb=" O   VAL H  36 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.759A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 101 through 121
      removed outlier: 3.720A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.004A  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 'B' and resid 96 through 98
      removed outlier: 6.447A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.439A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102
      removed outlier: 7.007A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.102A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.665A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78

    380 hydrogen bonds defined for protein.
    1134 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      306 hydrogen bonds
      612 hydrogen bond angles
      0 basepair planarities
      123 basepair parallelities
      249 stacking parallelities
  Total time for adding SS restraints: 2.22

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1411
        1.32 -     1.44: 4779
        1.44 -     1.56: 6161
        1.56 -     1.69: 576
        1.69 -     1.81: 24
  Bond restraints: 12951
  Sorted by residual:
  bond pdb=" N   ASP C  90 "
       pdb=" CA  ASP C  90 "
    ideal  model  delta    sigma   weight residual
    1.456  1.529 -0.074 1.25e-02 6.40e+03 3.47e+01
  bond pdb=" CA  SER D  35 "
       pdb=" CB  SER D  35 "
    ideal  model  delta    sigma   weight residual
    1.535  1.480  0.055 1.58e-02 4.01e+03 1.19e+01
  bond pdb=" O3'  DG I  12 "
       pdb=" P    DG I  13 "
    ideal  model  delta    sigma   weight residual
    1.607  1.658 -0.051 1.50e-02 4.44e+03 1.15e+01
  bond pdb=" O3'  DG I -66 "
       pdb=" P    DG I -65 "
    ideal  model  delta    sigma   weight residual
    1.607  1.654 -0.047 1.50e-02 4.44e+03 1.00e+01
  bond pdb=" N   ARG A 129 "
       pdb=" CA  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.29e-02 6.01e+03 9.90e+00
  ... (remaining 12946 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 18152
        2.16 -     4.33: 523
        4.33 -     6.49: 36
        6.49 -     8.65: 5
        8.65 -    10.81: 2
  Bond angle restraints: 18718
  Sorted by residual:
  angle pdb=" C   TYR D  34 "
        pdb=" CA  TYR D  34 "
        pdb=" CB  TYR D  34 "
      ideal   model   delta    sigma   weight residual
     112.12  103.64    8.48 1.50e+00 4.44e-01 3.20e+01
  angle pdb=" N   LEU A 126 "
        pdb=" CA  LEU A 126 "
        pdb=" C   LEU A 126 "
      ideal   model   delta    sigma   weight residual
     112.87  106.38    6.49 1.20e+00 6.94e-01 2.92e+01
  angle pdb=" N   ARG A 128 "
        pdb=" CA  ARG A 128 "
        pdb=" C   ARG A 128 "
      ideal   model   delta    sigma   weight residual
     110.80   99.99   10.81 2.13e+00 2.20e-01 2.58e+01
  angle pdb=" N   ASP C  90 "
        pdb=" CA  ASP C  90 "
        pdb=" C   ASP C  90 "
      ideal   model   delta    sigma   weight residual
     110.35  117.18   -6.83 1.36e+00 5.41e-01 2.52e+01
  angle pdb=" N   PHE F 100 "
        pdb=" CA  PHE F 100 "
        pdb=" C   PHE F 100 "
      ideal   model   delta    sigma   weight residual
     113.18  107.27    5.91 1.21e+00 6.83e-01 2.38e+01
  ... (remaining 18713 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.87: 5636
       30.87 -    61.74: 1444
       61.74 -    92.61: 24
       92.61 -   123.48: 0
      123.48 -   154.35: 1
  Dihedral angle restraints: 7105
    sinusoidal: 4844
      harmonic: 2261
  Sorted by residual:
  dihedral pdb=" N   ASP C  90 "
           pdb=" C   ASP C  90 "
           pdb=" CA  ASP C  90 "
           pdb=" CB  ASP C  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.60  -12.80     0      2.50e+00 1.60e-01 2.62e+01
  dihedral pdb=" C   ASP C  90 "
           pdb=" N   ASP C  90 "
           pdb=" CA  ASP C  90 "
           pdb=" CB  ASP C  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.28   10.68     0      2.50e+00 1.60e-01 1.83e+01
  dihedral pdb=" C   ARG C  20 "
           pdb=" N   ARG C  20 "
           pdb=" CA  ARG C  20 "
           pdb=" CB  ARG C  20 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.22   10.62     0      2.50e+00 1.60e-01 1.81e+01
  ... (remaining 7102 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 1989
       0.080 -    0.160: 110
       0.160 -    0.240: 16
       0.240 -    0.320: 7
       0.320 -    0.400: 1
  Chirality restraints: 2123
  Sorted by residual:
  chirality pdb=" CA  ASP C  90 "
            pdb=" N   ASP C  90 "
            pdb=" C   ASP C  90 "
            pdb=" CB  ASP C  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.01e+00
  chirality pdb=" CA  TYR D  34 "
            pdb=" N   TYR D  34 "
            pdb=" C   TYR D  34 "
            pdb=" CB  TYR D  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" CA  ARG C  20 "
            pdb=" N   ARG C  20 "
            pdb=" C   ARG C  20 "
            pdb=" CB  ARG C  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.47e+00
  ... (remaining 2120 not shown)

  Planarity restraints: 1365
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C  90 "    0.017 2.00e-02 2.50e+03   3.47e-02 1.21e+01
        pdb=" C   ASP C  90 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   ASP C  90 "    0.022 2.00e-02 2.50e+03
        pdb=" N   GLU C  91 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C  88 "   -0.012 2.00e-02 2.50e+03   2.43e-02 5.90e+00
        pdb=" C   ARG C  88 "    0.042 2.00e-02 2.50e+03
        pdb=" O   ARG C  88 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASN C  89 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 125 "    0.008 2.00e-02 2.50e+03   1.61e-02 2.58e+00
        pdb=" C   GLN A 125 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   GLN A 125 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A 126 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1362 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1458
        2.75 -     3.29: 10271
        3.29 -     3.83: 22498
        3.83 -     4.36: 25965
        4.36 -     4.90: 39112
  Nonbonded interactions: 99304
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  87 "
            pdb=" OE1 GLU D  90 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   GLU D 102 "
            pdb=" ND1 HIS D 106 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" O   ILE A 119 "
            pdb=" OG  SER B  47 "
     model   vdw
     2.398 3.040
  nonbonded pdb=" N2   DG I -28 "
            pdb=" N3   DC J  28 "
     model   vdw
     2.416 3.200
  nonbonded pdb=" NH1 ARG G  32 "
            pdb=" OP1  DC J -44 "
     model   vdw
     2.430 3.120
  ... (remaining 99299 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and (resid 36 through 134 or (resid 135 and (name N or name CA or nam \ 
e C or name O or name CB ))))
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 24 through 121)
  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:             1.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.140
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
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      :  0.005   0.074  12951  Z= 0.310
  Angle     :  0.727  10.814  18718  Z= 0.489
  Chirality :  0.044   0.400   2123
  Planarity :  0.003   0.035   1365
  Dihedral  : 26.094 154.348   5647
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  4.71 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  :  5.08 %
    Favored  : 90.91 %
  Cbeta Deviations :  0.41 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.28), residues: 765
  helix:  0.89 (0.22), residues: 510
  sheet:  None (None), residues: 0
  loop : -2.20 (0.30), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 131 
 TYR   0.015   0.001   TYR D  34 
 PHE   0.021   0.001   PHE F 100 
 HIS   0.004   0.001   HIS H  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (12951)
  covalent geometry    : angle       0.72728 (18718)
  hydrogen bonds       : bond        0.12146 (  686)
  hydrogen bonds       : angle       4.20261 ( 1746)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: B   79 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7696 (mttp)
REVERT: C   15 LYS cc_start: 0.7457 (mtpp) cc_final: 0.7038 (tttp)
REVERT: D   30 ARG cc_start: 0.5004 (ptm-80) cc_final: 0.4200 (mtp85)
REVERT: F   35 ARG cc_start: 0.8054 (mtt-85) cc_final: 0.7353 (mtm-85)
REVERT: G   15 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7554 (tttt)
REVERT: H   25 LYS cc_start: 0.3299 (OUTLIER) cc_final: 0.2115 (ptmt)
  outliers start: 26
  outliers final: 4
  residues processed: 141
  average time/residue: 0.2156
  time to fit residues: 37.0738
Evaluate side-chains
  70 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue  100 PHE
Chi-restraints excluded: chain H residue   25 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0370
   overall best weight:    0.9060

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

Flipped N/Q/H residues before XYZ refinement:
C  84 GLN
D  44 GLN
D  46 HIS
D  60 ASN
F  25 ASN
H  44 GLN
H  46 HIS
H  81 ASN
H  92 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.176430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.134283 restraints weight = 15117.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.132523 restraints weight = 29269.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.133510 restraints weight = 27427.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.133701 restraints weight = 21711.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.133740 restraints weight = 23486.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12951  Z= 0.146
  Angle     :  0.524   6.398  18718  Z= 0.315
  Chirality :  0.032   0.167   2123
  Planarity :  0.004   0.039   1365
  Dihedral  : 29.862 157.978   4091
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.01 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  8.47 %
    Favored  : 90.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.29), residues: 765
  helix:  2.11 (0.22), residues: 531
  sheet:  None (None), residues: 0
  loop : -1.81 (0.33), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  40 
 TYR   0.010   0.001   TYR D 118 
 PHE   0.008   0.001   PHE H  62 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (12951)
  covalent geometry    : angle       0.52425 (18718)
  hydrogen bonds       : bond        0.05047 (  686)
  hydrogen bonds       : angle       2.47600 ( 1746)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: D   30 ARG cc_start: 0.5788 (ptm-80) cc_final: 0.4933 (mtp-110)
REVERT: D   34 TYR cc_start: 0.8302 (m-80) cc_final: 0.7979 (m-80)
REVERT: F   35 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.7633 (mtm110)
REVERT: G   15 LYS cc_start: 0.8308 (mtpt) cc_final: 0.7899 (tttt)
REVERT: H   96 ARG cc_start: 0.7683 (mtp180) cc_final: 0.7472 (mtm180)
REVERT: H   98 LEU cc_start: 0.8803 (mm) cc_final: 0.8539 (mm)
  outliers start: 8
  outliers final: 7
  residues processed: 92
  average time/residue: 0.1549
  time to fit residues: 18.8039
Evaluate side-chains
  78 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   84 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0270
   chunk 35 optimal weight:    4.9990
   chunk 77 optimal weight:   10.0000
   chunk 72 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 81 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   overall best weight:    1.1642

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  27 GLN
E  68 GLN
F  75 HIS
G  84 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.169822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.126264 restraints weight = 15001.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.124842 restraints weight = 26183.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.125722 restraints weight = 22766.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.125880 restraints weight = 19106.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.125984 restraints weight = 20857.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12951  Z= 0.149
  Angle     :  0.510   6.189  18718  Z= 0.308
  Chirality :  0.032   0.163   2123
  Planarity :  0.004   0.035   1365
  Dihedral  : 29.764 161.076   4083
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.66 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  8.78 %
    Favored  : 89.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.11 (0.30), residues: 765
  helix:  2.60 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -1.67 (0.34), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  40 
 TYR   0.012   0.001   TYR F  51 
 PHE   0.012   0.002   PHE F 100 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (12951)
  covalent geometry    : angle       0.51036 (18718)
  hydrogen bonds       : bond        0.05579 (  686)
  hydrogen bonds       : angle       2.48531 ( 1746)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 TYR cc_start: 0.9167 (m-80) cc_final: 0.8914 (m-80)
REVERT: B   95 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7015 (ptm160)
REVERT: C   38 ASN cc_start: 0.8277 (t0) cc_final: 0.7993 (m-40)
REVERT: D   30 ARG cc_start: 0.5789 (ptm-80) cc_final: 0.5067 (mtp180)
REVERT: F   35 ARG cc_start: 0.7849 (mtt-85) cc_final: 0.7436 (mtm110)
REVERT: H   56 MET cc_start: 0.8107 (tpp) cc_final: 0.7906 (mmt)
REVERT: H   73 GLU cc_start: 0.8624 (tp30) cc_final: 0.8412 (tp30)
  outliers start: 12
  outliers final: 8
  residues processed: 85
  average time/residue: 0.1719
  time to fit residues: 18.7943
Evaluate side-chains
  73 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain G residue   35 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   84 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 97 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 82 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.167155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.121136 restraints weight = 14906.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.121199 restraints weight = 29703.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.121767 restraints weight = 27579.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.122154 restraints weight = 21370.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.122282 restraints weight = 21392.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.3686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12951  Z= 0.161
  Angle     :  0.521   5.690  18718  Z= 0.314
  Chirality :  0.033   0.178   2123
  Planarity :  0.004   0.038   1365
  Dihedral  : 29.787 162.488   4083
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.66 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  :  8.78 %
    Favored  : 88.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.29 (0.30), residues: 765
  helix:  2.75 (0.22), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.50 (0.35), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  20 
 TYR   0.014   0.001   TYR D 118 
 PHE   0.012   0.002   PHE F 100 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (12951)
  covalent geometry    : angle       0.52097 (18718)
  hydrogen bonds       : bond        0.05908 (  686)
  hydrogen bonds       : angle       2.58562 ( 1746)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 TYR cc_start: 0.9206 (m-80) cc_final: 0.8973 (m-80)
REVERT: C   38 ASN cc_start: 0.8299 (t0) cc_final: 0.8016 (m-40)
REVERT: F   35 ARG cc_start: 0.7880 (mtt-85) cc_final: 0.7420 (mtm110)
REVERT: H   73 GLU cc_start: 0.8603 (tp30) cc_final: 0.8325 (tp30)
  outliers start: 18
  outliers final: 13
  residues processed: 79
  average time/residue: 0.1441
  time to fit residues: 15.2326
Evaluate side-chains
  75 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   35 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 95 optimal weight:   10.0000
   chunk 82 optimal weight:    7.9990
   chunk 86 optimal weight:   10.0000
   chunk 20 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    2.3586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.162956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.115857 restraints weight = 14895.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.115556 restraints weight = 29115.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.116490 restraints weight = 29160.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.116740 restraints weight = 24306.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.117137 restraints weight = 25400.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.4226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12951  Z= 0.195
  Angle     :  0.563   6.179  18718  Z= 0.336
  Chirality :  0.035   0.194   2123
  Planarity :  0.004   0.055   1365
  Dihedral  : 30.092 163.298   4083
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.18 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  :  8.63 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.30), residues: 765
  helix:  2.50 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop : -1.51 (0.35), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  20 
 TYR   0.012   0.001   TYR F  51 
 PHE   0.013   0.002   PHE H  62 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (12951)
  covalent geometry    : angle       0.56293 (18718)
  hydrogen bonds       : bond        0.06952 (  686)
  hydrogen bonds       : angle       2.75225 ( 1746)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
REVERT: C   38 ASN cc_start: 0.8282 (t0) cc_final: 0.8013 (m-40)
REVERT: C   74 LYS cc_start: 0.7535 (mtmp) cc_final: 0.7179 (mtmm)
REVERT: E  134 ARG cc_start: 0.7554 (ttm-80) cc_final: 0.7224 (ttp80)
REVERT: H   73 GLU cc_start: 0.8619 (tp30) cc_final: 0.8352 (tp30)
REVERT: H   81 ASN cc_start: 0.8510 (m-40) cc_final: 0.8281 (m-40)
REVERT: H  109 SER cc_start: 0.8285 (t) cc_final: 0.8059 (m)
  outliers start: 18
  outliers final: 14
  residues processed: 78
  average time/residue: 0.1436
  time to fit residues: 14.9864
Evaluate side-chains
  77 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   35 ARG
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 80 optimal weight:    8.9990
   chunk 42 optimal weight:    0.6980
   chunk 85 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 81 optimal weight:    7.9990
   chunk 72 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 34 optimal weight:    5.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.171404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.129334 restraints weight = 14888.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.129117 restraints weight = 36739.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.130120 restraints weight = 33858.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.130218 restraints weight = 25945.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.130663 restraints weight = 27519.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.4078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12951  Z= 0.135
  Angle     :  0.487   5.013  18718  Z= 0.298
  Chirality :  0.031   0.181   2123
  Planarity :  0.003   0.034   1365
  Dihedral  : 29.870 163.290   4083
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.75 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 10.02 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.60 (0.31), residues: 765
  helix:  2.96 (0.22), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.30 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  20 
 TYR   0.006   0.001   TYR E  99 
 PHE   0.008   0.001   PHE F 100 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (12951)
  covalent geometry    : angle       0.48712 (18718)
  hydrogen bonds       : bond        0.04533 (  686)
  hydrogen bonds       : angle       2.40887 ( 1746)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 TYR cc_start: 0.9117 (m-80) cc_final: 0.8872 (m-80)
REVERT: B   95 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7437 (ptm160)
REVERT: F   35 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7339 (mtm110)
REVERT: H   68 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7075 (mm-30)
REVERT: H   73 GLU cc_start: 0.8595 (tp30) cc_final: 0.8345 (tp30)
  outliers start: 11
  outliers final: 9
  residues processed: 80
  average time/residue: 0.1302
  time to fit residues: 14.3551
Evaluate side-chains
  74 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain G residue   35 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 47 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 93 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 82 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    1.2384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.168638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.125485 restraints weight = 14764.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.125139 restraints weight = 36722.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.126311 restraints weight = 34927.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.126362 restraints weight = 24729.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.126530 restraints weight = 26147.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.4293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12951  Z= 0.147
  Angle     :  0.500   5.058  18718  Z= 0.305
  Chirality :  0.032   0.175   2123
  Planarity :  0.003   0.034   1365
  Dihedral  : 29.849 162.793   4083
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.40 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 10.63 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.56 (0.31), residues: 765
  helix:  2.89 (0.22), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.22 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  20 
 TYR   0.011   0.001   TYR D 118 
 PHE   0.010   0.001   PHE H  62 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (12951)
  covalent geometry    : angle       0.50043 (18718)
  hydrogen bonds       : bond        0.05448 (  686)
  hydrogen bonds       : angle       2.49376 ( 1746)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: B   95 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7424 (ptm160)
REVERT: C   72 ASP cc_start: 0.8015 (m-30) cc_final: 0.7791 (m-30)
REVERT: F   21 VAL cc_start: 0.4205 (OUTLIER) cc_final: 0.3980 (t)
REVERT: F   35 ARG cc_start: 0.8130 (mtt-85) cc_final: 0.7409 (mtm110)
REVERT: H   56 MET cc_start: 0.8202 (tpp) cc_final: 0.7780 (mmt)
REVERT: H   73 GLU cc_start: 0.8578 (tp30) cc_final: 0.8327 (tp30)
REVERT: H   81 ASN cc_start: 0.8158 (m-40) cc_final: 0.7842 (m-40)
  outliers start: 13
  outliers final: 10
  residues processed: 76
  average time/residue: 0.1289
  time to fit residues: 13.3518
Evaluate side-chains
  74 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 99 optimal weight:   10.0000
   chunk 73 optimal weight:    3.9990
   chunk 84 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 94 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.163962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.120153 restraints weight = 14738.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.119751 restraints weight = 36723.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.120782 restraints weight = 32319.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.121020 restraints weight = 25171.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.121563 restraints weight = 25890.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.4669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  12951  Z= 0.201
  Angle     :  0.569   5.802  18718  Z= 0.340
  Chirality :  0.036   0.182   2123
  Planarity :  0.004   0.035   1365
  Dihedral  : 30.102 163.228   4083
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.31 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 10.48 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.30), residues: 765
  helix:  2.46 (0.22), residues: 529
  sheet:  None (None), residues: 0
  loop : -1.46 (0.35), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C  20 
 TYR   0.032   0.002   TYR D 118 
 PHE   0.014   0.002   PHE H  62 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 (12951)
  covalent geometry    : angle       0.56924 (18718)
  hydrogen bonds       : bond        0.07114 (  686)
  hydrogen bonds       : angle       2.78044 ( 1746)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 TYR cc_start: 0.9184 (m-80) cc_final: 0.8921 (m-80)
REVERT: B   95 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7465 (ptm160)
REVERT: C   38 ASN cc_start: 0.8330 (t0) cc_final: 0.8075 (m-40)
REVERT: F   21 VAL cc_start: 0.4400 (OUTLIER) cc_final: 0.4170 (t)
REVERT: F   35 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7413 (mtm110)
REVERT: H   73 GLU cc_start: 0.8609 (tp30) cc_final: 0.8362 (tp30)
REVERT: H   81 ASN cc_start: 0.8534 (m-40) cc_final: 0.8290 (m-40)
  outliers start: 17
  outliers final: 15
  residues processed: 82
  average time/residue: 0.1535
  time to fit residues: 16.4207
Evaluate side-chains
  80 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   35 ARG
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 97 optimal weight:   10.0000
   chunk 30 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0270
   chunk 46 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 101 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9980
   overall best weight:    1.1440

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.168910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.126786 restraints weight = 14784.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.126478 restraints weight = 37320.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.127570 restraints weight = 35177.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.127667 restraints weight = 23741.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.127832 restraints weight = 24886.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.4538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12951  Z= 0.143
  Angle     :  0.497   4.977  18718  Z= 0.303
  Chirality :  0.032   0.167   2123
  Planarity :  0.003   0.036   1365
  Dihedral  : 29.945 163.446   4083
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.14 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 10.32 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.44 (0.31), residues: 765
  helix:  2.81 (0.22), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.28 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C  20 
 TYR   0.021   0.001   TYR D 118 
 PHE   0.008   0.001   PHE H  62 
 HIS   0.003   0.000   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (12951)
  covalent geometry    : angle       0.49665 (18718)
  hydrogen bonds       : bond        0.04940 (  686)
  hydrogen bonds       : angle       2.48494 ( 1746)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 TYR cc_start: 0.9130 (m-80) cc_final: 0.8833 (m-80)
REVERT: B   95 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7393 (ptm160)
REVERT: F   21 VAL cc_start: 0.4188 (OUTLIER) cc_final: 0.3946 (t)
REVERT: F   35 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7475 (mtm110)
REVERT: H   73 GLU cc_start: 0.8611 (tp30) cc_final: 0.8355 (tp30)
REVERT: H   81 ASN cc_start: 0.8093 (m-40) cc_final: 0.7756 (m-40)
  outliers start: 18
  outliers final: 15
  residues processed: 75
  average time/residue: 0.1525
  time to fit residues: 15.1551
Evaluate side-chains
  78 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   35 ARG
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0980
   chunk 29 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 92 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0970
   chunk 35 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.5978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.169477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.127169 restraints weight = 14820.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.126932 restraints weight = 36792.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.128006 restraints weight = 36140.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.128190 restraints weight = 23908.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.128366 restraints weight = 24566.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.4531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12951  Z= 0.132
  Angle     :  0.491   5.506  18718  Z= 0.301
  Chirality :  0.031   0.160   2123
  Planarity :  0.003   0.033   1365
  Dihedral  : 29.935 163.114   4083
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.40 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 11.09 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.60 (0.31), residues: 765
  helix:  2.93 (0.22), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.23 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  20 
 TYR   0.024   0.001   TYR D 118 
 PHE   0.007   0.001   PHE H  62 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (12951)
  covalent geometry    : angle       0.49066 (18718)
  hydrogen bonds       : bond        0.04707 (  686)
  hydrogen bonds       : angle       2.46081 ( 1746)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 TYR cc_start: 0.9117 (m-80) cc_final: 0.8824 (m-80)
REVERT: B   95 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7438 (ptm160)
REVERT: F   21 VAL cc_start: 0.4179 (OUTLIER) cc_final: 0.3950 (t)
REVERT: F   35 ARG cc_start: 0.8064 (mtt-85) cc_final: 0.7427 (mtm110)
REVERT: H   73 GLU cc_start: 0.8588 (tp30) cc_final: 0.8346 (tp30)
REVERT: H   81 ASN cc_start: 0.8024 (m-40) cc_final: 0.7680 (m-40)
  outliers start: 13
  outliers final: 11
  residues processed: 71
  average time/residue: 0.1636
  time to fit residues: 15.1692
Evaluate side-chains
  73 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain D residue   46 HIS
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   35 ARG
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   36 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 80 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 98 optimal weight:   10.0000
   chunk 91 optimal weight:    8.9990
   chunk 30 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0970
   chunk 94 optimal weight:    8.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    1.8184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.166749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.123163 restraints weight = 14741.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.122456 restraints weight = 37819.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.123514 restraints weight = 33273.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.123695 restraints weight = 24625.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.123952 restraints weight = 25696.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.4671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12951  Z= 0.168
  Angle     :  0.527   5.114  18718  Z= 0.319
  Chirality :  0.033   0.170   2123
  Planarity :  0.004   0.037   1365
  Dihedral  : 30.032 163.132   4083
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.44 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 10.94 %
    Favored  : 86.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.32 (0.30), residues: 765
  helix:  2.71 (0.22), residues: 529
  sheet:  None (None), residues: 0
  loop : -1.33 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  20 
 TYR   0.027   0.001   TYR D 118 
 PHE   0.012   0.002   PHE H  62 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (12951)
  covalent geometry    : angle       0.52724 (18718)
  hydrogen bonds       : bond        0.05984 (  686)
  hydrogen bonds       : angle       2.60208 ( 1746)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1558.96 seconds
wall clock time: 27 minutes 39.66 seconds (1659.66 seconds total)