Starting phenix.real_space_refine
on Sat Aug  8 18:29:27 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8c98_16505/08_2026/8c98_16505.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c98_16505/08_2026/8c98_16505.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c98_16505/08_2026/8c98_16505.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c98_16505/08_2026/8c98_16505.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8c98_16505/08_2026/8c98_16505.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8c98_16505/08_2026/8c98_16505.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c98_16505/08_2026/8c98_16505.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c98_16505/08_2026/8c98_16505.cif"
  }
  resolution = 3.66
  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=   0.023 sd=   0.113
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    1017      5.49       5
     S      20      5.16       5
     C   15050      2.51       5
     N    5646      2.21       5
     O    8551      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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 30284
  Number of models: 1
  Model: ""
    Number of chains: 12
    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: 671
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 671
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          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: "T"
      Number of atoms: 738
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 738
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 1, 'TRANS': 91}
    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: 449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 449
          Classifications: {'peptide': 58}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 55}
    Chain: "A"
      Number of atoms: 21846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1018, 21846
          Classifications: {'DNA': 1, 'RNAv2': 1017}
          Modifications used: {'rna2p_pur': 95, 'rna2p_pyr': 52, 'rna3p_pur': 499, 'rna3p_pyr': 371}
          Incomplete info: {'p_only': 1}
          Link IDs: {'rna2p': 147, 'rna3p': 870}
          Unresolved chain links: 2
          Chain breaks: 6
          Unresolved chain link angles: 5
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'  G:plan': 1, '  G:plan2': 1}
          Unresolved non-hydrogen planarities: 14
  Time building chain proxies: 4.75, per 1000 atoms: 0.16
  Number of scatterers: 30284
  At special positions: 0
  Unit cell: (131.25, 190, 167.5, 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      20     16.00
     P    1017     15.00
     O    8551      8.00
     N    5646      7.00
     C   15050      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: 2.06
  Conformation dependent library (CDL) restraints added in 452.3 milliseconds
  

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2006

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 12 sheets defined
      39.5% alpha, 13.6% beta
      335 base pairs and 521 stacking pairs defined.
    Time for finding SS restraints: 5.08
  Creating SS restraints...
    Processing helix  chain '2' and resid 10 through 17
    Processing helix  chain '2' and resid 17 through 24
      removed outlier: 3.894A  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
    Processing helix  chain 'E' and resid 97 through 115
    Processing helix  chain 'E' and resid 130 through 141
    Processing helix  chain 'E' and resid 154 through 164
      removed outlier: 4.359A  pdb=" N   ASN E 163 " --> pdb=" O   LEU E 159 " (cutoff:3.500A)
      removed outlier: 4.481A  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 176 through 183
    Processing helix  chain 'E' and resid 190 through 201
    Processing helix  chain 'J' and resid 25 through 37
    Processing helix  chain 'J' and resid 67 through 72
    Processing helix  chain 'J' and resid 89 through 96
    Processing helix  chain 'J' and resid 97 through 108
      removed outlier: 4.084A  pdb=" N   ILE J 101 " --> pdb=" O   PRO J  97 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 112 through 121
      removed outlier: 3.655A  pdb=" N   LYS J 121 " --> pdb=" O   ALA J 117 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 130 through 136
      removed outlier: 3.682A  pdb=" N   ALA J 134 " --> pdb=" O   ASN J 131 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 136
      removed outlier: 3.957A  pdb=" N   ALA L 134 " --> pdb=" O   GLY L 130 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 5 through 19
      removed outlier: 3.916A  pdb=" N   GLN Q  19 " --> pdb=" O   LYS Q  15 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 24 through 29
      removed outlier: 4.435A  pdb=" N   ARG Q  27 " --> pdb=" O   TYR Q  24 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 30 through 70
      removed outlier: 4.321A  pdb=" N   GLN Q  36 " --> pdb=" O   ARG Q  32 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ARG Q  50 " --> pdb=" O   TYR Q  46 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   LYS Q  53 " --> pdb=" O   ARG Q  49 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ARG Q  54 " --> pdb=" O   ARG Q  50 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLN Q  70 " --> pdb=" O   ALA Q  66 " (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: 4.000A  pdb=" N   PHE Q 105 " --> pdb=" O   ASP Q 101 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   ALA Q 117 " --> pdb=" O   LYS Q 113 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 13 through 23
      removed outlier: 3.865A  pdb=" N   LEU S  23 " --> pdb=" O   LEU S  19 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 38
      removed outlier: 3.860A  pdb=" N   ASP S  34 " --> pdb=" O   SER S  30 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   TYR S  38 " --> pdb=" O   ASP S  34 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 41 through 62
      removed outlier: 4.098A  pdb=" N   VAL S  45 " --> pdb=" O   LYS S  41 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU S  46 " --> pdb=" O   LYS S  42 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 4 through 11
      removed outlier: 3.840A  pdb=" N   LEU T  11 " --> pdb=" O   LEU T   7 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 17 through 27
      removed outlier: 3.857A  pdb=" N   GLU T  25 " --> pdb=" O   SER T  21 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 39 through 52
    Processing helix  chain 'Y' and resid 9 through 34
      removed outlier: 3.809A  pdb=" N   PHE Y  26 " --> pdb=" O   LEU Y  22 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 40 through 56
      removed outlier: 4.017A  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 118 through 121
      removed outlier: 3.843A  pdb=" N   VAL E 121 " --> pdb=" O   MET E 188 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   VAL E 146 " --> pdb=" O   ASP E 168 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   ARG E 170 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ILE E 148 " --> pdb=" O   ARG E 170 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 123 through 125
      removed outlier: 6.306A  pdb=" N   ILE J  54 " --> pdb=" O   LYS J 123 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   TYR J 125 " --> pdb=" O   ILE J  54 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   VAL J  56 " --> pdb=" O   TYR J 125 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'J' and resid 23 through 24
      removed outlier: 5.779A  pdb=" N   LYS J  23 " --> pdb=" O   ALA J  63 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'J' and resid 73 through 74
    Processing sheet with id=AA5, first strand: chain 'R' and resid 11 through 14
      removed outlier: 6.870A  pdb=" N   GLN R   6 " --> pdb=" O   VAL R  38 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   VAL R  38 " --> pdb=" O   GLN R   6 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'R' and resid 19 through 22
      removed outlier: 7.023A  pdb=" N   PHE R  93 " --> pdb=" O   HIS R  66 " (cutoff:3.500A)
      removed outlier: 5.270A  pdb=" N   HIS R  66 " --> pdb=" O   PHE R  93 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   ASP R  95 " --> pdb=" O   VAL R  64 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL R  64 " --> pdb=" O   ASP R  95 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   THR R  99 " --> pdb=" O   LYS R  60 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   LYS R  60 " --> pdb=" O   THR R  99 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'R' and resid 72 through 75
    Processing sheet with id=AA8, first strand: chain 'S' and resid 2 through 10
      removed outlier: 5.611A  pdb=" N   SER S 101 " --> pdb=" O   HIS S   9 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   HIS S 102 " --> pdb=" O   VAL S  76 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   VAL S  76 " --> pdb=" O   HIS S 102 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   THR S 104 " --> pdb=" O   ILE S  74 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   ILE S  74 " --> pdb=" O   THR S 104 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   VAL S 106 " --> pdb=" O   THR S  72 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'T' and resid 13 through 14
      removed outlier: 4.033A  pdb=" N   LYS T  81 " --> pdb=" O   VAL T  34 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   TRP T  80 " --> pdb=" O   VAL T  62 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   VAL T  62 " --> pdb=" O   TRP T  80 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   LYS T  82 " --> pdb=" O   THR T  60 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   THR T  60 " --> pdb=" O   LYS T  82 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   TYR T  84 " --> pdb=" O   VAL T  58 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   VAL T  58 " --> pdb=" O   TYR T  84 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   THR T  86 " --> pdb=" O   GLU T  56 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'U' and resid 64 through 65
      removed outlier: 6.676A  pdb=" N   LYS U  32 " --> pdb=" O   VAL U  27 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   VAL U  27 " --> pdb=" O   LYS U  32 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   ILE U  34 " --> pdb=" O   LYS U  25 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'U' and resid 82 through 86
    Processing sheet with id=AB3, first strand: chain 'Z' and resid 34 through 38

    340 hydrogen bonds defined for protein.
    981 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      853 hydrogen bonds
      1378 hydrogen bond angles
      0 basepair planarities
      335 basepair parallelities
      521 stacking parallelities
  Total time for adding SS restraints: 10.77

  Time building geometry restraints manager: 2.97 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: 4501
        1.33 -     1.45: 13501
        1.45 -     1.57: 12918
        1.57 -     1.69: 2027
        1.69 -     1.81: 40
  Bond restraints: 32987
  Sorted by residual:
  bond pdb=" C1'   U A 546 "
       pdb=" N1    U A 546 "
    ideal  model  delta    sigma   weight residual
    1.478  1.573 -0.095 2.00e-02 2.50e+03 2.28e+01
  bond pdb=" C1'   U A 827 "
       pdb=" N1    U A 827 "
    ideal  model  delta    sigma   weight residual
    1.478  1.573 -0.095 2.00e-02 2.50e+03 2.25e+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 3.08e+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 3.07e+00
  bond pdb=" N   MET T   1 "
       pdb=" CA  MET T   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.06e+00
  ... (remaining 32982 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 45104
        1.32 -     2.64: 2547
        2.64 -     3.96: 1707
        3.96 -     5.28: 198
        5.28 -     6.60: 2
  Bond angle restraints: 49558
  Sorted by residual:
  angle pdb=" C3'   U A1019 "
        pdb=" O3'   U A1019 "
        pdb=" P     A A1020 "
      ideal   model   delta    sigma   weight residual
     119.70  123.94   -4.24 1.20e+00 6.94e-01 1.25e+01
  angle pdb=" N   ALA S  64 "
        pdb=" CA  ALA S  64 "
        pdb=" C   ALA S  64 "
      ideal   model   delta    sigma   weight residual
     107.73  112.44   -4.71 1.34e+00 5.57e-01 1.24e+01
  angle pdb=" O3'   G A 271 "
        pdb=" C3'   G A 271 "
        pdb=" C2'   G A 271 "
      ideal   model   delta    sigma   weight residual
     113.80  107.20    6.60 2.00e+00 2.50e-01 1.09e+01
  angle pdb=" C3'   A A 404 "
        pdb=" O3'   A A 404 "
        pdb=" P     U A 405 "
      ideal   model   delta    sigma   weight residual
     119.70  123.51   -3.81 1.20e+00 6.94e-01 1.01e+01
  angle pdb=" C3'   U A 139 "
        pdb=" O3'   U A 139 "
        pdb=" P     C A 140 "
      ideal   model   delta    sigma   weight residual
     119.70  122.92   -3.22 1.20e+00 6.94e-01 7.18e+00
  ... (remaining 49553 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.81: 15746
       35.81 -    71.61: 1642
       71.61 -   107.42: 90
      107.42 -   143.23: 3
      143.23 -   179.04: 2
  Dihedral angle restraints: 17483
    sinusoidal: 14394
      harmonic: 3089
  Sorted by residual:
  dihedral pdb=" C4'   G A 271 "
           pdb=" C3'   G A 271 "
           pdb=" C2'   G A 271 "
           pdb=" C1'   G A 271 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -40.22   76.56     1      3.10e+00 1.04e-01 7.67e+02
  dihedral pdb=" C4'   A A 479 "
           pdb=" C3'   A A 479 "
           pdb=" C2'   A A 479 "
           pdb=" C1'   A A 479 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -37.83   74.17     1      3.10e+00 1.04e-01 7.26e+02
  dihedral pdb=" C4'   U A 395 "
           pdb=" C3'   U A 395 "
           pdb=" C2'   U A 395 "
           pdb=" C1'   U A 395 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -37.22   73.57     1      3.10e+00 1.04e-01 7.16e+02
  ... (remaining 17480 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 4041
       0.062 -    0.124: 1051
       0.124 -    0.186: 12
       0.186 -    0.248: 1086
       0.248 -    0.310: 218
  Chirality restraints: 6408
  Sorted by residual:
  chirality pdb=" P     A A1020 "
            pdb=" OP1   A A1020 "
            pdb=" OP2   A A1020 "
            pdb=" O5'   A A1020 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.48   -0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" P     U A 405 "
            pdb=" OP1   U A 405 "
            pdb=" OP2   U A 405 "
            pdb=" O5'   U A 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.48   -0.31 2.00e-01 2.50e+01 2.37e+00
  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     -2.50   -2.81    0.31 2.00e-01 2.50e+01 2.35e+00
  ... (remaining 6405 not shown)

  Planarity restraints: 2468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 259 "    0.009 2.00e-02 2.50e+03   1.47e-02 6.47e+00
        pdb=" N9    G A 259 "   -0.002 2.00e-02 2.50e+03
        pdb=" C8    G A 259 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    G A 259 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    G A 259 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G A 259 "   -0.011 2.00e-02 2.50e+03
        pdb=" O6    G A 259 "    0.013 2.00e-02 2.50e+03
        pdb=" N1    G A 259 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    G A 259 "   -0.039 2.00e-02 2.50e+03
        pdb=" N2    G A 259 "    0.025 2.00e-02 2.50e+03
        pdb=" N3    G A 259 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    G A 259 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A 269 "   -0.014 2.00e-02 2.50e+03   1.51e-02 5.13e+00
        pdb=" N1    C A 269 "    0.017 2.00e-02 2.50e+03
        pdb=" C2    C A 269 "    0.033 2.00e-02 2.50e+03
        pdb=" O2    C A 269 "   -0.019 2.00e-02 2.50e+03
        pdb=" N3    C A 269 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    C A 269 "    0.002 2.00e-02 2.50e+03
        pdb=" N4    C A 269 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5    C A 269 "   -0.007 2.00e-02 2.50e+03
        pdb=" C6    C A 269 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A 239 "   -0.009 2.00e-02 2.50e+03   1.44e-02 4.69e+00
        pdb=" N1    C A 239 "    0.007 2.00e-02 2.50e+03
        pdb=" C2    C A 239 "    0.035 2.00e-02 2.50e+03
        pdb=" O2    C A 239 "   -0.019 2.00e-02 2.50e+03
        pdb=" N3    C A 239 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    C A 239 "    0.007 2.00e-02 2.50e+03
        pdb=" N4    C A 239 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5    C A 239 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6    C A 239 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 2465 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 241
        2.52 -     3.11: 21985
        3.11 -     3.71: 57922
        3.71 -     4.30: 79359
        4.30 -     4.90: 110115
  Nonbonded interactions: 269622
  Sorted by model distance:
  nonbonded pdb=" O2'   A A 126 "
            pdb=" O4'   A A 127 "
     model   vdw
     1.923 3.040
  nonbonded pdb=" OD2 ASP Q  48 "
            pdb=" O2'   U A 534 "
     model   vdw
     1.941 3.040
  nonbonded pdb=" OP2   G A 117 "
            pdb=" O2'   A A 119 "
     model   vdw
     1.983 3.040
  nonbonded pdb=" O2'   A A1383 "
            pdb=" O4'   A A1384 "
     model   vdw
     1.996 3.040
  nonbonded pdb=" O2'   A A 299 "
            pdb=" O4'   A A 300 "
     model   vdw
     2.004 3.040
  ... (remaining 269617 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 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:             1.950
  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:             0.020
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.050
  Process input model:                     30.980
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
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      :  0.003   0.095  32987  Z= 0.135
  Angle     :  0.842   6.601  49558  Z= 0.343
  Chirality :  0.113   0.310   6408
  Planarity :  0.002   0.021   2468
  Dihedral  : 20.223 179.037  15477
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.35 (0.28), residues: 1050
  helix:  2.69 (0.27), residues: 369
  sheet:  0.18 (0.43), residues: 155
  loop : -0.16 (0.29), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG Q  27 
 TYR   0.006   0.001   TYR T  84 
 PHE   0.005   0.001   PHE S  75 
 TRP   0.002   0.000   TRP R  92 
 HIS   0.005   0.001   HIS Y  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.14 (32987)
  covalent geometry    : angle       0.84161 /  0.34 (49558)
  hydrogen bonds       : bond        0.09130 /  6.38 ( 1193)
  hydrogen bonds       : angle       4.23535 /  3.02 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.593 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   95 LEU cc_start: 0.4567 (pt) cc_final: 0.3917 (tt)
REVERT: T    1 MET cc_start: 0.4070 (pmm) cc_final: 0.3846 (pmm)
REVERT: Y    1 MET cc_start: 0.6249 (tpp) cc_final: 0.5874 (tpp)
REVERT: Z   36 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6380 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.2127
  time to fit residues: 23.4413
Evaluate side-chains
  41 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 194 optimal weight:    9.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:   10.0000
   chunk 200 optimal weight:   40.0000
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:   10.0000
   overall best weight:    9.1992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
J  47 HIS
Q  71 ASN
R   6 GLN
R  18 GLN
S  61 ASN
Y  41 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.051340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.037310 restraints weight = 293719.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.037960 restraints weight = 129168.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.038413 restraints weight = 88894.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.038564 restraints weight = 75138.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.038718 restraints weight = 70529.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.073  32987  Z= 0.410
  Angle     :  1.444  18.282  49558  Z= 0.577
  Chirality :  0.112   1.511   6408
  Planarity :  0.005   0.038   2468
  Dihedral  : 19.840 175.085  13361
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  5.91 %
    Favored  : 93.52 %
  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:  0.24 (0.26), residues: 1050
  helix:  1.42 (0.26), residues: 370
  sheet:  0.05 (0.44), residues: 140
  loop : -0.69 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R  90 
 TYR   0.015   0.002   TYR J  44 
 PHE   0.022   0.002   PHE 2  18 
 TRP   0.007   0.001   TRP J  15 
 HIS   0.008   0.002   HIS E 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00829 /  0.41 (32987)
  covalent geometry    : angle       1.44418 /  0.58 (49558)
  hydrogen bonds       : bond        0.09143 /  6.17 ( 1193)
  hydrogen bonds       : angle       3.83721 /  2.74 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
REVERT: L   95 LEU cc_start: 0.4426 (pt) cc_final: 0.4036 (tt)
REVERT: S    1 MET cc_start: 0.6644 (ttt) cc_final: 0.6233 (ttt)
REVERT: S  110 ARG cc_start: 0.6791 (mtm-85) cc_final: 0.6211 (mtm-85)
REVERT: T    1 MET cc_start: 0.3963 (pmm) cc_final: 0.3749 (pmm)
REVERT: Z   36 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6904 (mm-30)
  outliers start: 5
  outliers final: 4
  residues processed: 52
  average time/residue: 0.1772
  time to fit residues: 15.6954
Evaluate side-chains
  48 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   32 LEU
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain Z residue    4 ILE
Chi-restraints excluded: chain Z residue   34 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 183 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 161 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 64 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   chunk 132 optimal weight:    7.9990
   chunk 154 optimal weight:    9.9990
   chunk 36 optimal weight:    0.2980
   chunk 127 optimal weight:    9.9990
   chunk 135 optimal weight:    5.9990
   overall best weight:    4.8588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
T  48 GLN
** T  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
T  91 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.051524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.037599 restraints weight = 294039.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.038299 restraints weight = 127153.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.038746 restraints weight = 87592.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.038907 restraints weight = 74225.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.039042 restraints weight = 69642.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.3254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  32987  Z= 0.245
  Angle     :  1.108  13.786  49558  Z= 0.446
  Chirality :  0.087   1.058   6408
  Planarity :  0.004   0.034   2468
  Dihedral  : 19.706 179.890  13361
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  7.61 %
    Favored  : 91.14 %
  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: -0.00 (0.26), residues: 1050
  helix:  1.02 (0.26), residues: 384
  sheet:  0.04 (0.44), residues: 145
  loop : -0.76 (0.27), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Q  27 
 TYR   0.008   0.001   TYR T  84 
 PHE   0.048   0.002   PHE R  53 
 TRP   0.008   0.001   TRP Q  60 
 HIS   0.005   0.001   HIS R  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00502 /  0.25 (32987)
  covalent geometry    : angle       1.10783 /  0.45 (49558)
  hydrogen bonds       : bond        0.07645 /  5.12 ( 1193)
  hydrogen bonds       : angle       3.59221 /  2.57 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.614 
Fit side-chains
REVERT: L   95 LEU cc_start: 0.4457 (pt) cc_final: 0.4049 (tt)
  outliers start: 11
  outliers final: 5
  residues processed: 56
  average time/residue: 0.1677
  time to fit residues: 16.6544
Evaluate side-chains
  46 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain Z residue    4 ILE
Chi-restraints excluded: chain Z residue   34 THR
Chi-restraints excluded: chain Z residue   51 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 142 optimal weight:   30.0000
   chunk 60 optimal weight:   10.0000
   chunk 122 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 180 optimal weight:   10.0000
   chunk 74 optimal weight:    7.9990
   chunk 106 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   chunk 132 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    8.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
S   7 HIS
** T  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3651 r_free = 0.3651 target = 0.050628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.036498 restraints weight = 293060.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.037176 restraints weight = 129883.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.037613 restraints weight = 89592.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 64)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.037832 restraints weight = 75680.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.037903 restraints weight = 70345.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.4260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061  32987  Z= 0.363
  Angle     :  1.260  15.876  49558  Z= 0.507
  Chirality :  0.093   1.150   6408
  Planarity :  0.005   0.041   2468
  Dihedral  : 19.870 174.802  13361
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 10.45 %
    Favored  : 87.05 %
  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: -0.53 (0.25), residues: 1050
  helix:  0.61 (0.26), residues: 372
  sheet: -0.04 (0.42), residues: 149
  loop : -1.13 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG Z  37 
 TYR   0.012   0.002   TYR J  44 
 PHE   0.029   0.003   PHE 2  18 
 TRP   0.005   0.001   TRP J  15 
 HIS   0.006   0.002   HIS Y  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00743 /  0.36 (32987)
  covalent geometry    : angle       1.26041 /  0.51 (49558)
  hydrogen bonds       : bond        0.09671 /  6.61 ( 1193)
  hydrogen bonds       : angle       3.87575 /  2.75 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 47
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
REVERT: L   95 LEU cc_start: 0.4644 (pt) cc_final: 0.4204 (tt)
REVERT: R   55 ASP cc_start: 0.6299 (p0) cc_final: 0.5730 (m-30)
REVERT: S    1 MET cc_start: 0.6980 (ttt) cc_final: 0.6378 (ttp)
REVERT: S  110 ARG cc_start: 0.6535 (mtm-85) cc_final: 0.6215 (mtm-85)
  outliers start: 22
  outliers final: 16
  residues processed: 66
  average time/residue: 0.1728
  time to fit residues: 19.7371
Evaluate side-chains
  57 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 41
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   16 HIS
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain J residue  103 ILE
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain R residue   32 THR
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain R residue   98 ILE
Chi-restraints excluded: chain S residue    4 ILE
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain U residue   71 ILE
Chi-restraints excluded: chain Z residue   31 ILE
Chi-restraints excluded: chain Z residue   34 THR
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   53 MET
Chi-restraints excluded: chain Z residue   56 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 36 optimal weight:    9.9990
   chunk 194 optimal weight:    8.9990
   chunk 8 optimal weight:    9.9990
   chunk 83 optimal weight:    0.9990
   chunk 199 optimal weight:   30.0000
   chunk 85 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 125 optimal weight:   10.0000
   overall best weight:    2.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** T  70 HIS ** 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 = 0.3685 r_free = 0.3685 target = 0.051320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.037642 restraints weight = 293895.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.038133 restraints weight = 132531.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 72)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.038559 restraints weight = 89866.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 61)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.038775 restraints weight = 75532.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.038849 restraints weight = 70016.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.4160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  32987  Z= 0.185
  Angle     :  1.048  12.249  49558  Z= 0.421
  Chirality :  0.082   0.863   6408
  Planarity :  0.004   0.036   2468
  Dihedral  : 19.677 176.590  13361
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 12.73 %
    Favored  : 85.68 %
  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: -0.24 (0.26), residues: 1050
  helix:  0.91 (0.26), residues: 379
  sheet: -0.14 (0.41), residues: 152
  loop : -0.95 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG U  81 
 TYR   0.007   0.001   TYR T  84 
 PHE   0.011   0.001   PHE 2  18 
 TRP   0.004   0.001   TRP J  15 
 HIS   0.004   0.001   HIS R  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.18 (32987)
  covalent geometry    : angle       1.04818 /  0.42 (49558)
  hydrogen bonds       : bond        0.07232 /  4.91 ( 1193)
  hydrogen bonds       : angle       3.56212 /  2.56 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 40
  time to evaluate  : 0.690 
Fit side-chains
   revert: symmetry clash
REVERT: L   95 LEU cc_start: 0.4322 (pt) cc_final: 0.3944 (tt)
REVERT: R    1 MET cc_start: 0.7463 (tpt) cc_final: 0.7140 (tpp)
REVERT: S    1 MET cc_start: 0.6777 (ttt) cc_final: 0.6425 (ttp)
  outliers start: 14
  outliers final: 9
  residues processed: 52
  average time/residue: 0.1680
  time to fit residues: 15.8850
Evaluate side-chains
  46 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain Z residue   31 ILE
Chi-restraints excluded: chain Z residue   34 THR
Chi-restraints excluded: chain Z residue   51 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 110 optimal weight:   10.0000
   chunk 63 optimal weight:    9.9990
   chunk 146 optimal weight:   10.0000
   chunk 82 optimal weight:    3.9990
   chunk 165 optimal weight:   10.0000
   chunk 197 optimal weight:   20.0000
   chunk 139 optimal weight:   30.0000
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 119 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   overall best weight:    6.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** T  70 HIS ** 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 = 0.3670 r_free = 0.3670 target = 0.051033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.037347 restraints weight = 293530.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.037811 restraints weight = 131827.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.038139 restraints weight = 89754.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.038398 restraints weight = 76851.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.038496 restraints weight = 70956.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.4248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  32987  Z= 0.284
  Angle     :  1.109  13.123  49558  Z= 0.444
  Chirality :  0.084   0.884   6408
  Planarity :  0.004   0.036   2468
  Dihedral  : 19.685 175.413  13361
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 12.84 %
    Favored  : 84.77 %
  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: -0.37 (0.25), residues: 1050
  helix:  0.85 (0.26), residues: 378
  sheet: -0.18 (0.41), residues: 152
  loop : -1.08 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG Y  52 
 TYR   0.010   0.002   TYR J  74 
 PHE   0.019   0.002   PHE 2  18 
 TRP   0.003   0.001   TRP J  15 
 HIS   0.006   0.002   HIS E 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00580 /  0.28 (32987)
  covalent geometry    : angle       1.10906 /  0.44 (49558)
  hydrogen bonds       : bond        0.07858 /  5.36 ( 1193)
  hydrogen bonds       : angle       3.57704 /  2.56 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 41
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
REVERT: L   95 LEU cc_start: 0.4267 (pt) cc_final: 0.3836 (tt)
REVERT: R    1 MET cc_start: 0.7528 (tpt) cc_final: 0.7209 (tpp)
REVERT: S    1 MET cc_start: 0.6752 (ttt) cc_final: 0.6408 (ttp)
REVERT: T    1 MET cc_start: 0.3904 (pmm) cc_final: 0.3427 (pmm)
  outliers start: 21
  outliers final: 17
  residues processed: 59
  average time/residue: 0.1739
  time to fit residues: 18.0599
Evaluate side-chains
  56 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   16 HIS
Chi-restraints excluded: chain 2 residue   44 VAL
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain J residue    1 MET
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain T residue   61 LEU
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain U residue   67 SER
Chi-restraints excluded: chain U residue   71 ILE
Chi-restraints excluded: chain Z residue   31 ILE
Chi-restraints excluded: chain Z residue   34 THR
Chi-restraints excluded: chain Z residue   50 VAL
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   53 MET
Chi-restraints excluded: chain Z residue   56 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 176 optimal weight:   20.0000
   chunk 91 optimal weight:    8.9990
   chunk 144 optimal weight:   10.0000
   chunk 117 optimal weight:   30.0000
   chunk 183 optimal weight:   10.0000
   chunk 70 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 119 optimal weight:   10.0000
   chunk 175 optimal weight:   20.0000
   chunk 64 optimal weight:    7.9990
   chunk 33 optimal weight:    8.9990
   overall best weight:    7.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
J  58 ASN
J 128 ASN
** T  70 HIS ** 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 = 0.3656 r_free = 0.3656 target = 0.050709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.036892 restraints weight = 293888.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 72)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.037369 restraints weight = 132732.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.037802 restraints weight = 89646.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 63)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.038027 restraints weight = 75504.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.038100 restraints weight = 69953.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.4470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058  32987  Z= 0.351
  Angle     :  1.183  15.631  49558  Z= 0.474
  Chirality :  0.087   0.929   6408
  Planarity :  0.005   0.037   2468
  Dihedral  : 19.782 176.567  13361
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.48 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 13.86 %
    Favored  : 83.30 %
  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: -0.74 (0.25), residues: 1050
  helix:  0.55 (0.26), residues: 385
  sheet: -0.27 (0.41), residues: 152
  loop : -1.38 (0.26), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG Q  52 
 TYR   0.014   0.002   TYR J  74 
 PHE   0.024   0.002   PHE 2  18 
 TRP   0.003   0.001   TRP J  15 
 HIS   0.006   0.002   HIS Z  33 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00719 /  0.35 (32987)
  covalent geometry    : angle       1.18334 /  0.47 (49558)
  hydrogen bonds       : bond        0.08937 /  6.12 ( 1193)
  hydrogen bonds       : angle       3.71658 /  2.65 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 40
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
REVERT: J   92 MET cc_start: 0.7330 (tmm) cc_final: 0.6993 (tpp)
REVERT: L   95 LEU cc_start: 0.4183 (pt) cc_final: 0.3759 (tt)
  outliers start: 25
  outliers final: 18
  residues processed: 62
  average time/residue: 0.1630
  time to fit residues: 18.3669
Evaluate side-chains
  55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 37
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   16 HIS
Chi-restraints excluded: chain 2 residue   44 VAL
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain L residue   19 LEU
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain R residue   32 THR
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain S residue    4 ILE
Chi-restraints excluded: chain S residue   66 ILE
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain U residue   71 ILE
Chi-restraints excluded: chain Z residue   31 ILE
Chi-restraints excluded: chain Z residue   50 VAL
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   53 MET
Chi-restraints excluded: chain Z residue   56 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 153 optimal weight:    9.9990
   chunk 175 optimal weight:   20.0000
   chunk 155 optimal weight:   10.0000
   chunk 203 optimal weight:   40.0000
   chunk 28 optimal weight:    0.0070
   chunk 128 optimal weight:   10.0000
   chunk 35 optimal weight:    0.4980
   chunk 11 optimal weight:    2.9990
   chunk 113 optimal weight:   10.0000
   chunk 150 optimal weight:    9.9990
   overall best weight:    4.3004

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** T  70 HIS ** 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 = 0.3680 r_free = 0.3680 target = 0.051203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.037634 restraints weight = 294336.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.038101 restraints weight = 128526.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.038459 restraints weight = 87123.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 66)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.038697 restraints weight = 74244.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.038783 restraints weight = 68369.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.4510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  32987  Z= 0.217
  Angle     :  1.049  12.121  49558  Z= 0.420
  Chirality :  0.081   0.675   6408
  Planarity :  0.004   0.035   2468
  Dihedral  : 19.675 179.863  13361
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.34 %
    Favored  : 82.50 %
  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: -0.44 (0.25), residues: 1050
  helix:  0.85 (0.26), residues: 379
  sheet: -0.23 (0.40), residues: 152
  loop : -1.18 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG U  81 
 TYR   0.013   0.002   TYR J  74 
 PHE   0.011   0.001   PHE 2  18 
 TRP   0.003   0.001   TRP J  15 
 HIS   0.004   0.001   HIS E 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00443 /  0.22 (32987)
  covalent geometry    : angle       1.04912 /  0.42 (49558)
  hydrogen bonds       : bond        0.07367 /  5.04 ( 1193)
  hydrogen bonds       : angle       3.52354 /  2.53 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 42
  time to evaluate  : 0.620 
Fit side-chains
REVERT: J   92 MET cc_start: 0.7455 (tmm) cc_final: 0.6864 (tpt)
REVERT: L   95 LEU cc_start: 0.4263 (pt) cc_final: 0.3841 (tt)
REVERT: S    1 MET cc_start: 0.6776 (ttt) cc_final: 0.6355 (ttp)
  outliers start: 19
  outliers final: 15
  residues processed: 58
  average time/residue: 0.1683
  time to fit residues: 17.6416
Evaluate side-chains
  54 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 39
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   16 HIS
Chi-restraints excluded: chain 2 residue   44 VAL
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain J residue  103 ILE
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain R residue   54 VAL
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain S residue    4 ILE
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain Z residue   31 ILE
Chi-restraints excluded: chain Z residue   50 VAL
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   56 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 179 optimal weight:   10.0000
   chunk 197 optimal weight:   20.0000
   chunk 20 optimal weight:    0.9980
   chunk 135 optimal weight:   10.0000
   chunk 100 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 42 optimal weight:   20.0000
   chunk 191 optimal weight:    9.9990
   chunk 6 optimal weight:    0.9990
   chunk 188 optimal weight:   30.0000
   overall best weight:    3.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** T  70 HIS ** 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 = 0.3684 r_free = 0.3684 target = 0.051287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.037486 restraints weight = 294334.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.038174 restraints weight = 127456.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 69)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.038611 restraints weight = 87298.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.038783 restraints weight = 73780.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.038915 restraints weight = 69186.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.4553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  32987  Z= 0.202
  Angle     :  1.033  11.910  49558  Z= 0.414
  Chirality :  0.079   0.651   6408
  Planarity :  0.004   0.035   2468
  Dihedral  : 19.642 177.835  13361
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 16.02 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.31 (0.25), residues: 1050
  helix:  0.94 (0.26), residues: 378
  sheet: -0.13 (0.40), residues: 152
  loop : -1.09 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Q  52 
 TYR   0.008   0.001   TYR S  38 
 PHE   0.013   0.001   PHE 2  18 
 TRP   0.003   0.001   TRP T  80 
 HIS   0.004   0.001   HIS R  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00410 /  0.20 (32987)
  covalent geometry    : angle       1.03323 /  0.41 (49558)
  hydrogen bonds       : bond        0.07305 /  5.02 ( 1193)
  hydrogen bonds       : angle       3.49197 /  2.50 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 40
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
REVERT: J   92 MET cc_start: 0.7517 (tmm) cc_final: 0.6920 (tpt)
REVERT: L   95 LEU cc_start: 0.4262 (pt) cc_final: 0.3780 (tt)
REVERT: S    1 MET cc_start: 0.6816 (ttt) cc_final: 0.6402 (ttp)
REVERT: T    1 MET cc_start: 0.3610 (pmm) cc_final: 0.2983 (pmm)
  outliers start: 19
  outliers final: 17
  residues processed: 57
  average time/residue: 0.1646
  time to fit residues: 17.1417
Evaluate side-chains
  56 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   16 HIS
Chi-restraints excluded: chain 2 residue   44 VAL
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain J residue  103 ILE
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain R residue   54 VAL
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain S residue    4 ILE
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain T residue   61 LEU
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain Z residue   31 ILE
Chi-restraints excluded: chain Z residue   50 VAL
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   56 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 172 optimal weight:   20.0000
   chunk 7 optimal weight:   10.0000
   chunk 60 optimal weight:    6.9990
   chunk 187 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   chunk 94 optimal weight:    8.9990
   chunk 100 optimal weight:   20.0000
   chunk 59 optimal weight:   30.0000
   chunk 6 optimal weight:    1.9990
   overall best weight:    4.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** T  70 HIS ** 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 = 0.3683 r_free = 0.3683 target = 0.051271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.037730 restraints weight = 293295.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.038206 restraints weight = 127710.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.038602 restraints weight = 86702.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.038771 restraints weight = 73182.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.038890 restraints weight = 68649.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.4562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  32987  Z= 0.212
  Angle     :  1.036  11.922  49558  Z= 0.415
  Chirality :  0.080   0.651   6408
  Planarity :  0.004   0.035   2468
  Dihedral  : 19.638 177.777  13361
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.48 %
    Favored  : 81.48 %
  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 are not related in a simple way.
  whole: -0.31 (0.25), residues: 1050
  helix:  0.95 (0.26), residues: 378
  sheet: -0.11 (0.41), residues: 152
  loop : -1.10 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG U  81 
 TYR   0.008   0.001   TYR S  38 
 PHE   0.013   0.001   PHE 2  18 
 TRP   0.003   0.001   TRP J  15 
 HIS   0.004   0.001   HIS R  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00431 /  0.21 (32987)
  covalent geometry    : angle       1.03608 /  0.42 (49558)
  hydrogen bonds       : bond        0.07323 /  5.03 ( 1193)
  hydrogen bonds       : angle       3.48242 /  2.50 ( 2359)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 40
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
REVERT: J   92 MET cc_start: 0.7503 (tmm) cc_final: 0.6911 (tpt)
REVERT: L   95 LEU cc_start: 0.4244 (pt) cc_final: 0.3743 (tt)
REVERT: S    1 MET cc_start: 0.6819 (ttt) cc_final: 0.6407 (ttp)
REVERT: T    1 MET cc_start: 0.3644 (pmm) cc_final: 0.2957 (pmm)
  outliers start: 18
  outliers final: 18
  residues processed: 57
  average time/residue: 0.1791
  time to fit residues: 18.3911
Evaluate side-chains
  58 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 40
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 2 residue   16 HIS
Chi-restraints excluded: chain 2 residue   44 VAL
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   31 VAL
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain J residue  103 ILE
Chi-restraints excluded: chain Q residue   82 LEU
Chi-restraints excluded: chain R residue   54 VAL
Chi-restraints excluded: chain R residue   75 VAL
Chi-restraints excluded: chain S residue    4 ILE
Chi-restraints excluded: chain S residue   66 ILE
Chi-restraints excluded: chain S residue   74 ILE
Chi-restraints excluded: chain T residue   61 LEU
Chi-restraints excluded: chain T residue   93 LEU
Chi-restraints excluded: chain Z residue   31 ILE
Chi-restraints excluded: chain Z residue   50 VAL
Chi-restraints excluded: chain Z residue   51 SER
Chi-restraints excluded: chain Z residue   56 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 178 optimal weight:   40.0000
   chunk 0 optimal weight:   10.0000
   chunk 92 optimal weight:    2.9990
   chunk 107 optimal weight:   10.0000
   chunk 50 optimal weight:    5.9990
   chunk 159 optimal weight:    9.9990
   chunk 75 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 174 optimal weight:   30.0000
   chunk 200 optimal weight:   40.0000
   overall best weight:    6.7992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** T  70 HIS ** 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 = 0.3665 r_free = 0.3665 target = 0.050854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.036881 restraints weight = 294644.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.037580 restraints weight = 130706.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.037996 restraints weight = 90323.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.038165 restraints weight = 76565.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.038290 restraints weight = 71728.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.4694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  32987  Z= 0.301
  Angle     :  1.122  13.516  49558  Z= 0.448
  Chirality :  0.083   0.745   6408
  Planarity :  0.004   0.036   2468
  Dihedral  : 19.732 178.982  13361
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.25 %
    Favored  : 81.48 %
  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 are not related in a simple way.
  whole: -0.51 (0.25), residues: 1050
  helix:  0.79 (0.26), residues: 378
  sheet: -0.16 (0.41), residues: 151
  loop : -1.25 (0.26), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG Y  52 
 TYR   0.011   0.002   TYR J  44 
 PHE   0.022   0.002   PHE 2  18 
 TRP   0.002   0.001   TRP J  15 
 HIS   0.005   0.002   HIS E 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00616 /  0.30 (32987)
  covalent geometry    : angle       1.12235 /  0.45 (49558)
  hydrogen bonds       : bond        0.08380 /  5.77 ( 1193)
  hydrogen bonds       : angle       3.59314 /  2.56 ( 2359)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5702.88 seconds
wall clock time: 99 minutes 36.97 seconds (5976.97 seconds total)