Starting phenix.real_space_refine
on Thu Mar  5 23:59:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6w7w_21573/03_2026/6w7w_21573.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6w7w_21573/03_2026/6w7w_21573.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6w7w_21573/03_2026/6w7w_21573.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6w7w_21573/03_2026/6w7w_21573.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6w7w_21573/03_2026/6w7w_21573.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6w7w_21573/03_2026/6w7w_21573.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.999
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     871      5.49       5
     S      33      5.16       5
     C   13446      2.51       5
     N    5026      2.21       5
     O    7507      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 26883
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "2"
      Number of atoms: 18716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 871, 18716
          Classifications: {'RNA': 871}
          Modifications used: {'rna2p_pur': 68, 'rna2p_pyr': 42, 'rna3p_pur': 438, 'rna3p_pyr': 323}
          Link IDs: {'rna2p': 110, 'rna3p': 760}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1626
          Classifications: {'peptide': 205}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 198}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "D"
      Number of atoms: 1145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1145
          Classifications: {'peptide': 156}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 150}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "E"
      Number of atoms: 805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 805
          Classifications: {'peptide': 100}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "G"
      Number of atoms: 969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 969
          Classifications: {'peptide': 129}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "K"
      Number of atoms: 945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 945
          Classifications: {'peptide': 122}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 114}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "N"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 716
          Classifications: {'peptide': 88}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 87}
    Chain: "O"
      Number of atoms: 649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 649
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 79}
    Chain: "P"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 648
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 2, 'TRANS': 77}
    Chain: "S"
      Number of atoms: 664
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 664
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 1, 'TRANS': 83}
  Time building chain proxies: 5.43, per 1000 atoms: 0.20
  Number of scatterers: 26883
  At special positions: 0
  Unit cell: (143.782, 187.775, 158.804, 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      33     16.00
     P     871     15.00
     O    7507      8.00
     N    5026      7.00
     C   13446      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: 2.03
  Conformation dependent library (CDL) restraints added in 482.7 milliseconds
  

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1940

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 12 sheets defined
      40.5% alpha, 17.4% beta
      298 base pairs and 466 stacking pairs defined.
    Time for finding SS restraints: 4.22
  Creating SS restraints...
    Processing helix  chain 'C' and resid 8 through 16
      removed outlier: 3.868A  pdb=" N   SER C  12 " --> pdb=" O   LYS C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 31
    Processing helix  chain 'C' and resid 49 through 66
    Processing helix  chain 'C' and resid 68 through 82
    Processing helix  chain 'C' and resid 86 through 96
    Processing helix  chain 'C' and resid 97 through 106
    Processing helix  chain 'C' and resid 110 through 120
    Processing helix  chain 'C' and resid 152 through 165
      removed outlier: 3.839A  pdb=" N   LYS C 156 " --> pdb=" O   GLN C 152 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 205
    Processing helix  chain 'D' and resid 55 through 68
    Processing helix  chain 'D' and resid 109 through 117
      removed outlier: 3.964A  pdb=" N   ALA D 113 " --> pdb=" O   GLY D 109 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   VAL D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 132 through 146
    Processing helix  chain 'D' and resid 149 through 158
    Processing helix  chain 'D' and resid 160 through 165
    Processing helix  chain 'E' and resid 12 through 16
      removed outlier: 5.295A  pdb=" N   GLU E  16 " --> pdb=" O   ASP E  13 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 17 through 32
      removed outlier: 3.501A  pdb=" N   GLU E  23 " --> pdb=" O   PRO E  19 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 67 through 80
      removed outlier: 3.924A  pdb=" N   GLU E  75 " --> pdb=" O   ILE E  71 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   PHE E  80 " --> pdb=" O   THR E  76 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 5 through 21
    Processing helix  chain 'G' and resid 30 through 42
    Processing helix  chain 'G' and resid 94 through 99
      removed outlier: 3.621A  pdb=" N   ALA G  97 " --> pdb=" O   LYS G  94 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 113 through 120
    Processing helix  chain 'K' and resid 3 through 9
    Processing helix  chain 'K' and resid 113 through 118
      removed outlier: 3.965A  pdb=" N   TYR K 117 " --> pdb=" O   ALA K 113 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 3 through 15
    Processing helix  chain 'N' and resid 23 through 43
      removed outlier: 3.699A  pdb=" N   ALA N  29 " --> pdb=" O   GLU N  25 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   GLY N  40 " --> pdb=" O   ASN N  36 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   HIS N  41 " --> pdb=" O   HIS N  37 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 51 through 73
      removed outlier: 3.597A  pdb=" N   LEU N  55 " --> pdb=" O   SER N  51 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 73 through 85
      removed outlier: 4.071A  pdb=" N   TYR N  77 " --> pdb=" O   ASP N  73 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   GLU N  82 " --> pdb=" O   THR N  78 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   ARG N  83 " --> pdb=" O   ARG N  79 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU N  84 " --> pdb=" O   LEU N  80 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 53 through 63
    Processing helix  chain 'O' and resid 68 through 82
      removed outlier: 3.517A  pdb=" N   ALA O  72 " --> pdb=" O   SER O  68 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 4 through 42
      removed outlier: 3.548A  pdb=" N   VAL S  35 " --> pdb=" O   PHE S  31 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLY S  42 " --> pdb=" O   ALA S  38 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 43 through 64
      removed outlier: 3.759A  pdb=" N   ALA S  47 " --> pdb=" O   ASP S  43 " (cutoff:3.500A)
      Proline residue:  S  56  - end of helix
    Processing helix  chain 'S' and resid 68 through 86
      removed outlier: 3.616A  pdb=" N   ALA S  72 " --> pdb=" O   HIS S  68 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LEU S  86 " --> pdb=" O   GLN S  82 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 128 through 129
      removed outlier: 3.884A  pdb=" N   GLY C 180 " --> pdb=" O   VAL C 143 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 12 through 19
      removed outlier: 3.889A  pdb=" N   LYS D  14 " --> pdb=" O   VAL D  38 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   VAL D  38 " --> pdb=" O   LYS D  14 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   LEU D  36 " --> pdb=" O   ILE D  16 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   VAL D  18 " --> pdb=" O   THR D  34 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   THR D  34 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 22 through 24
      removed outlier: 3.707A  pdb=" N   LYS D  23 " --> pdb=" O   ILE D  30 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ILE D  30 " --> pdb=" O   LYS D  23 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'D' and resid 85 through 88
    Processing sheet with id=AA5, first strand: chain 'E' and resid 40 through 45
      removed outlier: 5.464A  pdb=" N   ASP E  41 " --> pdb=" O   LEU E  61 " (cutoff:3.500A)
      removed outlier: 7.234A  pdb=" N   LEU E  61 " --> pdb=" O   ASP E  41 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLY E  43 " --> pdb=" O   TYR E  59 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA E  57 " --> pdb=" O   ARG E  45 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   HIS E  58 " --> pdb=" O   VAL E  10 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL E  10 " --> pdb=" O   HIS E  58 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   VAL E  60 " --> pdb=" O   PHE E   8 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   PHE E   8 " --> pdb=" O   VAL E  60 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   GLU E   5 " --> pdb=" O   VAL E  89 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   VAL E  89 " --> pdb=" O   GLU E   5 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL E   7 " --> pdb=" O   SER E  87 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   SER E  87 " --> pdb=" O   VAL E   7 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   MET E   9 " --> pdb=" O   ILE E  85 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 24 through 28
      removed outlier: 4.506A  pdb=" N   ASP G  48 " --> pdb=" O   THR G  62 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 65 through 66
      removed outlier: 3.547A  pdb=" N   PHE G  66 " --> pdb=" O   LYS G  69 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 74 through 77
      removed outlier: 3.598A  pdb=" N   GLN G  76 " --> pdb=" O   TYR G 128 " (cutoff:3.500A)
      removed outlier: 5.785A  pdb=" N   ILE G 125 " --> pdb=" O   SER G 105 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   SER G 105 " --> pdb=" O   ILE G 125 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   CYS G 127 " --> pdb=" O   VAL G 103 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   VAL G 104 " --> pdb=" O   MET G 111 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   MET G 111 " --> pdb=" O   VAL G 104 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'K' and resid 62 through 66
      removed outlier: 3.608A  pdb=" N   CYS K  53 " --> pdb=" O   SER K  65 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   ARG K  50 " --> pdb=" O   THR K  39 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   THR K  39 " --> pdb=" O   ARG K  50 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   VAL K  52 " --> pdb=" O   VAL K  37 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   VAL K  37 " --> pdb=" O   VAL K  52 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   ARG K  54 " --> pdb=" O   THR K  35 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS K  30 " --> pdb=" O   ILE K  82 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ILE K  82 " --> pdb=" O   LYS K  30 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'O' and resid 2 through 8
      removed outlier: 3.728A  pdb=" N   GLU O  34 " --> pdb=" O   VAL O  21 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'O' and resid 38 through 39
    Processing sheet with id=AB3, first strand: chain 'P' and resid 8 through 14
      removed outlier: 8.875A  pdb=" N   GLN P   9 " --> pdb=" O   GLU P  26 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   GLU P  26 " --> pdb=" O   GLN P   9 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   VAL P  22 " --> pdb=" O   VAL P  13 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   TRP P  73 " --> pdb=" O   HIS P  45 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   LEU P  75 " --> pdb=" O   HIS P  47 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   GLU P  60 " --> pdb=" O   VAL P  76 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   VAL P  78 " --> pdb=" O   VAL P  58 " (cutoff:3.500A)
      removed outlier: 7.702A  pdb=" N   VAL P  58 " --> pdb=" O   VAL P  78 " (cutoff:3.500A)

    359 hydrogen bonds defined for protein.
    1023 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      754 hydrogen bonds
      1214 hydrogen bond angles
      0 basepair planarities
      298 basepair parallelities
      466 stacking parallelities
  Total time for adding SS restraints: 7.85

  Time building geometry restraints manager: 2.79 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: 3950
        1.33 -     1.45: 12379
        1.45 -     1.57: 11112
        1.57 -     1.69: 1739
        1.69 -     1.81: 58
  Bond restraints: 29238
  Sorted by residual:
  bond pdb=" N1    U 2 287 "
       pdb=" C2    U 2 287 "
    ideal  model  delta    sigma   weight residual
    1.381  1.402 -0.021 2.00e-02 2.50e+03 1.11e+00
  bond pdb=" C2    C 2 613 "
       pdb=" O2    C 2 613 "
    ideal  model  delta    sigma   weight residual
    1.240  1.220  0.020 2.00e-02 2.50e+03 9.98e-01
  bond pdb=" CA  ARG C  47 "
       pdb=" CB  ARG C  47 "
    ideal  model  delta    sigma   weight residual
    1.524  1.537 -0.012 1.22e-02 6.72e+03 9.92e-01
  bond pdb=" C   VAL E  18 "
       pdb=" N   PRO E  19 "
    ideal  model  delta    sigma   weight residual
    1.335  1.347 -0.012 1.28e-02 6.10e+03 9.21e-01
  bond pdb=" N9    G 2 627 "
       pdb=" C4    G 2 627 "
    ideal  model  delta    sigma   weight residual
    1.375  1.393 -0.018 2.00e-02 2.50e+03 7.93e-01
  ... (remaining 29233 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 43253
        1.78 -     3.56: 494
        3.56 -     5.34: 44
        5.34 -     7.12: 13
        7.12 -     8.90: 4
  Bond angle restraints: 43808
  Sorted by residual:
  angle pdb=" C   GLU N  44 "
        pdb=" N   HIS N  45 "
        pdb=" CA  HIS N  45 "
      ideal   model   delta    sigma   weight residual
     121.54  127.57   -6.03 1.91e+00 2.74e-01 9.98e+00
  angle pdb=" C2'   G 2 628 "
        pdb=" C1'   G 2 628 "
        pdb=" N9    G 2 628 "
      ideal   model   delta    sigma   weight residual
     112.00  116.57   -4.57 1.50e+00 4.44e-01 9.30e+00
  angle pdb=" C1'   U 2 287 "
        pdb=" N1    U 2 287 "
        pdb=" C2    U 2 287 "
      ideal   model   delta    sigma   weight residual
     117.70  126.60   -8.90 3.00e+00 1.11e-01 8.79e+00
  angle pdb=" C   ALA K 101 "
        pdb=" N   LEU K 102 "
        pdb=" CA  LEU K 102 "
      ideal   model   delta    sigma   weight residual
     121.54  127.15   -5.61 1.91e+00 2.74e-01 8.63e+00
  angle pdb=" N   VAL O  36 "
        pdb=" CA  VAL O  36 "
        pdb=" C   VAL O  36 "
      ideal   model   delta    sigma   weight residual
     111.62  109.37    2.25 7.90e-01 1.60e+00 8.14e+00
  ... (remaining 43803 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.40: 16323
       35.40 -    70.79: 2167
       70.79 -   106.19: 249
      106.19 -   141.58: 5
      141.58 -   176.97: 6
  Dihedral angle restraints: 18750
    sinusoidal: 15746
      harmonic: 3004
  Sorted by residual:
  dihedral pdb=" O4'   U 2 439 "
           pdb=" C1'   U 2 439 "
           pdb=" N1    U 2 439 "
           pdb=" C2    U 2 439 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   40.35  159.65     1      1.50e+01 4.44e-03 8.27e+01
  dihedral pdb=" O4'   U 2   4 "
           pdb=" C1'   U 2   4 "
           pdb=" N1    U 2   4 "
           pdb=" C2    U 2   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   45.13  154.87     1      1.50e+01 4.44e-03 8.13e+01
  dihedral pdb=" O4'   U 2 365 "
           pdb=" C1'   U 2 365 "
           pdb=" N1    U 2 365 "
           pdb=" C2    U 2 365 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   62.24  137.76     1      1.50e+01 4.44e-03 7.43e+01
  ... (remaining 18747 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 5302
       0.060 -    0.120: 279
       0.120 -    0.179: 19
       0.179 -    0.239: 4
       0.239 -    0.299: 2
  Chirality restraints: 5606
  Sorted by residual:
  chirality pdb=" CB  ILE D 106 "
            pdb=" CA  ILE D 106 "
            pdb=" CG1 ILE D 106 "
            pdb=" CG2 ILE D 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" C1'   G 2 628 "
            pdb=" O4'   G 2 628 "
            pdb=" C2'   G 2 628 "
            pdb=" N9    G 2 628 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.16    0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" C1'   C 2 754 "
            pdb=" O4'   C 2 754 "
            pdb=" C2'   C 2 754 "
            pdb=" N1    C 2 754 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.26    0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 5603 not shown)

  Planarity restraints: 2307
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C 2 613 "   -0.010 2.00e-02 2.50e+03   2.05e-02 9.42e+00
        pdb=" N1    C 2 613 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    C 2 613 "    0.051 2.00e-02 2.50e+03
        pdb=" O2    C 2 613 "   -0.026 2.00e-02 2.50e+03
        pdb=" N3    C 2 613 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4    C 2 613 "    0.011 2.00e-02 2.50e+03
        pdb=" N4    C 2 613 "   -0.013 2.00e-02 2.50e+03
        pdb=" C5    C 2 613 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6    C 2 613 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G 2 628 "    0.035 2.00e-02 2.50e+03   1.48e-02 6.58e+00
        pdb=" N9    G 2 628 "   -0.032 2.00e-02 2.50e+03
        pdb=" C8    G 2 628 "   -0.012 2.00e-02 2.50e+03
        pdb=" N7    G 2 628 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    G 2 628 "    0.006 2.00e-02 2.50e+03
        pdb=" C6    G 2 628 "    0.006 2.00e-02 2.50e+03
        pdb=" O6    G 2 628 "    0.009 2.00e-02 2.50e+03
        pdb=" N1    G 2 628 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    G 2 628 "   -0.006 2.00e-02 2.50e+03
        pdb=" N2    G 2 628 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G 2 628 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    G 2 628 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A 2 629 "    0.030 2.00e-02 2.50e+03   1.44e-02 5.71e+00
        pdb=" N9    A 2 629 "   -0.035 2.00e-02 2.50e+03
        pdb=" C8    A 2 629 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    A 2 629 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    A 2 629 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A 2 629 "    0.006 2.00e-02 2.50e+03
        pdb=" N6    A 2 629 "    0.008 2.00e-02 2.50e+03
        pdb=" N1    A 2 629 "    0.000 2.00e-02 2.50e+03
        pdb=" C2    A 2 629 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3    A 2 629 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    A 2 629 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 2304 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.70: 1957
        2.70 -     3.25: 25511
        3.25 -     3.80: 54890
        3.80 -     4.35: 67062
        4.35 -     4.90: 89200
  Nonbonded interactions: 238620
  Sorted by model distance:
  nonbonded pdb=" O2    U 2  49 "
            pdb=" N2    G 2 361 "
     model   vdw
     2.156 3.120
  nonbonded pdb=" OP2   G 2  82 "
            pdb=" N2    G 2  82 "
     model   vdw
     2.162 3.120
  nonbonded pdb=" O4    U 2 652 "
            pdb=" O2'   G 2 752 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O2    U 2 835 "
            pdb=" O6    G 2 851 "
     model   vdw
     2.213 2.432
  nonbonded pdb=" O2'   C 2 136 "
            pdb=" O   GLY O  64 "
     model   vdw
     2.228 3.040
  ... (remaining 238615 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:             1.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.030
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.050
  Process input model:                     28.220
  Find NCS groups from input model:        0.100
  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:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  29238  Z= 0.106
  Angle     :  0.495   8.896  43808  Z= 0.265
  Chirality :  0.029   0.299   5606
  Planarity :  0.003   0.054   2307
  Dihedral  : 23.619 176.975  16810
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.29 %
    Favored  : 96.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.82 (0.23), residues: 1029
  helix: -0.94 (0.23), residues: 378
  sheet: -2.67 (0.35), residues: 166
  loop : -2.29 (0.25), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  47 
 TYR   0.005   0.001   TYR E   4 
 PHE   0.005   0.001   PHE P  28 
 TRP   0.005   0.001   TRP O  60 
 HIS   0.006   0.001   HIS E   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00186 (29238)
  covalent geometry    : angle       0.49483 (43808)
  hydrogen bonds       : bond        0.12140 ( 1113)
  hydrogen bonds       : angle       4.85911 ( 2237)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 272
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   54 GLN cc_start: 0.8947 (mt0) cc_final: 0.8742 (mt0)
REVERT: C   93 LEU cc_start: 0.9195 (mp) cc_final: 0.8717 (tp)
REVERT: C  124 MET cc_start: 0.8030 (mtp) cc_final: 0.7698 (mtm)
REVERT: D   20 ARG cc_start: 0.7837 (ttt-90) cc_final: 0.7402 (ttm-80)
REVERT: D   64 MET cc_start: 0.8918 (tmm) cc_final: 0.8689 (tmm)
REVERT: D   66 LYS cc_start: 0.7822 (ttmt) cc_final: 0.7347 (tmtt)
REVERT: D   71 MET cc_start: 0.7390 (mmp) cc_final: 0.5913 (mmp)
REVERT: D   82 GLN cc_start: 0.7433 (mm-40) cc_final: 0.6615 (mm-40)
REVERT: D   95 PHE cc_start: 0.8898 (t80) cc_final: 0.8687 (t80)
REVERT: D  132 ASN cc_start: 0.7613 (t0) cc_final: 0.7397 (t0)
REVERT: G  125 ILE cc_start: 0.8879 (mt) cc_final: 0.8629 (mt)
REVERT: N   14 PHE cc_start: 0.8525 (m-80) cc_final: 0.7748 (m-80)
REVERT: N   58 MET cc_start: 0.6012 (ptt) cc_final: 0.5785 (tmm)
REVERT: O   25 ARG cc_start: 0.9230 (mtm110) cc_final: 0.8952 (ptp90)
REVERT: O   63 GLN cc_start: 0.8751 (mm110) cc_final: 0.8226 (mm-40)
REVERT: O   80 LYS cc_start: 0.9399 (tmmt) cc_final: 0.8831 (ptpt)
REVERT: P   11 ARG cc_start: 0.8286 (mtp85) cc_final: 0.7956 (ttm-80)
REVERT: P   81 LYS cc_start: 0.9039 (ttpp) cc_final: 0.8777 (tptp)
REVERT: S   32 ILE cc_start: 0.9205 (pt) cc_final: 0.8983 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 273
  average time/residue: 0.2069
  time to fit residues: 85.2121
Evaluate side-chains
  200 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:   20.0000
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    9.9990
   overall best weight:    7.9990

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

Flipped N/Q/H residues before XYZ refinement:
D  73 ASN
E  52 ASN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  96 HIS
O  26 ASN
O  63 GLN
O  79 ASN
** P  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.055227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.041733 restraints weight = 192452.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.042918 restraints weight = 88002.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.042823 restraints weight = 42909.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.042870 restraints weight = 41748.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.042869 restraints weight = 39523.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.071  29238  Z= 0.398
  Angle     :  0.804   9.423  43808  Z= 0.401
  Chirality :  0.041   0.301   5606
  Planarity :  0.006   0.081   2307
  Dihedral  : 24.421 171.604  14772
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 21.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.66 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.14 (0.25), residues: 1029
  helix: -0.35 (0.24), residues: 386
  sheet: -2.26 (0.37), residues: 177
  loop : -1.93 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG N  71 
 TYR   0.022   0.002   TYR E  49 
 PHE   0.037   0.003   PHE N  42 
 TRP   0.008   0.002   TRP E  42 
 HIS   0.008   0.002   HIS S  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00760 (29238)
  covalent geometry    : angle       0.80441 (43808)
  hydrogen bonds       : bond        0.09381 ( 1113)
  hydrogen bonds       : angle       4.17296 ( 2237)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 215
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  124 MET cc_start: 0.8142 (mtp) cc_final: 0.7693 (mtm)
REVERT: C  202 GLU cc_start: 0.8898 (pt0) cc_final: 0.8514 (tp30)
REVERT: D   20 ARG cc_start: 0.7482 (ttt-90) cc_final: 0.7170 (ttm-80)
REVERT: D   82 GLN cc_start: 0.7361 (mm-40) cc_final: 0.6587 (mm-40)
REVERT: D   97 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8420 (pt0)
REVERT: D  132 ASN cc_start: 0.7597 (t0) cc_final: 0.7316 (t0)
REVERT: D  148 ASN cc_start: 0.8645 (m110) cc_final: 0.8418 (m-40)
REVERT: E    9 MET cc_start: 0.7619 (pmm) cc_final: 0.6929 (ppp)
REVERT: G   12 THR cc_start: 0.9474 (p) cc_final: 0.9223 (t)
REVERT: G   16 ASN cc_start: 0.9079 (m-40) cc_final: 0.8840 (m-40)
REVERT: K   75 GLN cc_start: 0.8655 (pp30) cc_final: 0.8361 (pp30)
REVERT: K   83 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7742 (pmt-80)
REVERT: N   25 GLU cc_start: 0.9469 (mp0) cc_final: 0.9138 (pm20)
REVERT: N   31 LEU cc_start: 0.8886 (mm) cc_final: 0.8607 (mm)
REVERT: N   62 ARG cc_start: 0.8512 (ttp-110) cc_final: 0.8212 (ttm-80)
REVERT: O   25 ARG cc_start: 0.9381 (mtm110) cc_final: 0.9074 (ptp90)
REVERT: O   63 GLN cc_start: 0.9295 (mm-40) cc_final: 0.8770 (mm-40)
REVERT: O   80 LYS cc_start: 0.9483 (tmmt) cc_final: 0.8960 (pttm)
REVERT: P   11 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7823 (ttm-80)
REVERT: P   26 GLU cc_start: 0.8824 (tt0) cc_final: 0.7104 (tt0)
REVERT: P   63 GLU cc_start: 0.8238 (tt0) cc_final: 0.7965 (mt-10)
  outliers start: 26
  outliers final: 18
  residues processed: 227
  average time/residue: 0.1907
  time to fit residues: 66.3166
Evaluate side-chains
  213 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 193
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue   97 GLN
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain G residue   46 ILE
Chi-restraints excluded: chain G residue   51 VAL
Chi-restraints excluded: chain G residue   72 VAL
Chi-restraints excluded: chain K residue   35 THR
Chi-restraints excluded: chain K residue   83 ARG
Chi-restraints excluded: chain K residue   89 ASP
Chi-restraints excluded: chain N residue   55 LEU
Chi-restraints excluded: chain O residue   19 VAL
Chi-restraints excluded: chain O residue   20 VAL
Chi-restraints excluded: chain P residue    5 ILE
Chi-restraints excluded: chain P residue   28 PHE
Chi-restraints excluded: chain P residue   48 ASP
Chi-restraints excluded: chain P residue   50 ASN
Chi-restraints excluded: chain P residue   57 ASP
Chi-restraints excluded: chain S residue   59 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 178 optimal weight:    3.9990
   chunk 148 optimal weight:    5.9990
   chunk 69 optimal weight:   20.0000
   chunk 55 optimal weight:    7.9990
   chunk 58 optimal weight:    8.9990
   chunk 121 optimal weight:    5.9990
   chunk 122 optimal weight:    6.9990
   chunk 41 optimal weight:   10.0000
   chunk 151 optimal weight:    6.9990
   chunk 157 optimal weight:    4.9990
   chunk 57 optimal weight:    9.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 136 GLN
C 140 ASN
** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  63 ASN
** P  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  55 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.055678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.042503 restraints weight = 191147.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.043722 restraints weight = 81949.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.043727 restraints weight = 38736.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.043798 restraints weight = 38723.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.043828 restraints weight = 35287.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  29238  Z= 0.287
  Angle     :  0.685  11.643  43808  Z= 0.346
  Chirality :  0.038   0.305   5606
  Planarity :  0.005   0.046   2307
  Dihedral  : 24.324 173.149  14772
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 16.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 22.42 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.78 (0.25), residues: 1029
  helix:  0.02 (0.25), residues: 382
  sheet: -2.19 (0.39), residues: 165
  loop : -1.77 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  47 
 TYR   0.014   0.002   TYR E  49 
 PHE   0.053   0.003   PHE N  42 
 TRP   0.004   0.001   TRP P  73 
 HIS   0.017   0.002   HIS C  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 (29238)
  covalent geometry    : angle       0.68541 (43808)
  hydrogen bonds       : bond        0.07659 ( 1113)
  hydrogen bonds       : angle       3.80694 ( 2237)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 207
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   47 ARG cc_start: 0.8923 (ttp80) cc_final: 0.8677 (ttp80)
REVERT: C   93 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9010 (tt)
REVERT: C  124 MET cc_start: 0.8037 (mtp) cc_final: 0.7668 (mtm)
REVERT: C  202 GLU cc_start: 0.8866 (pt0) cc_final: 0.8288 (tp30)
REVERT: D   14 LYS cc_start: 0.8794 (ptpp) cc_final: 0.8487 (ptpp)
REVERT: D   20 ARG cc_start: 0.7532 (ttt-90) cc_final: 0.7327 (ttm-80)
REVERT: D   33 PHE cc_start: 0.7542 (m-80) cc_final: 0.7338 (m-10)
REVERT: D   82 GLN cc_start: 0.7250 (mm-40) cc_final: 0.6917 (mm-40)
REVERT: D   97 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8475 (pt0)
REVERT: D  122 ASN cc_start: 0.7521 (m110) cc_final: 0.7121 (t0)
REVERT: D  132 ASN cc_start: 0.7684 (t0) cc_final: 0.7013 (t0)
REVERT: D  152 MET cc_start: 0.8709 (tmm) cc_final: 0.8326 (tmm)
REVERT: E    9 MET cc_start: 0.7575 (pmm) cc_final: 0.7055 (ppp)
REVERT: E   55 HIS cc_start: 0.8540 (p90) cc_final: 0.8330 (p90)
REVERT: E   90 MET cc_start: 0.7864 (mmm) cc_final: 0.6477 (ttm)
REVERT: G   12 THR cc_start: 0.9409 (p) cc_final: 0.9176 (t)
REVERT: G   16 ASN cc_start: 0.9196 (m-40) cc_final: 0.8912 (m-40)
REVERT: K   75 GLN cc_start: 0.8670 (pp30) cc_final: 0.8409 (pp30)
REVERT: K   83 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7724 (pmt-80)
REVERT: N   25 GLU cc_start: 0.9498 (mp0) cc_final: 0.9173 (pm20)
REVERT: O   25 ARG cc_start: 0.9365 (mtm110) cc_final: 0.9065 (ptp90)
REVERT: O   63 GLN cc_start: 0.9332 (mm-40) cc_final: 0.8512 (mm-40)
REVERT: O   80 LYS cc_start: 0.9513 (tmmt) cc_final: 0.8915 (ptpt)
REVERT: P   11 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7827 (ttm-80)
REVERT: P   26 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7822 (tt0)
REVERT: P   27 ARG cc_start: 0.8218 (tpt-90) cc_final: 0.7900 (tpt90)
REVERT: P   39 LYS cc_start: 0.8981 (ptpt) cc_final: 0.8132 (ptpt)
  outliers start: 38
  outliers final: 22
  residues processed: 227
  average time/residue: 0.1862
  time to fit residues: 64.8364
Evaluate side-chains
  217 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 191
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  140 ASN
Chi-restraints excluded: chain C residue  141 ASP
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue   88 VAL
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain D residue   97 GLN
Chi-restraints excluded: chain G residue   46 ILE
Chi-restraints excluded: chain G residue   51 VAL
Chi-restraints excluded: chain K residue   57 LEU
Chi-restraints excluded: chain K residue   83 ARG
Chi-restraints excluded: chain K residue   87 VAL
Chi-restraints excluded: chain K residue   89 ASP
Chi-restraints excluded: chain K residue   90 LEU
Chi-restraints excluded: chain K residue   98 VAL
Chi-restraints excluded: chain N residue   55 LEU
Chi-restraints excluded: chain N residue   80 LEU
Chi-restraints excluded: chain O residue   19 VAL
Chi-restraints excluded: chain O residue   20 VAL
Chi-restraints excluded: chain O residue   21 VAL
Chi-restraints excluded: chain P residue    5 ILE
Chi-restraints excluded: chain P residue   26 GLU
Chi-restraints excluded: chain P residue   28 PHE
Chi-restraints excluded: chain P residue   48 ASP
Chi-restraints excluded: chain P residue   57 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 121 optimal weight:    2.9990
   chunk 165 optimal weight:    0.3980
   chunk 131 optimal weight:    5.9990
   chunk 148 optimal weight:    6.9990
   chunk 56 optimal weight:   10.0000
   chunk 142 optimal weight:    5.9990
   chunk 153 optimal weight:    3.9990
   chunk 101 optimal weight:    5.9990
   chunk 98 optimal weight:    4.9990
   chunk 85 optimal weight:   10.0000
   chunk 113 optimal weight:    0.8980
   overall best weight:    2.6586

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

Flipped N/Q/H residues before XYZ refinement:
** C  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  46 GLN
** P  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.056788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.043676 restraints weight = 185546.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.045070 restraints weight = 79812.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.044998 restraints weight = 36648.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.045022 restraints weight = 36499.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.045115 restraints weight = 33367.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  29238  Z= 0.166
  Angle     :  0.605  11.065  43808  Z= 0.306
  Chirality :  0.034   0.293   5606
  Planarity :  0.004   0.033   2307
  Dihedral  : 24.208 173.127  14772
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 23.47 %
    Favored  : 72.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.43 (0.26), residues: 1029
  helix:  0.28 (0.25), residues: 392
  sheet: -1.98 (0.39), residues: 160
  loop : -1.59 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG N  62 
 TYR   0.010   0.001   TYR G 128 
 PHE   0.038   0.002   PHE N  42 
 TRP   0.007   0.001   TRP P  73 
 HIS   0.016   0.001   HIS E   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (29238)
  covalent geometry    : angle       0.60544 (43808)
  hydrogen bonds       : bond        0.06556 ( 1113)
  hydrogen bonds       : angle       3.50906 ( 2237)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 216
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 GLN cc_start: 0.8373 (tp40) cc_final: 0.7891 (tp40)
REVERT: C   47 ARG cc_start: 0.8845 (ttp80) cc_final: 0.8556 (ttp80)
REVERT: C  124 MET cc_start: 0.7943 (mtp) cc_final: 0.7728 (mtm)
REVERT: D   14 LYS cc_start: 0.8747 (ptpp) cc_final: 0.8428 (ptpp)
REVERT: D   20 ARG cc_start: 0.7507 (ttt-90) cc_final: 0.7270 (ttm-80)
REVERT: D   33 PHE cc_start: 0.7380 (m-80) cc_final: 0.7141 (m-10)
REVERT: D   82 GLN cc_start: 0.7244 (mm-40) cc_final: 0.7015 (mm-40)
REVERT: D   88 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8224 (m)
REVERT: D  122 ASN cc_start: 0.7769 (m110) cc_final: 0.7260 (t0)
REVERT: D  152 MET cc_start: 0.8605 (tmm) cc_final: 0.8400 (tmm)
REVERT: E    9 MET cc_start: 0.7654 (pmm) cc_final: 0.7151 (ppp)
REVERT: E   55 HIS cc_start: 0.8745 (p90) cc_final: 0.8502 (p90)
REVERT: E   90 MET cc_start: 0.7888 (mmm) cc_final: 0.6793 (mtt)
REVERT: G   12 THR cc_start: 0.9354 (p) cc_final: 0.9086 (t)
REVERT: G   16 ASN cc_start: 0.9030 (m-40) cc_final: 0.8689 (m-40)
REVERT: K   75 GLN cc_start: 0.8642 (pp30) cc_final: 0.8355 (pp30)
REVERT: K   83 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7645 (pmt-80)
REVERT: N   25 GLU cc_start: 0.9509 (mp0) cc_final: 0.9151 (pm20)
REVERT: N   58 MET cc_start: 0.4988 (ptt) cc_final: 0.4508 (ttp)
REVERT: O   25 ARG cc_start: 0.9268 (mtm110) cc_final: 0.8962 (ptp90)
REVERT: O   63 GLN cc_start: 0.9260 (mm-40) cc_final: 0.8851 (mm-40)
REVERT: O   75 ILE cc_start: 0.9680 (pp) cc_final: 0.9459 (pp)
REVERT: O   80 LYS cc_start: 0.9504 (tmmt) cc_final: 0.8895 (ptpt)
REVERT: P   11 ARG cc_start: 0.8288 (mtp85) cc_final: 0.8032 (ttm-80)
REVERT: P   27 ARG cc_start: 0.8273 (tpt-90) cc_final: 0.7960 (tpt90)
  outliers start: 32
  outliers final: 18
  residues processed: 235
  average time/residue: 0.1795
  time to fit residues: 64.8853
Evaluate side-chains
  210 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 190
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain C residue  141 ASP
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue   88 VAL
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain G residue   51 VAL
Chi-restraints excluded: chain G residue   72 VAL
Chi-restraints excluded: chain K residue   27 CYS
Chi-restraints excluded: chain K residue   83 ARG
Chi-restraints excluded: chain K residue   89 ASP
Chi-restraints excluded: chain K residue   90 LEU
Chi-restraints excluded: chain K residue   98 VAL
Chi-restraints excluded: chain N residue   55 LEU
Chi-restraints excluded: chain N residue   80 LEU
Chi-restraints excluded: chain O residue   20 VAL
Chi-restraints excluded: chain O residue   21 VAL
Chi-restraints excluded: chain P residue   28 PHE
Chi-restraints excluded: chain P residue   63 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 119 optimal weight:   10.0000
   chunk 156 optimal weight:    6.9990
   chunk 160 optimal weight:    7.9990
   chunk 155 optimal weight:    2.9990
   chunk 126 optimal weight:    5.9990
   chunk 51 optimal weight:   10.0000
   chunk 59 optimal weight:   10.0000
   chunk 178 optimal weight:    0.4980
   chunk 9 optimal weight:   10.0000
   chunk 174 optimal weight:    5.9990
   chunk 103 optimal weight:   20.0000
   overall best weight:    4.4988

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

Flipped N/Q/H residues before XYZ refinement:
** C  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 140 ASN
** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  61 GLN
** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  46 GLN
** P  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  52 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.056091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.042923 restraints weight = 185629.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.044297 restraints weight = 80840.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.044215 restraints weight = 37334.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.044247 restraints weight = 36473.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.044316 restraints weight = 33804.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  29238  Z= 0.236
  Angle     :  0.648  10.980  43808  Z= 0.326
  Chirality :  0.036   0.285   5606
  Planarity :  0.005   0.052   2307
  Dihedral  : 24.202 173.174  14772
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 25.12 %
    Favored  : 71.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.42 (0.26), residues: 1029
  helix:  0.19 (0.26), residues: 384
  sheet: -1.99 (0.39), residues: 161
  loop : -1.45 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 138 
 TYR   0.011   0.002   TYR D  50 
 PHE   0.031   0.002   PHE N  42 
 TRP   0.007   0.001   TRP P  73 
 HIS   0.005   0.001   HIS C  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 (29238)
  covalent geometry    : angle       0.64777 (43808)
  hydrogen bonds       : bond        0.07060 ( 1113)
  hydrogen bonds       : angle       3.56311 ( 2237)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 202
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 GLN cc_start: 0.8401 (tp40) cc_final: 0.7899 (tp40)
REVERT: C   47 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8645 (ttp80)
REVERT: C  202 GLU cc_start: 0.8846 (pt0) cc_final: 0.8447 (tp30)
REVERT: D   33 PHE cc_start: 0.7466 (m-80) cc_final: 0.7210 (m-10)
REVERT: D   45 ARG cc_start: 0.7343 (mmm160) cc_final: 0.6999 (ttp80)
REVERT: D   88 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8199 (t)
REVERT: D  122 ASN cc_start: 0.7670 (m110) cc_final: 0.7203 (t0)
REVERT: E    9 MET cc_start: 0.7658 (pmm) cc_final: 0.7178 (ppp)
REVERT: E   55 HIS cc_start: 0.8772 (p90) cc_final: 0.8470 (p90)
REVERT: E   90 MET cc_start: 0.7862 (mmm) cc_final: 0.6769 (mtt)
REVERT: G   12 THR cc_start: 0.9388 (p) cc_final: 0.9102 (t)
REVERT: G   16 ASN cc_start: 0.9082 (m-40) cc_final: 0.8727 (m-40)
REVERT: K   75 GLN cc_start: 0.8661 (pp30) cc_final: 0.8370 (pp30)
REVERT: K   83 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7765 (pmt-80)
REVERT: N   25 GLU cc_start: 0.9456 (mp0) cc_final: 0.9140 (pm20)
REVERT: N   31 LEU cc_start: 0.8951 (mp) cc_final: 0.8282 (tp)
REVERT: O   25 ARG cc_start: 0.9305 (mtm110) cc_final: 0.9015 (ptp90)
REVERT: O   63 GLN cc_start: 0.9303 (mm-40) cc_final: 0.8751 (mm-40)
REVERT: O   80 LYS cc_start: 0.9523 (tmmt) cc_final: 0.8916 (ptpt)
REVERT: P   11 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7796 (ttm-80)
  outliers start: 32
  outliers final: 27
  residues processed: 224
  average time/residue: 0.1800
  time to fit residues: 61.9712
Evaluate side-chains
  219 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 190
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  140 ASN
Chi-restraints excluded: chain C residue  141 ASP
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue   88 VAL
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain G residue   11 LEU
Chi-restraints excluded: chain G residue   51 VAL
Chi-restraints excluded: chain G residue   72 VAL
Chi-restraints excluded: chain K residue   27 CYS
Chi-restraints excluded: chain K residue   35 THR
Chi-restraints excluded: chain K residue   83 ARG
Chi-restraints excluded: chain K residue   87 VAL
Chi-restraints excluded: chain K residue   89 ASP
Chi-restraints excluded: chain K residue   90 LEU
Chi-restraints excluded: chain K residue   98 VAL
Chi-restraints excluded: chain N residue   55 LEU
Chi-restraints excluded: chain N residue   80 LEU
Chi-restraints excluded: chain O residue   19 VAL
Chi-restraints excluded: chain O residue   20 VAL
Chi-restraints excluded: chain O residue   21 VAL
Chi-restraints excluded: chain P residue    5 ILE
Chi-restraints excluded: chain P residue   28 PHE
Chi-restraints excluded: chain P residue   48 ASP
Chi-restraints excluded: chain P residue   57 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 10 optimal weight:    8.9990
   chunk 100 optimal weight:    5.9990
   chunk 185 optimal weight:    0.9980
   chunk 14 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 143 optimal weight:    6.9990
   chunk 105 optimal weight:    9.9990
   chunk 119 optimal weight:   10.0000
   chunk 46 optimal weight:   10.0000
   chunk 59 optimal weight:   10.0000
   overall best weight:    6.5988

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

Flipped N/Q/H residues before XYZ refinement:
** C  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 140 ASN
** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  61 GLN
D  97 GLN
** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.055116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.041968 restraints weight = 190049.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.043307 restraints weight = 83117.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.043249 restraints weight = 38478.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.043246 restraints weight = 37632.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.043315 restraints weight = 35165.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  29238  Z= 0.335
  Angle     :  0.732  10.865  43808  Z= 0.368
  Chirality :  0.039   0.287   5606
  Planarity :  0.005   0.052   2307
  Dihedral  : 24.270 172.517  14772
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 18.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 26.41 %
    Favored  : 68.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.60 (0.25), residues: 1029
  helix:  0.01 (0.25), residues: 385
  sheet: -2.07 (0.39), residues: 164
  loop : -1.52 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  20 
 TYR   0.011   0.002   TYR D  50 
 PHE   0.016   0.002   PHE E  80 
 TRP   0.020   0.003   TRP P  73 
 HIS   0.008   0.001   HIS N  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00640 (29238)
  covalent geometry    : angle       0.73231 (43808)
  hydrogen bonds       : bond        0.08198 ( 1113)
  hydrogen bonds       : angle       3.76941 ( 2237)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 200
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 GLN cc_start: 0.8417 (tp40) cc_final: 0.7910 (tp40)
REVERT: C   47 ARG cc_start: 0.8835 (ttp80) cc_final: 0.8575 (ttp80)
REVERT: C  202 GLU cc_start: 0.8829 (pt0) cc_final: 0.8480 (tp30)
REVERT: D   33 PHE cc_start: 0.7612 (m-80) cc_final: 0.7098 (m-10)
REVERT: D  122 ASN cc_start: 0.7534 (m110) cc_final: 0.7107 (t0)
REVERT: D  135 ASN cc_start: 0.8620 (m-40) cc_final: 0.8365 (m110)
REVERT: D  151 GLU cc_start: 0.9233 (pm20) cc_final: 0.9010 (pm20)
REVERT: E    1 MET cc_start: 0.4902 (OUTLIER) cc_final: 0.3954 (mmp)
REVERT: E    9 MET cc_start: 0.7527 (pmm) cc_final: 0.7098 (ppp)
REVERT: E   55 HIS cc_start: 0.8675 (p90) cc_final: 0.8399 (p90)
REVERT: E   90 MET cc_start: 0.7855 (mmm) cc_final: 0.6730 (mtt)
REVERT: G   12 THR cc_start: 0.9400 (p) cc_final: 0.9117 (t)
REVERT: G   16 ASN cc_start: 0.9207 (m-40) cc_final: 0.8807 (m110)
REVERT: K   75 GLN cc_start: 0.8709 (pp30) cc_final: 0.8423 (pp30)
REVERT: K   83 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7838 (pmt-80)
REVERT: N   25 GLU cc_start: 0.9474 (mp0) cc_final: 0.9201 (pm20)
REVERT: N   62 ARG cc_start: 0.8101 (ttm110) cc_final: 0.7705 (ttm110)
REVERT: O   25 ARG cc_start: 0.9341 (mtm110) cc_final: 0.9045 (ptp90)
REVERT: O   63 GLN cc_start: 0.9330 (mm-40) cc_final: 0.8608 (mm-40)
REVERT: O   80 LYS cc_start: 0.9508 (tmmt) cc_final: 0.8895 (ptpt)
REVERT: P   11 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7832 (ttm-80)
  outliers start: 41
  outliers final: 31
  residues processed: 229
  average time/residue: 0.1940
  time to fit residues: 68.2114
Evaluate side-chains
  222 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 189
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  141 ASP
Chi-restraints excluded: chain C residue  178 MET
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue   88 VAL
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain E residue    1 MET
Chi-restraints excluded: chain G residue   11 LEU
Chi-restraints excluded: chain G residue   51 VAL
Chi-restraints excluded: chain G residue   72 VAL
Chi-restraints excluded: chain K residue   27 CYS
Chi-restraints excluded: chain K residue   35 THR
Chi-restraints excluded: chain K residue   52 VAL
Chi-restraints excluded: chain K residue   83 ARG
Chi-restraints excluded: chain K residue   87 VAL
Chi-restraints excluded: chain K residue   89 ASP
Chi-restraints excluded: chain K residue   90 LEU
Chi-restraints excluded: chain K residue   98 VAL
Chi-restraints excluded: chain N residue   55 LEU
Chi-restraints excluded: chain O residue   19 VAL
Chi-restraints excluded: chain O residue   20 VAL
Chi-restraints excluded: chain O residue   21 VAL
Chi-restraints excluded: chain P residue    5 ILE
Chi-restraints excluded: chain P residue   48 ASP
Chi-restraints excluded: chain P residue   57 ASP
Chi-restraints excluded: chain P residue   80 GLU
Chi-restraints excluded: chain S residue   39 ILE
Chi-restraints excluded: chain S residue   58 VAL
Chi-restraints excluded: chain S residue   59 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 176 optimal weight:    4.9990
   chunk 35 optimal weight:    8.9990
   chunk 174 optimal weight:    0.0770
   chunk 169 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 117 optimal weight:    6.9990
   chunk 109 optimal weight:   30.0000
   chunk 185 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    4.2146

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

Flipped N/Q/H residues before XYZ refinement:
C  36 GLN
** C  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 140 ASN
** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  52 ASN
** P  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.055923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.042828 restraints weight = 188605.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.044166 restraints weight = 84018.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.044092 restraints weight = 39141.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.044083 restraints weight = 39139.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.044154 restraints weight = 35911.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.3393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  29238  Z= 0.225
  Angle     :  0.658  13.242  43808  Z= 0.332
  Chirality :  0.036   0.285   5606
  Planarity :  0.004   0.033   2307
  Dihedral  : 24.218 172.139  14772
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 27.82 %
    Favored  : 67.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.41 (0.26), residues: 1029
  helix:  0.20 (0.26), residues: 393
  sheet: -2.00 (0.38), residues: 166
  loop : -1.45 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  20 
 TYR   0.011   0.001   TYR D  50 
 PHE   0.021   0.002   PHE D  95 
 TRP   0.014   0.002   TRP P  73 
 HIS   0.009   0.001   HIS N  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (29238)
  covalent geometry    : angle       0.65833 (43808)
  hydrogen bonds       : bond        0.07144 ( 1113)
  hydrogen bonds       : angle       3.62392 ( 2237)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 198
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 GLN cc_start: 0.8364 (tp-100) cc_final: 0.8014 (tp40)
REVERT: C   47 ARG cc_start: 0.8814 (ttp80) cc_final: 0.8554 (ttp80)
REVERT: C  141 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8591 (m-30)
REVERT: C  202 GLU cc_start: 0.8765 (pt0) cc_final: 0.8462 (tp30)
REVERT: D   33 PHE cc_start: 0.7536 (m-80) cc_final: 0.7109 (m-10)
REVERT: D   88 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8217 (m)
REVERT: D  135 ASN cc_start: 0.8719 (m-40) cc_final: 0.8430 (m110)
REVERT: E    9 MET cc_start: 0.7611 (pmm) cc_final: 0.7162 (ppp)
REVERT: E   55 HIS cc_start: 0.8685 (p90) cc_final: 0.8460 (p90)
REVERT: E   75 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7196 (pm20)
REVERT: E   90 MET cc_start: 0.7883 (mmm) cc_final: 0.6877 (mtt)
REVERT: G   12 THR cc_start: 0.9361 (p) cc_final: 0.9051 (t)
REVERT: G   16 ASN cc_start: 0.9021 (m-40) cc_final: 0.8638 (m-40)
REVERT: G   27 MET cc_start: 0.8989 (ptp) cc_final: 0.8761 (pmm)
REVERT: G   48 ASP cc_start: 0.8937 (t0) cc_final: 0.8661 (p0)
REVERT: K    5 ASN cc_start: 0.8436 (t0) cc_final: 0.7999 (t0)
REVERT: K   75 GLN cc_start: 0.8703 (pp30) cc_final: 0.8435 (pp30)
REVERT: K   83 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7810 (pmt-80)
REVERT: K  112 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8713 (pm20)
REVERT: N   25 GLU cc_start: 0.9474 (mp0) cc_final: 0.9169 (pm20)
REVERT: O    1 MET cc_start: 0.8373 (pmm) cc_final: 0.7864 (pmm)
REVERT: O   25 ARG cc_start: 0.9287 (mtm110) cc_final: 0.9010 (ptp90)
REVERT: O   63 GLN cc_start: 0.9311 (mm-40) cc_final: 0.8645 (mm-40)
REVERT: O   80 LYS cc_start: 0.9512 (tmmt) cc_final: 0.8852 (ptpp)
REVERT: P   11 ARG cc_start: 0.8272 (mtp85) cc_final: 0.7837 (ttm-80)
REVERT: P   67 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8592 (mm)
  outliers start: 37
  outliers final: 26
  residues processed: 225
  average time/residue: 0.1887
  time to fit residues: 65.8186
Evaluate side-chains
  220 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 188
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  140 ASN
Chi-restraints excluded: chain C residue  141 ASP
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue   88 VAL
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain G residue   11 LEU
Chi-restraints excluded: chain G residue   51 VAL
Chi-restraints excluded: chain G residue   72 VAL
Chi-restraints excluded: chain K residue   27 CYS
Chi-restraints excluded: chain K residue   35 THR
Chi-restraints excluded: chain K residue   83 ARG
Chi-restraints excluded: chain K residue   87 VAL
Chi-restraints excluded: chain K residue   89 ASP
Chi-restraints excluded: chain K residue   90 LEU
Chi-restraints excluded: chain K residue   98 VAL
Chi-restraints excluded: chain K residue  105 SER
Chi-restraints excluded: chain K residue  112 GLN
Chi-restraints excluded: chain N residue   55 LEU
Chi-restraints excluded: chain O residue   19 VAL
Chi-restraints excluded: chain O residue   20 VAL
Chi-restraints excluded: chain O residue   21 VAL
Chi-restraints excluded: chain O residue   78 VAL
Chi-restraints excluded: chain P residue   57 ASP
Chi-restraints excluded: chain P residue   67 LEU
Chi-restraints excluded: chain S residue   39 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 10 optimal weight:    8.9990
   chunk 105 optimal weight:    0.4980
   chunk 49 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 140 optimal weight:    4.9990
   chunk 59 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 160 optimal weight:    5.9990
   chunk 136 optimal weight:    5.9990
   chunk 154 optimal weight:    8.9990
   overall best weight:    5.2988

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

Flipped N/Q/H residues before XYZ refinement:
** C  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  45 HIS
** P  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.055571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.042489 restraints weight = 188540.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.043861 restraints weight = 81432.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.043813 restraints weight = 37225.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.043807 restraints weight = 37190.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.043904 restraints weight = 34187.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.3474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  29238  Z= 0.271
  Angle     :  0.694  14.949  43808  Z= 0.348
  Chirality :  0.037   0.285   5606
  Planarity :  0.005   0.039   2307
  Dihedral  : 24.224 172.119  14772
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 16.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 28.76 %
    Favored  : 67.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.44 (0.26), residues: 1029
  helix:  0.14 (0.26), residues: 393
  sheet: -1.85 (0.38), residues: 173
  loop : -1.48 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  20 
 TYR   0.014   0.002   TYR G 128 
 PHE   0.018   0.002   PHE E  80 
 TRP   0.013   0.002   TRP P  73 
 HIS   0.009   0.001   HIS N  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 (29238)
  covalent geometry    : angle       0.69391 (43808)
  hydrogen bonds       : bond        0.07475 ( 1113)
  hydrogen bonds       : angle       3.70361 ( 2237)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 191
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 GLN cc_start: 0.8392 (tp-100) cc_final: 0.8087 (tp40)
REVERT: C   47 ARG cc_start: 0.8815 (ttp80) cc_final: 0.8560 (ttp80)
REVERT: C  202 GLU cc_start: 0.8765 (pt0) cc_final: 0.8483 (tp30)
REVERT: D   33 PHE cc_start: 0.7489 (m-80) cc_final: 0.7085 (m-10)
REVERT: D   88 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8263 (t)
REVERT: D  135 ASN cc_start: 0.8747 (m-40) cc_final: 0.8438 (m110)
REVERT: E    9 MET cc_start: 0.7615 (pmm) cc_final: 0.7185 (ppp)
REVERT: E   55 HIS cc_start: 0.8654 (p90) cc_final: 0.8422 (p90)
REVERT: E   75 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7220 (pm20)
REVERT: E   91 ARG cc_start: 0.6981 (mtp180) cc_final: 0.6411 (mtm-85)
REVERT: G   12 THR cc_start: 0.9357 (p) cc_final: 0.9048 (t)
REVERT: G   16 ASN cc_start: 0.9071 (m-40) cc_final: 0.8618 (m110)
REVERT: G   27 MET cc_start: 0.8952 (ptp) cc_final: 0.8693 (pmm)
REVERT: G   48 ASP cc_start: 0.8929 (t0) cc_final: 0.8664 (p0)
REVERT: K    5 ASN cc_start: 0.8499 (t0) cc_final: 0.8056 (t0)
REVERT: K   75 GLN cc_start: 0.8708 (pp30) cc_final: 0.8441 (pp30)
REVERT: K   83 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7850 (pmt-80)
REVERT: N   25 GLU cc_start: 0.9471 (mp0) cc_final: 0.9164 (pm20)
REVERT: O    1 MET cc_start: 0.8314 (pmm) cc_final: 0.7852 (pmm)
REVERT: O   63 GLN cc_start: 0.9303 (mm-40) cc_final: 0.8623 (mm-40)
REVERT: P   11 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7803 (ttm-80)
REVERT: P   67 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8591 (mm)
  outliers start: 34
  outliers final: 29
  residues processed: 218
  average time/residue: 0.1774
  time to fit residues: 60.5116
Evaluate side-chains
  221 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 188
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  124 MET
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue   81 LEU
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue   88 VAL
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain G residue   11 LEU
Chi-restraints excluded: chain G residue   51 VAL
Chi-restraints excluded: chain G residue   72 VAL
Chi-restraints excluded: chain G residue  125 ILE
Chi-restraints excluded: chain K residue   27 CYS
Chi-restraints excluded: chain K residue   35 THR
Chi-restraints excluded: chain K residue   52 VAL
Chi-restraints excluded: chain K residue   83 ARG
Chi-restraints excluded: chain K residue   87 VAL
Chi-restraints excluded: chain K residue   89 ASP
Chi-restraints excluded: chain K residue   90 LEU
Chi-restraints excluded: chain K residue   98 VAL
Chi-restraints excluded: chain N residue   55 LEU
Chi-restraints excluded: chain O residue   19 VAL
Chi-restraints excluded: chain O residue   20 VAL
Chi-restraints excluded: chain O residue   21 VAL
Chi-restraints excluded: chain P residue    5 ILE
Chi-restraints excluded: chain P residue   57 ASP
Chi-restraints excluded: chain P residue   63 GLU
Chi-restraints excluded: chain P residue   67 LEU
Chi-restraints excluded: chain S residue   39 ILE
Chi-restraints excluded: chain S residue   58 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 161 optimal weight:    8.9990
   chunk 179 optimal weight:    0.4980
   chunk 92 optimal weight:    4.9990
   chunk 163 optimal weight:    5.9990
   chunk 39 optimal weight:    8.9990
   chunk 138 optimal weight:    0.0050
   chunk 137 optimal weight:    0.6980
   chunk 10 optimal weight:    7.9990
   chunk 183 optimal weight:    8.9990
   chunk 162 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    2.4398

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

Flipped N/Q/H residues before XYZ refinement:
** C  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  51 ASN ** 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 = 0.3451 r_free = 0.3451 target = 0.059944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.047680 restraints weight = 207382.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.048907 restraints weight = 93597.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.048878 restraints weight = 44904.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.048724 restraints weight = 41532.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.048883 restraints weight = 40103.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  29238  Z= 0.153
  Angle     :  0.618  11.854  43808  Z= 0.311
  Chirality :  0.034   0.281   5606
  Planarity :  0.004   0.032   2307
  Dihedral  : 24.082 172.432  14772
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 29.69 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.18 (0.26), residues: 1029
  helix:  0.33 (0.26), residues: 392
  sheet: -1.67 (0.38), residues: 165
  loop : -1.34 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  20 
 TYR   0.010   0.001   TYR D  50 
 PHE   0.033   0.002   PHE D  95 
 TRP   0.009   0.002   TRP P  73 
 HIS   0.006   0.001   HIS N  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (29238)
  covalent geometry    : angle       0.61757 (43808)
  hydrogen bonds       : bond        0.06340 ( 1113)
  hydrogen bonds       : angle       3.55889 ( 2237)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 199
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 GLN cc_start: 0.8408 (tp-100) cc_final: 0.8108 (tp40)
REVERT: C   47 ARG cc_start: 0.8740 (ttp80) cc_final: 0.8480 (ttp80)
REVERT: C  202 GLU cc_start: 0.8675 (pt0) cc_final: 0.8402 (tp30)
REVERT: D   22 SER cc_start: 0.8189 (OUTLIER) cc_final: 0.7297 (t)
REVERT: D   33 PHE cc_start: 0.7340 (m-80) cc_final: 0.6998 (m-10)
REVERT: D   88 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8253 (m)
REVERT: E    9 MET cc_start: 0.7783 (pmm) cc_final: 0.7196 (ppp)
REVERT: E   75 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7176 (pm20)
REVERT: E   91 ARG cc_start: 0.6781 (mtp180) cc_final: 0.6372 (mtm-85)
REVERT: G   12 THR cc_start: 0.9350 (p) cc_final: 0.9053 (t)
REVERT: G   16 ASN cc_start: 0.8908 (m-40) cc_final: 0.8440 (m110)
REVERT: G   27 MET cc_start: 0.9060 (ptp) cc_final: 0.8781 (pmm)
REVERT: K    5 ASN cc_start: 0.8452 (t0) cc_final: 0.7996 (t0)
REVERT: K   75 GLN cc_start: 0.8722 (pp30) cc_final: 0.8500 (pp30)
REVERT: K   83 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7726 (pmt-80)
REVERT: K  112 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8792 (pm20)
REVERT: N   25 GLU cc_start: 0.9471 (mp0) cc_final: 0.9052 (pm20)
REVERT: O   25 ARG cc_start: 0.9231 (mtm110) cc_final: 0.8929 (ptp90)
REVERT: O   55 ASP cc_start: 0.8607 (p0) cc_final: 0.8182 (p0)
REVERT: O   63 GLN cc_start: 0.9215 (mm-40) cc_final: 0.8916 (mm-40)
REVERT: O   80 LYS cc_start: 0.9276 (ptmm) cc_final: 0.8572 (pttm)
REVERT: P   11 ARG cc_start: 0.8298 (mtp85) cc_final: 0.8043 (ttm-80)
REVERT: P   39 LYS cc_start: 0.9282 (tttt) cc_final: 0.9031 (tptm)
REVERT: P   67 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8583 (mm)
  outliers start: 31
  outliers final: 20
  residues processed: 222
  average time/residue: 0.1943
  time to fit residues: 67.2283
Evaluate side-chains
  214 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 188
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  124 MET
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue   88 VAL
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain G residue   72 VAL
Chi-restraints excluded: chain K residue   27 CYS
Chi-restraints excluded: chain K residue   83 ARG
Chi-restraints excluded: chain K residue   87 VAL
Chi-restraints excluded: chain K residue   89 ASP
Chi-restraints excluded: chain K residue   90 LEU
Chi-restraints excluded: chain K residue   98 VAL
Chi-restraints excluded: chain K residue  112 GLN
Chi-restraints excluded: chain N residue   55 LEU
Chi-restraints excluded: chain O residue   19 VAL
Chi-restraints excluded: chain O residue   20 VAL
Chi-restraints excluded: chain O residue   21 VAL
Chi-restraints excluded: chain P residue    6 ARG
Chi-restraints excluded: chain P residue   28 PHE
Chi-restraints excluded: chain P residue   57 ASP
Chi-restraints excluded: chain P residue   67 LEU
Chi-restraints excluded: chain S residue   39 ILE
Chi-restraints excluded: chain S residue   58 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 119 optimal weight:   10.0000
   chunk 39 optimal weight:   10.0000
   chunk 162 optimal weight:    9.9990
   chunk 38 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 175 optimal weight:    9.9990
   chunk 170 optimal weight:    1.9990
   chunk 167 optimal weight:    0.0020
   chunk 23 optimal weight:   10.0000
   chunk 136 optimal weight:    9.9990
   overall best weight:    6.3996

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

Flipped N/Q/H residues before XYZ refinement:
** C  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  51 ASN ** 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 = 0.3370 r_free = 0.3370 target = 0.055166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.042020 restraints weight = 189239.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.043361 restraints weight = 82684.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.043326 restraints weight = 38407.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.043320 restraints weight = 38496.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.043421 restraints weight = 35524.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.085  29238  Z= 0.321
  Angle     :  0.733  12.546  43808  Z= 0.368
  Chirality :  0.039   0.283   5606
  Planarity :  0.005   0.056   2307
  Dihedral  : 24.193 171.312  14772
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 18.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 29.69 %
    Favored  : 66.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.39 (0.26), residues: 1029
  helix:  0.16 (0.26), residues: 393
  sheet: -1.77 (0.38), residues: 167
  loop : -1.47 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG P  62 
 TYR   0.013   0.002   TYR O  17 
 PHE   0.022   0.002   PHE E  80 
 TRP   0.014   0.003   TRP P  73 
 HIS   0.014   0.002   HIS E  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00620 (29238)
  covalent geometry    : angle       0.73325 (43808)
  hydrogen bonds       : bond        0.07844 ( 1113)
  hydrogen bonds       : angle       3.75647 ( 2237)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 188
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 GLN cc_start: 0.8458 (tp-100) cc_final: 0.8144 (tp40)
REVERT: C   47 ARG cc_start: 0.8775 (ttp80) cc_final: 0.8504 (ttp80)
REVERT: C  202 GLU cc_start: 0.8745 (pt0) cc_final: 0.8499 (tp30)
REVERT: D   14 LYS cc_start: 0.8728 (ptpp) cc_final: 0.8413 (ptpp)
REVERT: D   22 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.7481 (t)
REVERT: D   66 LYS cc_start: 0.7986 (ttmt) cc_final: 0.7470 (tttt)
REVERT: D  135 ASN cc_start: 0.8785 (m-40) cc_final: 0.8402 (m-40)
REVERT: E    9 MET cc_start: 0.7716 (pmm) cc_final: 0.7262 (ppp)
REVERT: E   75 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7303 (pm20)
REVERT: E   91 ARG cc_start: 0.7002 (mtp180) cc_final: 0.6541 (mtm-85)
REVERT: G   12 THR cc_start: 0.9406 (p) cc_final: 0.9084 (t)
REVERT: G   16 ASN cc_start: 0.9082 (m-40) cc_final: 0.8640 (m110)
REVERT: G   27 MET cc_start: 0.8869 (ptp) cc_final: 0.8580 (pmm)
REVERT: K    5 ASN cc_start: 0.8548 (t0) cc_final: 0.8037 (t0)
REVERT: K   75 GLN cc_start: 0.8757 (pp30) cc_final: 0.8483 (pp30)
REVERT: K   83 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7917 (pmt-80)
REVERT: N   25 GLU cc_start: 0.9465 (mp0) cc_final: 0.9063 (pm20)
REVERT: O    1 MET cc_start: 0.8285 (pmm) cc_final: 0.7819 (pmm)
REVERT: O   63 GLN cc_start: 0.9307 (mm-40) cc_final: 0.8628 (mm-40)
REVERT: O   80 LYS cc_start: 0.9201 (ptmm) cc_final: 0.8498 (pttm)
REVERT: P   26 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7807 (tm-30)
REVERT: P   39 LYS cc_start: 0.9304 (tttt) cc_final: 0.9015 (tptm)
REVERT: P   67 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8587 (mm)
  outliers start: 29
  outliers final: 23
  residues processed: 210
  average time/residue: 0.1989
  time to fit residues: 65.1448
Evaluate side-chains
  211 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 184
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  124 MET
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue   88 VAL
Chi-restraints excluded: chain D residue   94 VAL
Chi-restraints excluded: chain E residue   75 GLU
Chi-restraints excluded: chain G residue   51 VAL
Chi-restraints excluded: chain G residue   72 VAL
Chi-restraints excluded: chain K residue   27 CYS
Chi-restraints excluded: chain K residue   83 ARG
Chi-restraints excluded: chain K residue   87 VAL
Chi-restraints excluded: chain K residue   89 ASP
Chi-restraints excluded: chain K residue   90 LEU
Chi-restraints excluded: chain K residue   98 VAL
Chi-restraints excluded: chain N residue   55 LEU
Chi-restraints excluded: chain O residue   19 VAL
Chi-restraints excluded: chain O residue   20 VAL
Chi-restraints excluded: chain O residue   21 VAL
Chi-restraints excluded: chain P residue    6 ARG
Chi-restraints excluded: chain P residue   28 PHE
Chi-restraints excluded: chain P residue   57 ASP
Chi-restraints excluded: chain P residue   67 LEU
Chi-restraints excluded: chain S residue   39 ILE
Chi-restraints excluded: chain S residue   58 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 61 optimal weight:    8.9990
   chunk 50 optimal weight:   10.0000
   chunk 187 optimal weight:    5.9990
   chunk 154 optimal weight:    3.9990
   chunk 162 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 68 optimal weight:   30.0000
   chunk 87 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 94 optimal weight:    0.9990
   chunk 138 optimal weight:    9.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  51 ASN ** 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 = 0.3397 r_free = 0.3397 target = 0.056001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.042938 restraints weight = 188993.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.044186 restraints weight = 81545.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.044164 restraints weight = 39051.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.044315 restraints weight = 38027.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.044304 restraints weight = 36123.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  29238  Z= 0.217
  Angle     :  0.665  12.600  43808  Z= 0.336
  Chirality :  0.036   0.282   5606
  Planarity :  0.005   0.049   2307
  Dihedral  : 24.148 170.434  14772
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 15.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 30.63 %
    Favored  : 65.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.29 (0.26), residues: 1029
  helix:  0.23 (0.26), residues: 393
  sheet: -1.73 (0.37), residues: 176
  loop : -1.38 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  20 
 TYR   0.015   0.002   TYR C 135 
 PHE   0.033   0.002   PHE D  95 
 TRP   0.007   0.002   TRP P  73 
 HIS   0.009   0.001   HIS N  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (29238)
  covalent geometry    : angle       0.66488 (43808)
  hydrogen bonds       : bond        0.07024 ( 1113)
  hydrogen bonds       : angle       3.66123 ( 2237)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3698.22 seconds
wall clock time: 65 minutes 22.76 seconds (3922.76 seconds total)