Starting phenix.real_space_refine
on Mon Aug 25 10:37:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c99_16506/08_2025/8c99_16506.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c99_16506/08_2025/8c99_16506.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c99_16506/08_2025/8c99_16506.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c99_16506/08_2025/8c99_16506.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c99_16506/08_2025/8c99_16506.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c99_16506/08_2025/8c99_16506.cif"
  }
  resolution = 3.29
  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=   0.005 sd=   0.091
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     945      5.49       5
     S      18      5.16       5
     C   13888      2.51       5
     N    5234      2.21       5
     O    7903      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 27988
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "2"
      Number of atoms: 286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 286
          Classifications: {'peptide': 35}
          Link IDs: {'TRANS': 34}
    Chain: "E"
      Number of atoms: 1454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1454
          Classifications: {'peptide': 189}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 184}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 1055
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1055
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 125}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 676
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Chain breaks: 1
    Chain: "Q"
      Number of atoms: 947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 947
          Classifications: {'peptide': 117}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 116}
    Chain: "R"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 816
          Classifications: {'peptide': 103}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 101}
    Chain: "S"
      Number of atoms: 734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 734
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 93}
          Chain breaks: 1
    Chain: "U"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 779
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 3, 'TRANS': 98}
    Chain: "Y"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 509
          Classifications: {'peptide': 63}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 62}
    Chain: "Z"
      Number of atoms: 439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 439
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 2, 'TRANS': 54}
    Chain: "A"
      Number of atoms: 20293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 945, 20293
          Classifications: {'DNA': 1, 'RNA': 944}
          Modifications used: {'rna2p_pur': 92, 'rna2p_pyr': 44, 'rna3p_pur': 465, 'rna3p_pyr': 343}
          Incomplete info: {'p_only': 1}
          Link IDs: {'rna2p': 136, 'rna3p': 808}
          Unresolved chain links: 1
          Chain breaks: 4
          Unresolved chain link angles: 7
          Unresolved chain link dihedrals: 5
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'  G:plan': 1, '  G:plan2': 1}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 5.68, per 1000 atoms: 0.20
  Number of scatterers: 27988
  At special positions: 0
  Unit cell: (132.5, 176.25, 168.75, 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      18     16.00
     P     945     15.00
     O    7903      8.00
     N    5234      7.00
     C   13888      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: 2.31
  Conformation dependent library (CDL) restraints added in 449.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1828

  Finding SS restraints...
Warning! O4 atom is missing from residue    U A 358  
  Was trying to link:    A A 282 N6 with    U A 358 O4, Saenger class: 20
Warning! O4 atom is missing from residue    U A 358  
  Was trying to link:    A A 282 N6 with    U A 358 O4, Saenger class: 23
    Secondary structure from input PDB file:
      34 helices and 11 sheets defined
      41.6% alpha, 12.4% beta
      310 base pairs and 465 stacking pairs defined.
    Time for finding SS restraints: 4.19
  Creating SS restraints...
    Processing helix  chain '2' and resid 10 through 17
      removed outlier: 3.535A  pdb=" N   SER 2  15 " --> pdb=" O   LYS 2  11 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 17 through 24
      removed outlier: 3.976A  pdb=" N   THR 2  24 " --> pdb=" O   ALA 2  20 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 24 through 38
    Processing helix  chain 'E' and resid 15 through 20
    Processing helix  chain 'E' and resid 24 through 39
      removed outlier: 3.516A  pdb=" N   ALA E  39 " --> pdb=" O   TYR E  35 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 115
    Processing helix  chain 'E' and resid 130 through 141
      removed outlier: 3.513A  pdb=" N   LEU E 134 " --> pdb=" O   LYS E 130 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 154 through 164
      removed outlier: 4.416A  pdb=" N   ASN E 163 " --> pdb=" O   LEU E 159 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   LEU E 164 " --> pdb=" O   ALA E 160 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 173 through 175
      No H-bonds generated for 'chain 'E' and resid 173 through 175'
    Processing helix  chain 'E' and resid 178 through 183
      removed outlier: 3.548A  pdb=" N   PHE E 183 " --> pdb=" O   SER E 179 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 201
    Processing helix  chain 'J' and resid 7 through 11
      removed outlier: 3.681A  pdb=" N   VAL J  11 " --> pdb=" O   PRO J   8 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 24 through 37
    Processing helix  chain 'J' and resid 58 through 62
    Processing helix  chain 'J' and resid 67 through 72
    Processing helix  chain 'J' and resid 88 through 96
    Processing helix  chain 'J' and resid 96 through 108
      removed outlier: 4.151A  pdb=" N   VAL J 100 " --> pdb=" O   ARG J  96 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ILE J 101 " --> pdb=" O   PRO J  97 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 112 through 122
      removed outlier: 3.786A  pdb=" N   LYS J 121 " --> pdb=" O   ALA J 117 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   LEU J 122 " --> pdb=" O   MET J 118 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 130 through 136
      removed outlier: 4.028A  pdb=" N   ALA J 134 " --> pdb=" O   ASN J 131 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 135
      removed outlier: 4.419A  pdb=" N   ALA L 134 " --> pdb=" O   GLY L 130 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 5 through 19
      removed outlier: 3.919A  pdb=" N   GLN Q  19 " --> pdb=" O   LYS Q  15 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 25 through 30
    Processing helix  chain 'Q' and resid 30 through 71
      removed outlier: 4.351A  pdb=" N   GLN Q  36 " --> pdb=" O   ARG Q  32 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ARG Q  50 " --> pdb=" O   TYR Q  46 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   LYS Q  53 " --> pdb=" O   ARG Q  49 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ARG Q  54 " --> pdb=" O   ARG Q  50 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ASN Q  71 " --> pdb=" O   ALA Q  67 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 74 through 85
    Processing helix  chain 'Q' and resid 90 through 101
    Processing helix  chain 'Q' and resid 101 through 117
      removed outlier: 3.890A  pdb=" N   PHE Q 105 " --> pdb=" O   ASP Q 101 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ALA Q 117 " --> pdb=" O   LYS Q 113 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 13 through 22
      removed outlier: 3.512A  pdb=" N   VAL S  20 " --> pdb=" O   LYS S  16 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 38
      removed outlier: 4.106A  pdb=" N   ASP S  34 " --> pdb=" O   SER S  30 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   TYR S  38 " --> pdb=" O   ASP S  34 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 41 through 62
      removed outlier: 4.193A  pdb=" N   VAL S  45 " --> pdb=" O   LYS S  41 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   LEU S  46 " --> pdb=" O   LYS S  42 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 3 through 8
      removed outlier: 4.108A  pdb=" N   ARG Y   7 " --> pdb=" O   LYS Y   4 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 9 through 34
      removed outlier: 4.351A  pdb=" N   PHE Y  26 " --> pdb=" O   LEU Y  22 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 40 through 56
      removed outlier: 3.590A  pdb=" N   LYS Y  44 " --> pdb=" O   SER Y  40 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 16 through 27
    Processing helix  chain 'Z' and resid 40 through 50
    Processing sheet with id=AA1, first strand: chain 'E' and resid 2 through 3
      removed outlier: 3.648A  pdb=" N   LEU E   3 " --> pdb=" O   LEU E  12 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 118 through 121
      removed outlier: 3.924A  pdb=" N   VAL E 121 " --> pdb=" O   MET E 188 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   LEU E 147 " --> pdb=" O   VAL E 187 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   THR E 189 " --> pdb=" O   LEU E 147 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   ILE E 149 " --> pdb=" O   THR E 189 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'J' and resid 123 through 124
    Processing sheet with id=AA4, first strand: chain 'R' and resid 2 through 6
    Processing sheet with id=AA5, first strand: chain 'R' and resid 20 through 22
      removed outlier: 6.556A  pdb=" N   PHE R  93 " --> pdb=" O   HIS R  66 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   HIS R  66 " --> pdb=" O   PHE R  93 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ASP R  95 " --> pdb=" O   VAL R  64 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   LYS R  60 " --> pdb=" O   THR R  99 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'R' and resid 72 through 74
    Processing sheet with id=AA7, first strand: chain 'S' and resid 3 through 10
      removed outlier: 3.624A  pdb=" N   HIS S   9 " --> pdb=" O   SER S 101 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   SER S 101 " --> pdb=" O   HIS S   9 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LYS S  73 " --> pdb=" O   VAL S 106 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   SER S 108 " --> pdb=" O   VAL S  71 " (cutoff:3.500A)
      removed outlier: 5.463A  pdb=" N   VAL S  71 " --> pdb=" O   SER S 108 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'U' and resid 64 through 65
      removed outlier: 6.887A  pdb=" N   LYS U  32 " --> pdb=" O   VAL U  27 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   VAL U  27 " --> pdb=" O   LYS U  32 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   ILE U  34 " --> pdb=" O   LYS U  25 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'U' and resid 40 through 44
    Processing sheet with id=AB1, first strand: chain 'U' and resid 82 through 86
    Processing sheet with id=AB2, first strand: chain 'Z' and resid 34 through 37

    317 hydrogen bonds defined for protein.
    897 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      790 hydrogen bonds
      1254 hydrogen bond angles
      0 basepair planarities
      310 basepair parallelities
      465 stacking parallelities
  Total time for adding SS restraints: 7.26

  Time building geometry restraints manager: 3.16 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4015
        1.33 -     1.45: 12679
        1.45 -     1.57: 11893
        1.57 -     1.69: 1884
        1.69 -     1.81: 36
  Bond restraints: 30507
  Sorted by residual:
  bond pdb=" C1'   U A 827 "
       pdb=" N1    U A 827 "
    ideal  model  delta    sigma   weight residual
    1.480  1.573 -0.093 1.50e-02 4.44e+03 3.87e+01
  bond pdb=" C1'   A A 526 "
       pdb=" N9    A A 526 "
    ideal  model  delta    sigma   weight residual
    1.475  1.391  0.084 1.50e-02 4.44e+03 3.14e+01
  bond pdb=" N   MET Y   1 "
       pdb=" CA  MET Y   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.95e+00
  bond pdb=" N   MET J   1 "
       pdb=" CA  MET J   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.94e+00
  bond pdb=" N   MET S   1 "
       pdb=" CA  MET S   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.90e+00
  ... (remaining 30502 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 45386
        1.40 -     2.80: 422
        2.80 -     4.20: 49
        4.20 -     5.60: 5
        5.60 -     6.99: 4
  Bond angle restraints: 45866
  Sorted by residual:
  angle pdb=" N   VAL Q  33 "
        pdb=" CA  VAL Q  33 "
        pdb=" C   VAL Q  33 "
      ideal   model   delta    sigma   weight residual
     112.96  109.37    3.59 1.00e+00 1.00e+00 1.29e+01
  angle pdb=" N   ILE L 103 "
        pdb=" CA  ILE L 103 "
        pdb=" C   ILE L 103 "
      ideal   model   delta    sigma   weight residual
     111.62  108.83    2.79 7.90e-01 1.60e+00 1.25e+01
  angle pdb=" C   SER U  97 "
        pdb=" N   ASN U  98 "
        pdb=" CA  ASN U  98 "
      ideal   model   delta    sigma   weight residual
     121.54  128.08   -6.54 1.91e+00 2.74e-01 1.17e+01
  angle pdb=" N   ILE U  38 "
        pdb=" CA  ILE U  38 "
        pdb=" C   ILE U  38 "
      ideal   model   delta    sigma   weight residual
     112.12  109.29    2.83 8.40e-01 1.42e+00 1.14e+01
  angle pdb=" C4'   A A 404 "
        pdb=" C3'   A A 404 "
        pdb=" O3'   A A 404 "
      ideal   model   delta    sigma   weight residual
     109.40  112.84   -3.44 1.50e+00 4.44e-01 5.25e+00
  ... (remaining 45861 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.09: 17159
       35.09 -    70.19: 2066
       70.19 -   105.28: 248
      105.28 -   140.38: 6
      140.38 -   175.47: 3
  Dihedral angle restraints: 19482
    sinusoidal: 16664
      harmonic: 2818
  Sorted by residual:
  dihedral pdb=" O4'   U A 545 "
           pdb=" C1'   U A 545 "
           pdb=" N1    U A 545 "
           pdb=" C2    U A 545 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   15.06 -175.06     1      1.50e+01 4.44e-03 8.52e+01
  dihedral pdb=" O4'   C A 323 "
           pdb=" C1'   C A 323 "
           pdb=" N1    C A 323 "
           pdb=" C2    C A 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   36.76 -164.76     1      1.70e+01 3.46e-03 6.53e+01
  dihedral pdb=" C4'   G A 271 "
           pdb=" C3'   G A 271 "
           pdb=" O3'   G A 271 "
           pdb=" P     A A 272 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00   65.47 -175.47     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 19479 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 4776
       0.033 -    0.065: 962
       0.065 -    0.098: 120
       0.098 -    0.131: 63
       0.131 -    0.163: 4
  Chirality restraints: 5925
  Sorted by residual:
  chirality pdb=" C1'   U A 827 "
            pdb=" O4'   U A 827 "
            pdb=" C2'   U A 827 "
            pdb=" N1    U A 827 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.63   -0.16 2.00e-01 2.50e+01 6.68e-01
  chirality pdb=" C1'   A A 526 "
            pdb=" O4'   A A 526 "
            pdb=" C2'   A A 526 "
            pdb=" N9    A A 526 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.31    0.15 2.00e-01 2.50e+01 5.71e-01
  chirality pdb=" C3'   G A 271 "
            pdb=" C4'   G A 271 "
            pdb=" O3'   G A 271 "
            pdb=" C2'   G A 271 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.60   -0.15 2.00e-01 2.50e+01 5.56e-01
  ... (remaining 5922 not shown)

  Planarity restraints: 2271
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A1138 "   -0.028 2.00e-02 2.50e+03   1.20e-02 4.35e+00
        pdb=" N9    G A1138 "    0.027 2.00e-02 2.50e+03
        pdb=" C8    G A1138 "    0.005 2.00e-02 2.50e+03
        pdb=" N7    G A1138 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G A1138 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G A1138 "   -0.008 2.00e-02 2.50e+03
        pdb=" O6    G A1138 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    G A1138 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G A1138 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2    G A1138 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    G A1138 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    G A1138 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 481 "    0.024 2.00e-02 2.50e+03   1.09e-02 3.54e+00
        pdb=" N9    G A 481 "   -0.028 2.00e-02 2.50e+03
        pdb=" C8    G A 481 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    G A 481 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    G A 481 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    G A 481 "    0.003 2.00e-02 2.50e+03
        pdb=" O6    G A 481 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    G A 481 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    G A 481 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G A 481 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    G A 481 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    G A 481 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 308 "   -0.023 2.00e-02 2.50e+03   1.03e-02 3.21e+00
        pdb=" N9    G A 308 "    0.026 2.00e-02 2.50e+03
        pdb=" C8    G A 308 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    G A 308 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G A 308 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G A 308 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6    G A 308 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    G A 308 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G A 308 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G A 308 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G A 308 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G A 308 "    0.002 2.00e-02 2.50e+03
  ... (remaining 2268 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 229
        2.55 -     3.13: 21171
        3.13 -     3.72: 53007
        3.72 -     4.31: 72752
        4.31 -     4.90: 101233
  Nonbonded interactions: 248392
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP Q  48 "
            pdb=" O2'   U A 534 "
     model   vdw
     1.957 3.040
  nonbonded pdb=" OP2   G A 117 "
            pdb=" O2'   A A 119 "
     model   vdw
     1.962 3.040
  nonbonded pdb=" O2'   A A 126 "
            pdb=" O4'   A A 127 "
     model   vdw
     1.968 3.040
  nonbonded pdb=" O2'   U A 369 "
            pdb=" OP2   A A 422 "
     model   vdw
     2.002 3.040
  nonbonded pdb=" O2'   C A 957 "
            pdb=" OP1   A A 959 "
     model   vdw
     2.011 3.040
  ... (remaining 248387 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.650
  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:             0.020
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.070
  Process input model:                     27.460
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.093  30507  Z= 0.106
  Angle     :  0.392   6.995  45866  Z= 0.210
  Chirality :  0.027   0.163   5925
  Planarity :  0.003   0.039   2271
  Dihedral  : 22.330 175.471  17654
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.28), residues: 959
  helix:  2.46 (0.29), residues: 337
  sheet:  0.07 (0.50), residues: 120
  loop : -0.48 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Q  50 
 TYR   0.023   0.001   TYR Q  24 
 PHE   0.016   0.001   PHE R  53 
 TRP   0.001   0.000   TRP R  92 
 HIS   0.002   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00190 (30507)
  covalent geometry    : angle       0.39221 (45866)
  hydrogen bonds       : bond        0.08803 ( 1107)
  hydrogen bonds       : angle       3.87751 ( 2151)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
REVERT: J   16 TYR cc_start: 0.8401 (m-80) cc_final: 0.8156 (m-10)
REVERT: J  138 GLN cc_start: 0.7310 (tt0) cc_final: 0.7022 (tt0)
REVERT: L  126 ARG cc_start: 0.4765 (mtm180) cc_final: 0.3627 (tpt-90)
REVERT: Q   96 ASP cc_start: 0.7714 (t70) cc_final: 0.7457 (t70)
REVERT: Z   44 ARG cc_start: 0.8049 (mmp80) cc_final: 0.7705 (mmt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1703
  time to fit residues: 30.3832
Evaluate side-chains
  74 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:   20.0000
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.4980
   chunk 130 optimal weight:   30.0000
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    9.9990
   chunk 149 optimal weight:   10.0000
   overall best weight:    6.0988

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

Flipped N/Q/H residues before XYZ refinement:
J 132 HIS
Q  80 ASN
R  18 GLN
S  57 ASN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  31 GLN
Z  19 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.075858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.051606 restraints weight = 124136.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 1.91
r_work: 0.3021 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.2728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.070  30507  Z= 0.380
  Angle     :  0.728   8.882  45866  Z= 0.366
  Chirality :  0.039   0.241   5925
  Planarity :  0.005   0.053   2271
  Dihedral  : 23.041 179.345  15736
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  7.38 %
    Favored  : 90.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.27), residues: 959
  helix:  0.81 (0.27), residues: 359
  sheet: -0.51 (0.45), residues: 148
  loop : -0.92 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG 2  34 
 TYR   0.026   0.003   TYR J  74 
 PHE   0.024   0.003   PHE E  23 
 TRP   0.008   0.001   TRP R  92 
 HIS   0.007   0.002   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00750 (30507)
  covalent geometry    : angle       0.72828 (45866)
  hydrogen bonds       : bond        0.08442 ( 1107)
  hydrogen bonds       : angle       3.59727 ( 2151)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: J  138 GLN cc_start: 0.7734 (tt0) cc_final: 0.7447 (tt0)
REVERT: J  142 ILE cc_start: 0.6065 (mt) cc_final: 0.5805 (mm)
REVERT: L  126 ARG cc_start: 0.4767 (mtm180) cc_final: 0.3907 (ttt-90)
REVERT: Q   80 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8482 (m-40)
REVERT: S   31 GLN cc_start: 0.8390 (mt0) cc_final: 0.8126 (mm-40)
REVERT: U  100 GLU cc_start: 0.8412 (tp30) cc_final: 0.7922 (tt0)
REVERT: Y    2 LYS cc_start: 0.7686 (mttm) cc_final: 0.6607 (mttp)
REVERT: Z   44 ARG cc_start: 0.7888 (mmp80) cc_final: 0.7641 (mmp80)
  outliers start: 13
  outliers final: 7
  residues processed: 92
  average time/residue: 0.1606
  time to fit residues: 23.7019
Evaluate side-chains
  84 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain Q residue   80 ASN
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain S residue    3 THR
Chi-restraints excluded: chain S residue   34 ASP
Chi-restraints excluded: chain S residue   69 LEU
Chi-restraints excluded: chain Z residue   34 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 99 optimal weight:   10.0000
   chunk 125 optimal weight:    5.9990
   chunk 104 optimal weight:    7.9990
   chunk 182 optimal weight:    5.9990
   chunk 113 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 164 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9980
   chunk 110 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 101 optimal weight:    8.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  18 GLN
R  43 ASN
** U  53 GLN ** 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 = 0.3803 r_free = 0.3803 target = 0.076368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.052106 restraints weight = 125939.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 1.76
r_work: 0.3042 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.2943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  30507  Z= 0.283
  Angle     :  0.601   9.934  45866  Z= 0.306
  Chirality :  0.035   0.217   5925
  Planarity :  0.004   0.043   2271
  Dihedral  : 23.077 179.069  15736
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.26 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.27), residues: 959
  helix:  0.89 (0.27), residues: 353
  sheet: -0.65 (0.46), residues: 136
  loop : -1.09 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG 2  34 
 TYR   0.016   0.002   TYR J  74 
 PHE   0.015   0.002   PHE E  23 
 TRP   0.007   0.001   TRP R  92 
 HIS   0.004   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 (30507)
  covalent geometry    : angle       0.60079 (45866)
  hydrogen bonds       : bond        0.06878 ( 1107)
  hydrogen bonds       : angle       3.37707 ( 2151)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J    1 MET cc_start: 0.7525 (tpp) cc_final: 0.7259 (tmm)
REVERT: J  138 GLN cc_start: 0.7683 (tt0) cc_final: 0.7289 (tt0)
REVERT: J  142 ILE cc_start: 0.6081 (mt) cc_final: 0.5725 (mm)
REVERT: S   31 GLN cc_start: 0.8438 (mt0) cc_final: 0.8218 (mm-40)
REVERT: U  100 GLU cc_start: 0.8431 (tp30) cc_final: 0.8000 (tt0)
REVERT: Y    2 LYS cc_start: 0.7693 (mttm) cc_final: 0.6568 (mttp)
REVERT: Z   44 ARG cc_start: 0.7903 (mmp80) cc_final: 0.7671 (mmp80)
  outliers start: 12
  outliers final: 8
  residues processed: 96
  average time/residue: 0.1715
  time to fit residues: 26.4548
Evaluate side-chains
  83 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain J residue    3 THR
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain S residue    3 THR
Chi-restraints excluded: chain S residue   69 LEU
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain U residue   11 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 123 optimal weight:    7.9990
   chunk 105 optimal weight:   10.0000
   chunk 147 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 106 optimal weight:   20.0000
   chunk 79 optimal weight:    0.9990
   chunk 124 optimal weight:    7.9990
   chunk 2 optimal weight:    0.6980
   chunk 129 optimal weight:   30.0000
   chunk 171 optimal weight:   10.0000
   chunk 166 optimal weight:   20.0000
   overall best weight:    4.3388

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

Flipped N/Q/H residues before XYZ refinement:
E  97 ASN
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  43 ASN
** U  53 GLN ** 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 = 0.3792 r_free = 0.3792 target = 0.076367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.052063 restraints weight = 129408.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 1.75
r_work: 0.3032 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  30507  Z= 0.273
  Angle     :  0.607  10.079  45866  Z= 0.309
  Chirality :  0.035   0.232   5925
  Planarity :  0.004   0.043   2271
  Dihedral  : 23.134 179.716  15736
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 14.39 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.61 (0.26), residues: 959
  helix:  0.94 (0.28), residues: 349
  sheet: -0.88 (0.44), residues: 138
  loop : -1.28 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG 2  34 
 TYR   0.017   0.002   TYR J  74 
 PHE   0.013   0.002   PHE Q  56 
 TRP   0.007   0.001   TRP R  92 
 HIS   0.005   0.001   HIS Z  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00539 (30507)
  covalent geometry    : angle       0.60678 (45866)
  hydrogen bonds       : bond        0.07010 ( 1107)
  hydrogen bonds       : angle       3.37541 ( 2151)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.8179 (ptp) cc_final: 0.7247 (ptp)
REVERT: E  105 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.7744 (mp)
REVERT: J    1 MET cc_start: 0.7531 (tpp) cc_final: 0.7240 (tmm)
REVERT: J  138 GLN cc_start: 0.7860 (tt0) cc_final: 0.7455 (tt0)
REVERT: J  142 ILE cc_start: 0.6144 (mt) cc_final: 0.5776 (mm)
REVERT: Y    2 LYS cc_start: 0.7702 (mttm) cc_final: 0.6572 (mttp)
  outliers start: 17
  outliers final: 13
  residues processed: 97
  average time/residue: 0.1670
  time to fit residues: 25.7332
Evaluate side-chains
  91 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue  105 LEU
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain J residue   74 TYR
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain S residue    3 THR
Chi-restraints excluded: chain S residue   66 ILE
Chi-restraints excluded: chain S residue   69 LEU
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain U residue   11 ILE
Chi-restraints excluded: chain Z residue   34 THR
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 4 optimal weight:    1.9990
   chunk 166 optimal weight:   20.0000
   chunk 45 optimal weight:    5.9990
   chunk 184 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 187 optimal weight:    7.9990
   chunk 49 optimal weight:    0.6980
   chunk 109 optimal weight:   30.0000
   chunk 172 optimal weight:    8.9990
   overall best weight:    3.5386

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

Flipped N/Q/H residues before XYZ refinement:
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.076606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 88)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.052429 restraints weight = 128519.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 1.78
r_work: 0.3043 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  30507  Z= 0.225
  Angle     :  0.555  10.182  45866  Z= 0.284
  Chirality :  0.033   0.234   5925
  Planarity :  0.004   0.038   2271
  Dihedral  : 23.135 178.524  15736
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 14.64 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.27), residues: 959
  helix:  1.09 (0.28), residues: 349
  sheet: -0.94 (0.45), residues: 135
  loop : -1.35 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG 2  34 
 TYR   0.014   0.002   TYR J  74 
 PHE   0.018   0.002   PHE R  53 
 TRP   0.006   0.001   TRP R  92 
 HIS   0.004   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (30507)
  covalent geometry    : angle       0.55515 (45866)
  hydrogen bonds       : bond        0.06436 ( 1107)
  hydrogen bonds       : angle       3.25728 ( 2151)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  105 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.7765 (mp)
REVERT: J    1 MET cc_start: 0.7616 (tpp) cc_final: 0.7309 (tmm)
REVERT: J   16 TYR cc_start: 0.8494 (m-80) cc_final: 0.8289 (m-10)
REVERT: J  138 GLN cc_start: 0.7826 (tt0) cc_final: 0.7500 (tt0)
REVERT: J  142 ILE cc_start: 0.5891 (mt) cc_final: 0.5503 (mm)
REVERT: Q   96 ASP cc_start: 0.8212 (t70) cc_final: 0.7917 (t0)
REVERT: Y    2 LYS cc_start: 0.7689 (mttm) cc_final: 0.6559 (mttp)
  outliers start: 21
  outliers final: 14
  residues processed: 101
  average time/residue: 0.1636
  time to fit residues: 26.8870
Evaluate side-chains
  93 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue  105 LEU
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain J residue    3 THR
Chi-restraints excluded: chain J residue  124 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain R residue   64 VAL
Chi-restraints excluded: chain S residue    3 THR
Chi-restraints excluded: chain S residue   36 LEU
Chi-restraints excluded: chain S residue   69 LEU
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain U residue   11 ILE
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 186 optimal weight:    7.9990
   chunk 124 optimal weight:    8.9990
   chunk 173 optimal weight:    8.9990
   chunk 126 optimal weight:    6.9990
   chunk 141 optimal weight:   10.0000
   chunk 149 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    2.9984

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

Flipped N/Q/H residues before XYZ refinement:
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  43 ASN
** U  53 GLN ** 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 = 0.3806 r_free = 0.3806 target = 0.076904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.052710 restraints weight = 128578.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 1.78
r_work: 0.3052 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.3548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  30507  Z= 0.197
  Angle     :  0.532  10.187  45866  Z= 0.274
  Chirality :  0.031   0.230   5925
  Planarity :  0.004   0.036   2271
  Dihedral  : 23.117 177.156  15736
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 15.02 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.49 (0.27), residues: 959
  helix:  1.12 (0.28), residues: 355
  sheet: -0.90 (0.42), residues: 148
  loop : -1.29 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG 2  39 
 TYR   0.013   0.002   TYR J  74 
 PHE   0.017   0.002   PHE R  53 
 TRP   0.006   0.001   TRP R  92 
 HIS   0.003   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (30507)
  covalent geometry    : angle       0.53235 (45866)
  hydrogen bonds       : bond        0.06275 ( 1107)
  hydrogen bonds       : angle       3.18625 ( 2151)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: J    1 MET cc_start: 0.7625 (tpp) cc_final: 0.7294 (tmm)
REVERT: J   16 TYR cc_start: 0.8511 (m-80) cc_final: 0.8295 (m-10)
REVERT: J  138 GLN cc_start: 0.7731 (tt0) cc_final: 0.7442 (tt0)
REVERT: J  142 ILE cc_start: 0.5913 (mt) cc_final: 0.5651 (mm)
REVERT: L   78 ARG cc_start: 0.2851 (OUTLIER) cc_final: 0.1187 (mtm-85)
REVERT: Y    2 LYS cc_start: 0.7674 (mttm) cc_final: 0.6621 (mttp)
REVERT: Y   26 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8501 (t80)
REVERT: Y   31 GLN cc_start: 0.8680 (mp10) cc_final: 0.8336 (mt0)
REVERT: Z   44 ARG cc_start: 0.7546 (mmt-90) cc_final: 0.7318 (mmt-90)
  outliers start: 24
  outliers final: 18
  residues processed: 101
  average time/residue: 0.1646
  time to fit residues: 27.0609
Evaluate side-chains
  97 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain J residue    3 THR
Chi-restraints excluded: chain J residue  124 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   78 ARG
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain R residue   47 VAL
Chi-restraints excluded: chain R residue   64 VAL
Chi-restraints excluded: chain S residue    3 THR
Chi-restraints excluded: chain S residue   36 LEU
Chi-restraints excluded: chain S residue   66 ILE
Chi-restraints excluded: chain S residue   69 LEU
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain U residue   11 ILE
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain Y residue   26 PHE
Chi-restraints excluded: chain Z residue   34 THR
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 162 optimal weight:   20.0000
   chunk 154 optimal weight:   50.0000
   chunk 16 optimal weight:    0.9990
   chunk 103 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9990
   chunk 37 optimal weight:    7.9990
   chunk 163 optimal weight:   10.0000
   chunk 108 optimal weight:   30.0000
   chunk 164 optimal weight:   20.0000
   chunk 147 optimal weight:   10.0000
   overall best weight:    4.1992

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

Flipped N/Q/H residues before XYZ refinement:
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  43 ASN
** U  53 GLN ** 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 = 0.3790 r_free = 0.3790 target = 0.076284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.051943 restraints weight = 128685.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 1.81
r_work: 0.3026 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  30507  Z= 0.260
  Angle     :  0.581   9.952  45866  Z= 0.297
  Chirality :  0.034   0.233   5925
  Planarity :  0.004   0.037   2271
  Dihedral  : 23.159 179.759  15736
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.15 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.64 (0.27), residues: 959
  helix:  1.02 (0.28), residues: 355
  sheet: -1.09 (0.44), residues: 141
  loop : -1.35 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG 2  34 
 TYR   0.011   0.002   TYR E 101 
 PHE   0.015   0.002   PHE Q  56 
 TRP   0.006   0.001   TRP R  92 
 HIS   0.005   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 (30507)
  covalent geometry    : angle       0.58081 (45866)
  hydrogen bonds       : bond        0.06865 ( 1107)
  hydrogen bonds       : angle       3.28581 ( 2151)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.8055 (ptp) cc_final: 0.7238 (ptp)
REVERT: J    1 MET cc_start: 0.7613 (tpp) cc_final: 0.7275 (tmm)
REVERT: J   16 TYR cc_start: 0.8486 (m-80) cc_final: 0.8259 (m-10)
REVERT: J  138 GLN cc_start: 0.7834 (tt0) cc_final: 0.7509 (tt0)
REVERT: J  142 ILE cc_start: 0.6023 (mt) cc_final: 0.5698 (mm)
REVERT: L   78 ARG cc_start: 0.2820 (OUTLIER) cc_final: 0.1496 (mtm-85)
REVERT: R   32 THR cc_start: 0.9129 (m) cc_final: 0.8680 (t)
REVERT: Y    2 LYS cc_start: 0.7663 (mttm) cc_final: 0.6611 (mttp)
REVERT: Y   26 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8507 (t80)
  outliers start: 23
  outliers final: 18
  residues processed: 100
  average time/residue: 0.1603
  time to fit residues: 26.1386
Evaluate side-chains
  98 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain J residue    3 THR
Chi-restraints excluded: chain J residue  124 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   78 ARG
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain R residue   64 VAL
Chi-restraints excluded: chain S residue    3 THR
Chi-restraints excluded: chain S residue   36 LEU
Chi-restraints excluded: chain S residue   66 ILE
Chi-restraints excluded: chain S residue   69 LEU
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain U residue   11 ILE
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain Y residue   26 PHE
Chi-restraints excluded: chain Z residue   34 THR
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 95 optimal weight:    6.9990
   chunk 150 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9990
   chunk 139 optimal weight:    6.9990
   chunk 82 optimal weight:    4.9990
   chunk 120 optimal weight:   30.0000
   chunk 44 optimal weight:    3.9990
   chunk 149 optimal weight:    8.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.077285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.053121 restraints weight = 130796.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 1.74
r_work: 0.3064 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.3678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  30507  Z= 0.170
  Angle     :  0.519  12.340  45866  Z= 0.266
  Chirality :  0.031   0.235   5925
  Planarity :  0.004   0.033   2271
  Dihedral  : 23.147 177.046  15736
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.40 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.27), residues: 959
  helix:  1.25 (0.28), residues: 355
  sheet: -1.06 (0.43), residues: 140
  loop : -1.31 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Z  44 
 TYR   0.010   0.001   TYR E 101 
 PHE   0.013   0.001   PHE R  77 
 TRP   0.006   0.001   TRP R  92 
 HIS   0.003   0.001   HIS S  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (30507)
  covalent geometry    : angle       0.51868 (45866)
  hydrogen bonds       : bond        0.06056 ( 1107)
  hydrogen bonds       : angle       3.16326 ( 2151)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.7986 (ptp) cc_final: 0.6985 (ptp)
REVERT: J    1 MET cc_start: 0.7638 (tpp) cc_final: 0.7293 (tmm)
REVERT: J   16 TYR cc_start: 0.8505 (m-80) cc_final: 0.8278 (m-10)
REVERT: J  138 GLN cc_start: 0.7734 (tt0) cc_final: 0.7407 (tt0)
REVERT: J  142 ILE cc_start: 0.5880 (mt) cc_final: 0.5649 (mm)
REVERT: L   78 ARG cc_start: 0.2731 (OUTLIER) cc_final: 0.1460 (mtm-85)
REVERT: R   32 THR cc_start: 0.9140 (m) cc_final: 0.8698 (t)
REVERT: Y    2 LYS cc_start: 0.7630 (mttm) cc_final: 0.6570 (mttp)
REVERT: Y   26 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8411 (t80)
REVERT: Y   31 GLN cc_start: 0.8683 (mp10) cc_final: 0.8320 (mt0)
  outliers start: 21
  outliers final: 17
  residues processed: 101
  average time/residue: 0.1598
  time to fit residues: 26.2554
Evaluate side-chains
  100 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain J residue    3 THR
Chi-restraints excluded: chain J residue  124 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   78 ARG
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain R residue   64 VAL
Chi-restraints excluded: chain R residue   79 ARG
Chi-restraints excluded: chain S residue   36 LEU
Chi-restraints excluded: chain S residue   69 LEU
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain U residue   11 ILE
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain Y residue   26 PHE
Chi-restraints excluded: chain Z residue   34 THR
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 134 optimal weight:   20.0000
   chunk 118 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   chunk 28 optimal weight:    7.9990
   chunk 17 optimal weight:    0.6980
   chunk 142 optimal weight:    7.9990
   chunk 174 optimal weight:   10.0000
   chunk 127 optimal weight:   10.0000
   chunk 166 optimal weight:   20.0000
   chunk 94 optimal weight:   10.0000
   overall best weight:    6.1388

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

Flipped N/Q/H residues before XYZ refinement:
J  58 ASN
J 128 ASN
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** 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 = 0.3765 r_free = 0.3765 target = 0.075302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.050921 restraints weight = 129655.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3108 rms_B_bonded: 1.98
r_work: 0.2997 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.4144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.070  30507  Z= 0.374
  Angle     :  0.689  11.406  45866  Z= 0.347
  Chirality :  0.039   0.241   5925
  Planarity :  0.005   0.038   2271
  Dihedral  : 23.263 177.037  15736
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.90 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.88 (0.27), residues: 959
  helix:  0.79 (0.28), residues: 356
  sheet: -1.49 (0.45), residues: 128
  loop : -1.39 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG 2  21 
 TYR   0.042   0.003   TYR Q  24 
 PHE   0.023   0.002   PHE Q  56 
 TRP   0.008   0.002   TRP R  92 
 HIS   0.004   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00736 (30507)
  covalent geometry    : angle       0.68868 (45866)
  hydrogen bonds       : bond        0.08054 ( 1107)
  hydrogen bonds       : angle       3.47086 ( 2151)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.8239 (ptp) cc_final: 0.7617 (ptp)
REVERT: J    1 MET cc_start: 0.7624 (tpp) cc_final: 0.7257 (tmm)
REVERT: J   16 TYR cc_start: 0.8532 (m-80) cc_final: 0.8290 (m-10)
REVERT: J  138 GLN cc_start: 0.7776 (tt0) cc_final: 0.7454 (tt0)
REVERT: J  142 ILE cc_start: 0.6246 (mt) cc_final: 0.5899 (mm)
REVERT: L   78 ARG cc_start: 0.2881 (OUTLIER) cc_final: 0.1399 (mtm-85)
REVERT: R   32 THR cc_start: 0.9134 (m) cc_final: 0.8682 (t)
REVERT: Y    2 LYS cc_start: 0.7734 (mttm) cc_final: 0.6626 (mttp)
REVERT: Y   36 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7477 (tm-30)
  outliers start: 23
  outliers final: 19
  residues processed: 98
  average time/residue: 0.1733
  time to fit residues: 27.6249
Evaluate side-chains
  99 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain J residue    3 THR
Chi-restraints excluded: chain J residue  124 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   78 ARG
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain R residue   47 VAL
Chi-restraints excluded: chain R residue   64 VAL
Chi-restraints excluded: chain S residue    3 THR
Chi-restraints excluded: chain S residue   36 LEU
Chi-restraints excluded: chain S residue   66 ILE
Chi-restraints excluded: chain S residue   69 LEU
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain U residue   11 ILE
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain Y residue   36 GLN
Chi-restraints excluded: chain Z residue   34 THR
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 184 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 175 optimal weight:   20.0000
   chunk 54 optimal weight:    2.9990
   chunk 181 optimal weight:    6.9990
   chunk 140 optimal weight:    5.9990
   chunk 32 optimal weight:    0.3980
   chunk 85 optimal weight:    5.9990
   chunk 174 optimal weight:    6.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.077321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.053274 restraints weight = 129611.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 1.73
r_work: 0.3070 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  30507  Z= 0.149
  Angle     :  0.524  10.950  45866  Z= 0.270
  Chirality :  0.031   0.243   5925
  Planarity :  0.004   0.032   2271
  Dihedral  : 23.212 176.396  15736
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 18.15 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.27), residues: 959
  helix:  1.23 (0.28), residues: 354
  sheet: -1.43 (0.44), residues: 132
  loop : -1.33 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG Z  44 
 TYR   0.037   0.002   TYR Q  24 
 PHE   0.012   0.001   PHE R  77 
 TRP   0.004   0.001   TRP R  92 
 HIS   0.004   0.001   HIS S  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (30507)
  covalent geometry    : angle       0.52391 (45866)
  hydrogen bonds       : bond        0.06060 ( 1107)
  hydrogen bonds       : angle       3.19122 ( 2151)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.7736 (ptp) cc_final: 0.6859 (ptp)
REVERT: J    1 MET cc_start: 0.7621 (tpp) cc_final: 0.7294 (tmm)
REVERT: J   16 TYR cc_start: 0.8545 (m-80) cc_final: 0.8309 (m-10)
REVERT: J  138 GLN cc_start: 0.7818 (tt0) cc_final: 0.7502 (tt0)
REVERT: J  142 ILE cc_start: 0.5966 (mt) cc_final: 0.5618 (mm)
REVERT: L   78 ARG cc_start: 0.3025 (OUTLIER) cc_final: 0.1609 (mtm-85)
REVERT: R   32 THR cc_start: 0.9103 (m) cc_final: 0.8583 (t)
REVERT: R   62 GLU cc_start: 0.8254 (pt0) cc_final: 0.7768 (mp0)
REVERT: Y    2 LYS cc_start: 0.7671 (mttm) cc_final: 0.6630 (mttp)
  outliers start: 17
  outliers final: 16
  residues processed: 95
  average time/residue: 0.1917
  time to fit residues: 29.3656
Evaluate side-chains
  95 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue   33 VAL
Chi-restraints excluded: chain E residue  147 LEU
Chi-restraints excluded: chain J residue    3 THR
Chi-restraints excluded: chain J residue  124 VAL
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   78 ARG
Chi-restraints excluded: chain Q residue    3 VAL
Chi-restraints excluded: chain R residue   26 ASP
Chi-restraints excluded: chain R residue   64 VAL
Chi-restraints excluded: chain R residue   79 ARG
Chi-restraints excluded: chain S residue   36 LEU
Chi-restraints excluded: chain S residue   69 LEU
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain U residue   11 ILE
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 137 optimal weight:    7.9990
   chunk 102 optimal weight:   10.0000
   chunk 138 optimal weight:    7.9990
   chunk 23 optimal weight:    9.9990
   chunk 65 optimal weight:    0.0870
   chunk 14 optimal weight:    4.9990
   chunk 92 optimal weight:    6.9990
   chunk 156 optimal weight:   10.0000
   chunk 94 optimal weight:   10.0000
   chunk 73 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9990
   overall best weight:    3.8166

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

Flipped N/Q/H residues before XYZ refinement:
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.076122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.052328 restraints weight = 123666.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 1.70
r_work: 0.3043 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.4004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  30507  Z= 0.243
  Angle     :  0.576  11.946  45866  Z= 0.294
  Chirality :  0.033   0.236   5925
  Planarity :  0.004   0.034   2271
  Dihedral  : 23.218 179.781  15736
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 18.15 %
    Favored  : 79.60 %
  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 aren not related in a simple way.
  whole: -0.68 (0.27), residues: 959
  helix:  1.10 (0.28), residues: 354
  sheet: -1.47 (0.44), residues: 133
  loop : -1.36 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Z  44 
 TYR   0.037   0.002   TYR Q  24 
 PHE   0.015   0.002   PHE Q  56 
 TRP   0.005   0.001   TRP R  92 
 HIS   0.004   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 (30507)
  covalent geometry    : angle       0.57638 (45866)
  hydrogen bonds       : bond        0.06740 ( 1107)
  hydrogen bonds       : angle       3.28341 ( 2151)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6382.96 seconds
wall clock time: 110 minutes 16.61 seconds (6616.61 seconds total)