Starting phenix.real_space_refine
on Thu Sep 26 00:24:56 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/09_2024/8c91_16498.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/09_2024/8c91_16498.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/09_2024/8c91_16498.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/09_2024/8c91_16498.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/09_2024/8c91_16498.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/09_2024/8c91_16498.cif"
  }
  resolution = 4.19
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.082
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    2077      5.49       5
     S      41      5.16       5
     C   28981      2.51       5
     N   11042      2.21       5
     O   16969      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 59110
  Number of models: 1
  Model: ""
    Number of chains: 18
    Chain: "C"
      Number of atoms: 1195
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1195
          Classifications: {'peptide': 156}
          Link IDs: {'PTRANS': 10, 'TRANS': 145}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1348
          Classifications: {'peptide': 180}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 175}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1461
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1461
          Classifications: {'peptide': 190}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 184}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 1121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1121
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 133}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 929
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 5, 'TRANS': 115}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 769
          Classifications: {'peptide': 108}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 105}
          Chain breaks: 1
    Chain: "N"
      Number of atoms: 960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 960
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "P"
      Number of atoms: 917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 917
          Classifications: {'peptide': 114}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 110}
    Chain: "Q"
      Number of atoms: 947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 947
          Classifications: {'peptide': 117}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 116}
    Chain: "R"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 816
          Classifications: {'peptide': 103}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 101}
    Chain: "S"
      Number of atoms: 786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 786
          Classifications: {'peptide': 101}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 99}
          Chain breaks: 1
    Chain: "T"
      Number of atoms: 730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 730
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 1, 'TRANS': 90}
    Chain: "U"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 779
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 3, 'TRANS': 98}
    Chain: "Y"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 509
          Classifications: {'peptide': 63}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 62}
    Chain: "0"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 444
          Classifications: {'peptide': 56}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 54}
    Chain: "2"
      Number of atoms: 315
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 315
          Classifications: {'peptide': 39}
          Link IDs: {'PTRANS': 1, 'TRANS': 37}
    Chain: "Z"
      Number of atoms: 449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 449
          Classifications: {'peptide': 58}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 55}
    Chain: "A"
      Number of atoms: 44635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2077, 44635
          Classifications: {'RNA': 2077}
          Modifications used: {'rna2p_pur': 200, 'rna2p_pyr': 108, 'rna3p_pur': 1021, 'rna3p_pyr': 748}
          Link IDs: {'rna2p': 308, 'rna3p': 1768}
          Chain breaks: 5
  Time building chain proxies: 25.71, per 1000 atoms: 0.43
  Number of scatterers: 59110
  At special positions: 0
  Unit cell: (170, 203.75, 203.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      41     16.00
     P    2077     15.00
     O   16969      8.00
     N   11042      7.00
     C   28981      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: 10.75
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3414

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 27 sheets defined
      31.5% alpha, 18.8% beta
      678 base pairs and 1000 stacking pairs defined.
    Time for finding SS restraints: 22.52
  Creating SS restraints...
    Processing helix  chain 'C' and resid 132 through 134
      No H-bonds generated for 'chain 'C' and resid 132 through 134'
    Processing helix  chain 'D' and resid 56 through 60
    Processing helix  chain 'D' and resid 61 through 72
    Processing helix  chain 'D' and resid 98 through 103
      removed outlier: 4.295A  pdb=" N   ASP D 103 " --> pdb=" O   LEU D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 126
    Processing helix  chain 'E' and resid 15 through 20
    Processing helix  chain 'E' and resid 25 through 40
    Processing helix  chain 'E' and resid 97 through 115
    Processing helix  chain 'E' and resid 130 through 141
    Processing helix  chain 'E' and resid 154 through 160
      removed outlier: 4.083A  pdb=" N   ALA E 160 " --> pdb=" O   ASN E 156 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 176 through 183
    Processing helix  chain 'E' and resid 189 through 201
      removed outlier: 3.886A  pdb=" N   LYS E 194 " --> pdb=" O   ALA E 190 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 7 through 11
    Processing helix  chain 'J' and resid 24 through 38
    Processing helix  chain 'J' and resid 58 through 62
      removed outlier: 3.687A  pdb=" N   LYS J  61 " --> pdb=" O   ASN J  58 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL J  62 " --> pdb=" O   ALA J  59 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 58 through 62'
    Processing helix  chain 'J' and resid 88 through 96
    Processing helix  chain 'J' and resid 96 through 109
      removed outlier: 4.168A  pdb=" N   VAL J 100 " --> pdb=" O   ARG J  96 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 112 through 120
    Processing helix  chain 'J' and resid 131 through 136
      removed outlier: 4.374A  pdb=" N   ALA J 134 " --> pdb=" O   ASN J 131 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 109 through 111
      No H-bonds generated for 'chain 'K' and resid 109 through 111'
    Processing helix  chain 'K' and resid 112 through 117
      removed outlier: 3.957A  pdb=" N   SER K 117 " --> pdb=" O   MET K 113 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 29 through 33
      removed outlier: 3.782A  pdb=" N   GLY L  32 " --> pdb=" O   LYS L  29 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 94 through 99
    Processing helix  chain 'L' and resid 135 through 139
    Processing helix  chain 'N' and resid 13 through 32
    Processing helix  chain 'N' and resid 38 through 55
      removed outlier: 4.779A  pdb=" N   ARG N  46 " --> pdb=" O   LYS N  42 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   VAL N  47 " --> pdb=" O   GLU N  43 " (cutoff:3.500A)
      Proline residue:  N  50  - end of helix
    Processing helix  chain 'N' and resid 59 through 68
    Processing helix  chain 'N' and resid 72 through 79
    Processing helix  chain 'N' and resid 82 through 89
      removed outlier: 4.584A  pdb=" N   SER N  89 " --> pdb=" O   PRO N  85 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 11
      removed outlier: 3.676A  pdb=" N   GLN P  11 " --> pdb=" O   LEU P   7 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 52 through 55
      removed outlier: 3.585A  pdb=" N   HIS P  55 " --> pdb=" O   ARG P  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 52 through 55'
    Processing helix  chain 'P' and resid 96 through 102
      removed outlier: 4.011A  pdb=" N   ARG P 100 " --> pdb=" O   TYR P  97 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   GLU P 101 " --> pdb=" O   TYR P  98 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ARG P 102 " --> pdb=" O   LEU P  99 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 103 through 107
    Processing helix  chain 'Q' and resid 5 through 20
      removed outlier: 3.637A  pdb=" N   GLN Q  19 " --> pdb=" O   LYS Q  15 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 24 through 29
      removed outlier: 4.383A  pdb=" N   ARG Q  27 " --> pdb=" O   TYR Q  24 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 30 through 72
      removed outlier: 4.078A  pdb=" N   GLN Q  36 " --> pdb=" O   ARG Q  32 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   LYS Q  53 " --> pdb=" O   ARG Q  49 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   ARG Q  54 " --> pdb=" O   ARG Q  50 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 74 through 85
    Processing helix  chain 'Q' and resid 90 through 101
    Processing helix  chain 'Q' and resid 101 through 115
      removed outlier: 3.637A  pdb=" N   PHE Q 105 " --> pdb=" O   ASP Q 101 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 15 through 25
      removed outlier: 3.777A  pdb=" N   LEU S  23 " --> pdb=" O   LEU S  19 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ILE S  24 " --> pdb=" O   VAL S  20 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 38
      removed outlier: 3.879A  pdb=" N   ASP S  34 " --> pdb=" O   SER S  30 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   TYR S  38 " --> pdb=" O   ASP S  34 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 42 through 62
      removed outlier: 4.377A  pdb=" N   LEU S  46 " --> pdb=" O   LYS S  42 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 65 through 69
      removed outlier: 3.543A  pdb=" N   LEU S  69 " --> pdb=" O   ILE S  66 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 4 through 10
      removed outlier: 3.660A  pdb=" N   VAL T  10 " --> pdb=" O   ARG T   6 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 17 through 27
    Processing helix  chain 'T' and resid 39 through 51
    Processing helix  chain 'Y' and resid 2 through 7
    Processing helix  chain 'Y' and resid 9 through 32
      removed outlier: 3.843A  pdb=" N   GLN Y  25 " --> pdb=" O   LEU Y  21 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   PHE Y  26 " --> pdb=" O   LEU Y  22 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 42 through 56
      removed outlier: 3.680A  pdb=" N   VAL Y  46 " --> pdb=" O   LEU Y  42 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ARG Y  47 " --> pdb=" O   LEU Y  43 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   ARG Y  48 " --> pdb=" O   LYS Y  44 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 8 through 16
      removed outlier: 3.670A  pdb=" N   ARG 0  12 " --> pdb=" O   THR 0   8 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 8 through 17
    Processing helix  chain '2' and resid 17 through 24
      removed outlier: 3.971A  pdb=" N   THR 2  24 " --> pdb=" O   ALA 2  20 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 24 through 38
      removed outlier: 3.898A  pdb=" N   ARG 2  28 " --> pdb=" O   THR 2  24 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLN 2  29 " --> pdb=" O   LYS 2  25 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 16 through 27
    Processing helix  chain 'Z' and resid 40 through 50
    Processing sheet with id=AA1, first strand: chain 'C' and resid 100 through 104
      removed outlier: 7.011A  pdb=" N   ILE C  90 " --> pdb=" O   LEU C  80 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   LEU C  80 " --> pdb=" O   ILE C  90 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LEU C  92 " --> pdb=" O   GLU C  78 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 128 through 130
    Processing sheet with id=AA3, first strand: chain 'C' and resid 162 through 163
    Processing sheet with id=AA4, first strand: chain 'D' and resid 21 through 28
      removed outlier: 6.866A  pdb=" N   ILE D  22 " --> pdb=" O   ARG D  13 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   ARG D  13 " --> pdb=" O   ILE D  22 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   VAL D  24 " --> pdb=" O   MET D  11 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   MET D  11 " --> pdb=" O   VAL D  24 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   VAL D  26 " --> pdb=" O   VAL D   9 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   ASP D 200 " --> pdb=" O   THR D 112 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   THR D 112 " --> pdb=" O   ASP D 200 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   VAL D 109 " --> pdb=" O   GLN D 173 " (cutoff:3.500A)
      removed outlier: 5.336A  pdb=" N   GLN D 173 " --> pdb=" O   VAL D 109 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   GLY D 111 " --> pdb=" O   THR D 171 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   THR D 171 " --> pdb=" O   GLY D 111 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 80 through 83
      removed outlier: 3.589A  pdb=" N   GLN D  36 " --> pdb=" O   GLN D  49 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   THR D  51 " --> pdb=" O   VAL D  34 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   VAL D  34 " --> pdb=" O   THR D  51 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASN D  32 " --> pdb=" O   ILE D  96 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 117 through 118
      removed outlier: 4.052A  pdb=" N   GLY D 117 " --> pdb=" O   MET D 165 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   MET D 165 " --> pdb=" O   GLY D 117 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'D' and resid 180 through 181
    Processing sheet with id=AA8, first strand: chain 'E' and resid 2 through 3
      removed outlier: 4.242A  pdb=" N   LEU E   3 " --> pdb=" O   LEU E  12 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   LEU E  12 " --> pdb=" O   LEU E   3 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.828A  pdb=" N   ASP E 168 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'J' and resid 122 through 124
      removed outlier: 6.602A  pdb=" N   TYR J  16 " --> pdb=" O   ILE J  55 " (cutoff:3.500A)
      removed outlier: 7.990A  pdb=" N   LEU J  57 " --> pdb=" O   TYR J  16 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   VAL J  18 " --> pdb=" O   LEU J  57 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   TRP J  15 " --> pdb=" O   GLN J 138 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'J' and resid 74 through 76
      removed outlier: 4.250A  pdb=" N   TYR J  74 " --> pdb=" O   ALA J  87 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   ALA J  87 " --> pdb=" O   TYR J  74 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   HIS J  76 " --> pdb=" O   LYS J  85 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 7 through 10
      removed outlier: 3.517A  pdb=" N   LEU K   8 " --> pdb=" O   VAL K  19 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   VAL K  10 " --> pdb=" O   ARG K  17 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   ARG K  17 " --> pdb=" O   VAL K  10 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ALA K  16 " --> pdb=" O   ALA K  46 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   ALA K  46 " --> pdb=" O   ALA K  16 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ARG K  18 " --> pdb=" O   LYS K  44 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   LYS K  40 " --> pdb=" O   ILE K  22 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   ALA K  83 " --> pdb=" O   VAL K  63 " (cutoff:3.500A)
      removed outlier: 8.716A  pdb=" N   CYS K  84 " --> pdb=" O   MET K   7 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ASN K   9 " --> pdb=" O   CYS K  84 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   LEU K  86 " --> pdb=" O   ASN K   9 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'K' and resid 69 through 70
      removed outlier: 3.637A  pdb=" N   VAL K  69 " --> pdb=" O   ILE K  77 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   VAL K  76 " --> pdb=" O   VAL P  72 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL P  72 " --> pdb=" O   VAL K  76 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   ALA P  57 " --> pdb=" O   ILE P  49 " (cutoff:3.500A)
      removed outlier: 5.045A  pdb=" N   ILE P  49 " --> pdb=" O   ALA P  57 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   THR P  59 " --> pdb=" O   ILE P  47 " (cutoff:3.500A)
      removed outlier: 5.736A  pdb=" N   ILE P  63 " --> pdb=" O   GLU P  43 " (cutoff:3.500A)
      removed outlier: 8.621A  pdb=" N   GLU P  43 " --> pdb=" O   ILE P  63 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ARG P  87 " --> pdb=" O   THR P  24 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   GLU P  26 " --> pdb=" O   VAL P  85 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   VAL P  85 " --> pdb=" O   GLU P  26 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   LYS P  28 " --> pdb=" O   ILE P  83 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   ILE P  83 " --> pdb=" O   LYS P  28 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   TRP P  30 " --> pdb=" O   ASP P  81 " (cutoff:3.500A)
      removed outlier: 7.168A  pdb=" N   ASP P  81 " --> pdb=" O   TRP P  30 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'N' and resid 33 through 37
      removed outlier: 3.518A  pdb=" N   GLU N 114 " --> pdb=" O   ARG N  96 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'N' and resid 33 through 37
      removed outlier: 5.759A  pdb=" N   MET N 110 " --> pdb=" O   CYS N 100 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'R' and resid 11 through 15
      removed outlier: 3.736A  pdb=" N   MET R  40 " --> pdb=" O   VAL R   4 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'R' and resid 19 through 23
      removed outlier: 3.946A  pdb=" N   VAL R  20 " --> pdb=" O   VAL R  96 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL R  96 " --> pdb=" O   VAL R  20 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ASP R  95 " --> pdb=" O   ALA R  65 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ALA R  65 " --> pdb=" O   ASP R  95 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   LYS R  97 " --> pdb=" O   VAL R  63 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   VAL R  63 " --> pdb=" O   LYS R  97 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'R' and resid 72 through 78
      removed outlier: 4.344A  pdb=" N   TYR R  83 " --> pdb=" O   ARG R  78 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'S' and resid 3 through 10
      removed outlier: 5.483A  pdb=" N   ILE S   4 " --> pdb=" O   VAL S 107 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   VAL S 107 " --> pdb=" O   ILE S   4 " (cutoff:3.500A)
      removed outlier: 5.252A  pdb=" N   LYS S   6 " --> pdb=" O   VAL S 105 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   VAL S 105 " --> pdb=" O   LYS S   6 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   ARG S   8 " --> pdb=" O   ILE S 103 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ILE S 103 " --> pdb=" O   ARG S   8 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LYS S  73 " --> pdb=" O   VAL S 106 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   SER S 108 " --> pdb=" O   VAL S  71 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   VAL S  71 " --> pdb=" O   SER S 108 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'T' and resid 11 through 14
      removed outlier: 6.849A  pdb=" N   LYS T  33 " --> pdb=" O   ARG T  12 " (cutoff:3.500A)
      removed outlier: 8.309A  pdb=" N   VAL T  31 " --> pdb=" O   PRO T  14 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LYS T  81 " --> pdb=" O   VAL T  34 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   TRP T  80 " --> pdb=" O   VAL T  62 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   VAL T  62 " --> pdb=" O   TRP T  80 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   LYS T  82 " --> pdb=" O   THR T  60 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   THR T  60 " --> pdb=" O   LYS T  82 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   TYR T  84 " --> pdb=" O   VAL T  58 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   VAL T  58 " --> pdb=" O   TYR T  84 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   THR T  86 " --> pdb=" O   GLU T  56 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'T' and resid 67 through 68
    Processing sheet with id=AC4, first strand: chain 'U' and resid 64 through 65
      removed outlier: 6.402A  pdb=" N   LYS U  32 " --> pdb=" O   VAL U  27 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   VAL U  27 " --> pdb=" O   LYS U  32 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ILE U  34 " --> pdb=" O   LYS U  25 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   GLU U   9 " --> pdb=" O   PHE U  72 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE U  72 " --> pdb=" O   GLU U   9 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ASN U  73 " --> pdb=" O   LYS U  78 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LYS U  78 " --> pdb=" O   ASN U  73 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'U' and resid 40 through 44
    Processing sheet with id=AC6, first strand: chain 'U' and resid 83 through 86
    Processing sheet with id=AC7, first strand: chain '0' and resid 27 through 29
    Processing sheet with id=AC8, first strand: chain '0' and resid 47 through 48
      removed outlier: 3.667A  pdb=" N   TYR 0  48 " --> pdb=" O   ARG 0  51 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'Z' and resid 35 through 38

    494 hydrogen bonds defined for protein.
    1371 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      1723 hydrogen bonds
      2784 hydrogen bond angles
      0 basepair planarities
      678 basepair parallelities
      1000 stacking parallelities
  Total time for adding SS restraints: 53.44

  Time building geometry restraints manager: 13.28 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: 8654
        1.33 -     1.45: 27776
        1.45 -     1.57: 23988
        1.57 -     1.69: 4148
        1.69 -     1.81: 78
  Bond restraints: 64644
  Sorted by residual:
  bond pdb=" O5'   A A1566 "
       pdb=" C5'   A A1566 "
    ideal  model  delta    sigma   weight residual
    1.424  1.453 -0.029 1.50e-02 4.44e+03 3.62e+00
  bond pdb=" N   GLU T   4 "
       pdb=" CA  GLU T   4 "
    ideal  model  delta    sigma   weight residual
    1.457  1.481 -0.024 1.29e-02 6.01e+03 3.41e+00
  bond pdb=" N   MET K   1 "
       pdb=" CA  MET K   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.18e+00
  bond pdb=" N   ILE T   2 "
       pdb=" CA  ILE T   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.06e+00
  bond pdb=" N   MET E   1 "
       pdb=" CA  MET E   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.04e+00
  ... (remaining 64639 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 96343
        1.17 -     2.33: 1078
        2.33 -     3.50: 159
        3.50 -     4.66: 33
        4.66 -     5.83: 10
  Bond angle restraints: 97623
  Sorted by residual:
  angle pdb=" C3'   A A1566 "
        pdb=" C2'   A A1566 "
        pdb=" C1'   A A1566 "
      ideal   model   delta    sigma   weight residual
     101.50   97.70    3.80 1.00e+00 1.00e+00 1.44e+01
  angle pdb=" N   ALA E 161 "
        pdb=" CA  ALA E 161 "
        pdb=" C   ALA E 161 "
      ideal   model   delta    sigma   weight residual
     114.62  110.72    3.90 1.14e+00 7.69e-01 1.17e+01
  angle pdb=" CA  ALA E 161 "
        pdb=" C   ALA E 161 "
        pdb=" N   ARG E 162 "
      ideal   model   delta    sigma   weight residual
     119.71  116.36    3.35 1.17e+00 7.31e-01 8.18e+00
  angle pdb=" N   ARG T   3 "
        pdb=" CA  ARG T   3 "
        pdb=" C   ARG T   3 "
      ideal   model   delta    sigma   weight residual
     113.29  107.84    5.45 2.00e+00 2.50e-01 7.43e+00
  angle pdb=" O   ARG T   3 "
        pdb=" C   ARG T   3 "
        pdb=" N   GLU T   4 "
      ideal   model   delta    sigma   weight residual
     121.88  124.75   -2.87 1.07e+00 8.73e-01 7.18e+00
  ... (remaining 97618 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.78: 36231
       34.78 -    69.57: 4551
       69.57 -   104.35: 534
      104.35 -   139.14: 12
      139.14 -   173.92: 6
  Dihedral angle restraints: 41334
    sinusoidal: 36052
      harmonic: 5282
  Sorted by residual:
  dihedral pdb=" O4'   U A1174 "
           pdb=" C1'   U A1174 "
           pdb=" N1    U A1174 "
           pdb=" C2    U A1174 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   41.18  158.82     1      1.50e+01 4.44e-03 8.24e+01
  dihedral pdb=" O4'   U A 545 "
           pdb=" C1'   U A 545 "
           pdb=" N1    U A 545 "
           pdb=" C2    U A 545 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   53.21  146.79     1      1.50e+01 4.44e-03 7.84e+01
  dihedral pdb=" O4'   U A1340 "
           pdb=" C1'   U A1340 "
           pdb=" N1    U A1340 "
           pdb=" C2    U A1340 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   45.92 -173.92     1      1.70e+01 3.46e-03 6.62e+01
  ... (remaining 41331 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 12403
       0.084 -    0.167: 226
       0.167 -    0.251: 1
       0.251 -    0.334: 0
       0.334 -    0.418: 1
  Chirality restraints: 12631
  Sorted by residual:
  chirality pdb=" P     A A1566 "
            pdb=" OP1   A A1566 "
            pdb=" OP2   A A1566 "
            pdb=" O5'   A A1566 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.83   -0.42 2.00e-01 2.50e+01 4.36e+00
  chirality pdb=" CA  ILE T   2 "
            pdb=" N   ILE T   2 "
            pdb=" C   ILE T   2 "
            pdb=" CB  ILE T   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.25e-01
  chirality pdb=" CA  ILE S 103 "
            pdb=" N   ILE S 103 "
            pdb=" C   ILE S 103 "
            pdb=" CB  ILE S 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.42e-01
  ... (remaining 12628 not shown)

  Planarity restraints: 4596
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A  32 "   -0.003 2.00e-02 2.50e+03   1.45e-02 4.74e+00
        pdb=" N1    C A  32 "    0.006 2.00e-02 2.50e+03
        pdb=" C2    C A  32 "    0.035 2.00e-02 2.50e+03
        pdb=" O2    C A  32 "   -0.022 2.00e-02 2.50e+03
        pdb=" N3    C A  32 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4    C A  32 "    0.005 2.00e-02 2.50e+03
        pdb=" N4    C A  32 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    C A  32 "   -0.007 2.00e-02 2.50e+03
        pdb=" C6    C A  32 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A1351 "    0.001 2.00e-02 2.50e+03   1.26e-02 3.57e+00
        pdb=" N1    C A1351 "   -0.011 2.00e-02 2.50e+03
        pdb=" C2    C A1351 "    0.021 2.00e-02 2.50e+03
        pdb=" O2    C A1351 "    0.000 2.00e-02 2.50e+03
        pdb=" N3    C A1351 "   -0.024 2.00e-02 2.50e+03
        pdb=" C4    C A1351 "    0.017 2.00e-02 2.50e+03
        pdb=" N4    C A1351 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    C A1351 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    C A1351 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 175 "    0.018 2.00e-02 2.50e+03   1.07e-02 3.42e+00
        pdb=" N9    G A 175 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8    G A 175 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    G A 175 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G A 175 "    0.003 2.00e-02 2.50e+03
        pdb=" C6    G A 175 "    0.013 2.00e-02 2.50e+03
        pdb=" O6    G A 175 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1    G A 175 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    G A 175 "    0.014 2.00e-02 2.50e+03
        pdb=" N2    G A 175 "   -0.009 2.00e-02 2.50e+03
        pdb=" N3    G A 175 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    G A 175 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 4593 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 442
        2.50 -     3.10: 40295
        3.10 -     3.70: 110989
        3.70 -     4.30: 155656
        4.30 -     4.90: 213311
  Nonbonded interactions: 520693
  Sorted by model distance:
  nonbonded pdb=" O2'   C A1462 "
            pdb=" O2'   G A2702 "
     model   vdw
     1.896 3.040
  nonbonded pdb=" O2'   G A 175 "
            pdb=" O5'   A A 176 "
     model   vdw
     1.898 3.040
  nonbonded pdb=" O2'   C A1351 "
            pdb=" O2'   A A1571 "
     model   vdw
     1.914 3.040
  nonbonded pdb=" O2'   G A 636 "
            pdb=" O2'   G A 638 "
     model   vdw
     1.925 3.040
  nonbonded pdb=" O2'   A A 299 "
            pdb=" O4'   A A 300 "
     model   vdw
     1.937 3.040
  ... (remaining 520688 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:             1.640
  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:             0.060
  Extract box with map and model:          1.870
  Check model and map are aligned:         0.350
  Set scattering table:                    0.440
  Process input model:                     143.380
  Find NCS groups from input model:        0.540
  Set up NCS constraints:                  0.180
  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:             0.020
  Load rotamer database and sin/cos tables:2.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  151.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
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      :  0.001   0.034  64644  Z= 0.082
  Angle     :  0.357   5.830  97623  Z= 0.186
  Chirality :  0.025   0.418  12631
  Planarity :  0.002   0.029   4596
  Dihedral  : 22.463 173.924  37920
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.75 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.24 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.20), residues: 1812
  helix:  1.76 (0.25), residues: 504
  sheet:  0.49 (0.31), residues: 309
  loop : -0.59 (0.20), residues: 999

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP T  80 
 HIS   0.002   0.000   HIS E 165 
 PHE   0.010   0.001   PHE Z  52 
 TYR   0.005   0.001   TYR Q  44 
 ARG   0.004   0.000   ARG T   3 

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  363 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 362
  time to evaluate  : 2.400 
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: C   82 TYR cc_start: 0.8968 (t80) cc_final: 0.8695 (t80)
REVERT: C   89 ASN cc_start: 0.7518 (t0) cc_final: 0.6814 (t0)
REVERT: C   90 ILE cc_start: 0.8676 (pt) cc_final: 0.7848 (tp)
REVERT: D  108 ASP cc_start: 0.8379 (m-30) cc_final: 0.8145 (m-30)
REVERT: D  175 LEU cc_start: 0.9175 (mt) cc_final: 0.8970 (mt)
REVERT: D  202 ILE cc_start: 0.9053 (mt) cc_final: 0.8724 (mm)
REVERT: E  158 PHE cc_start: 0.7451 (t80) cc_final: 0.7022 (t80)
REVERT: J   16 TYR cc_start: 0.8011 (m-80) cc_final: 0.6936 (m-80)
REVERT: J   36 LEU cc_start: 0.8809 (mt) cc_final: 0.8471 (mt)
REVERT: J   96 ARG cc_start: 0.7503 (mtt180) cc_final: 0.7292 (ptp-110)
REVERT: K    4 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8129 (tp30)
REVERT: K   67 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8085 (ttmm)
REVERT: L    3 LEU cc_start: 0.6871 (pt) cc_final: 0.6479 (mt)
REVERT: L   18 ARG cc_start: 0.8230 (mtp-110) cc_final: 0.7979 (mtp180)
REVERT: L   77 ILE cc_start: 0.3806 (mm) cc_final: 0.3222 (mm)
REVERT: N    1 MET cc_start: 0.7686 (tmm) cc_final: 0.7325 (tmm)
REVERT: N    5 LYS cc_start: 0.7453 (tptt) cc_final: 0.7251 (ttpp)
REVERT: N  106 ASP cc_start: 0.8401 (p0) cc_final: 0.7657 (p0)
REVERT: N  107 ASN cc_start: 0.8274 (m110) cc_final: 0.7817 (m110)
REVERT: P   54 LEU cc_start: 0.8948 (tp) cc_final: 0.8541 (tp)
REVERT: Q   96 ASP cc_start: 0.8590 (m-30) cc_final: 0.8348 (m-30)
REVERT: S   16 LYS cc_start: 0.8760 (mttt) cc_final: 0.8485 (mttm)
REVERT: S   65 ASP cc_start: 0.8930 (t0) cc_final: 0.8668 (t0)
REVERT: T   50 LEU cc_start: 0.9390 (tp) cc_final: 0.9145 (tt)
REVERT: T   51 PHE cc_start: 0.8322 (m-80) cc_final: 0.8057 (m-80)
REVERT: 0   30 ASP cc_start: 0.7506 (t0) cc_final: 0.7182 (t70)
REVERT: 2   18 PHE cc_start: 0.8680 (t80) cc_final: 0.8329 (t80)
REVERT: 2   41 ARG cc_start: 0.8859 (tmm-80) cc_final: 0.8582 (tmm-80)
REVERT: Z   31 ILE cc_start: 0.8831 (mp) cc_final: 0.8410 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 363
  average time/residue: 0.6425
  time to fit residues: 379.5029
Evaluate side-chains
  245 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 244
  time to evaluate  : 2.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 387
   random chunks:
   chunk 326 optimal weight:   20.0000
   chunk 293 optimal weight:   10.0000
   chunk 162 optimal weight:    7.9990
   chunk 100 optimal weight:    7.9990
   chunk 197 optimal weight:   20.0000
   chunk 156 optimal weight:    6.9990
   chunk 303 optimal weight:   20.0000
   chunk 117 optimal weight:   10.0000
   chunk 184 optimal weight:   10.0000
   chunk 225 optimal weight:   10.0000
   chunk 351 optimal weight:   20.0000
   overall best weight:    8.5994

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

Flipped N/Q/H residues before XYZ refinement:
** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 127 ASN
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  30 GLN
** E  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  80 HIS
P  40 GLN
Q  19 GLN
Q  43 GLN
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S   9 HIS
Y  20 ASN
0  18 HIS
2  29 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.4057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078  64644  Z= 0.353
  Angle     :  0.800  15.014  97623  Z= 0.395
  Chirality :  0.038   0.238  12631
  Planarity :  0.007   0.154   4596
  Dihedral  : 23.896 174.240  34296
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 22.96
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.40 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  4.82 %
    Favored  : 94.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.19), residues: 1812
  helix:  0.14 (0.22), residues: 519
  sheet: -0.46 (0.28), residues: 352
  loop : -1.05 (0.19), residues: 941

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D  80 
 HIS   0.008   0.002   HIS S   9 
 PHE   0.028   0.003   PHE Q 105 
 TYR   0.017   0.003   TYR J  74 
 ARG   0.013   0.001   ARG R  78 

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 285
  time to evaluate  : 2.368 
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: C   89 ASN cc_start: 0.7881 (t0) cc_final: 0.7097 (p0)
REVERT: D  186 LEU cc_start: 0.8959 (mt) cc_final: 0.8462 (mt)
REVERT: D  188 LEU cc_start: 0.9454 (mp) cc_final: 0.8806 (mt)
REVERT: D  202 ILE cc_start: 0.9305 (mt) cc_final: 0.9004 (mm)
REVERT: J   16 TYR cc_start: 0.7902 (m-80) cc_final: 0.7624 (m-80)
REVERT: J   92 MET cc_start: 0.8229 (ptp) cc_final: 0.7906 (ptp)
REVERT: J  109 LEU cc_start: 0.9560 (tp) cc_final: 0.9272 (tt)
REVERT: J  118 MET cc_start: 0.8938 (mtp) cc_final: 0.8598 (mtp)
REVERT: K   25 LEU cc_start: 0.8981 (tp) cc_final: 0.8547 (mp)
REVERT: K   67 LYS cc_start: 0.8795 (ttmt) cc_final: 0.8567 (mtpt)
REVERT: L   18 ARG cc_start: 0.8820 (mtp-110) cc_final: 0.8462 (ttt180)
REVERT: N    1 MET cc_start: 0.7774 (tmm) cc_final: 0.7564 (tmm)
REVERT: N   72 ASP cc_start: 0.8964 (t0) cc_final: 0.8626 (t70)
REVERT: Q   44 TYR cc_start: 0.7952 (m-80) cc_final: 0.7103 (m-80)
REVERT: Q   48 ASP cc_start: 0.8793 (m-30) cc_final: 0.8550 (m-30)
REVERT: Q   89 ILE cc_start: 0.9255 (mm) cc_final: 0.8880 (mm)
REVERT: Q   93 ILE cc_start: 0.9242 (mm) cc_final: 0.8999 (mm)
REVERT: Q   96 ASP cc_start: 0.8716 (m-30) cc_final: 0.8402 (m-30)
REVERT: R   37 GLU cc_start: 0.8981 (mp0) cc_final: 0.8399 (tp30)
REVERT: R   87 GLN cc_start: 0.8584 (pp30) cc_final: 0.8367 (pp30)
REVERT: S   65 ASP cc_start: 0.9014 (t0) cc_final: 0.8772 (t0)
REVERT: T    4 GLU cc_start: 0.8637 (tp30) cc_final: 0.7938 (tp30)
REVERT: T    5 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8863 (mm-30)
REVERT: T   24 MET cc_start: 0.9391 (tpp) cc_final: 0.9068 (tpt)
REVERT: T   32 LEU cc_start: 0.9356 (pp) cc_final: 0.9091 (pp)
REVERT: 2   39 ARG cc_start: 0.9126 (ttp-110) cc_final: 0.8727 (ttp-110)
REVERT: 2   41 ARG cc_start: 0.9022 (tmm-80) cc_final: 0.8243 (ttp80)
REVERT: Z   28 LEU cc_start: 0.8296 (mm) cc_final: 0.7792 (tp)
  outliers start: 3
  outliers final: 2
  residues processed: 287
  average time/residue: 0.6034
  time to fit residues: 286.7681
Evaluate side-chains
  216 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 214
  time to evaluate  : 2.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 387
   random chunks:
   chunk 195 optimal weight:   20.0000
   chunk 109 optimal weight:    4.9990
   chunk 292 optimal weight:   10.0000
   chunk 239 optimal weight:   10.0000
   chunk 96 optimal weight:    8.9990
   chunk 352 optimal weight:   10.0000
   chunk 380 optimal weight:   10.0000
   chunk 313 optimal weight:   20.0000
   chunk 349 optimal weight:   40.0000
   chunk 120 optimal weight:    3.9990
   chunk 282 optimal weight:   10.0000
   overall best weight:    7.5994

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

Flipped N/Q/H residues before XYZ refinement:
** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  77 HIS
K  88 ASN
Q  19 GLN
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  40 ASN
0  18 HIS
** 2  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.4779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  64644  Z= 0.277
  Angle     :  0.620  11.204  97623  Z= 0.314
  Chirality :  0.034   0.212  12631
  Planarity :  0.005   0.139   4596
  Dihedral  : 23.950 177.154  34296
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 18.32
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.41 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.19), residues: 1812
  helix:  0.40 (0.23), residues: 509
  sheet: -0.55 (0.27), residues: 381
  loop : -1.15 (0.20), residues: 922

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP D  80 
 HIS   0.007   0.002   HIS 0  37 
 PHE   0.017   0.002   PHE T  51 
 TYR   0.015   0.002   TYR K  32 
 ARG   0.008   0.001   ARG R  78 

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 2.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   90 ILE cc_start: 0.8815 (pt) cc_final: 0.7983 (tp)
REVERT: D    1 MET cc_start: 0.8258 (ttp) cc_final: 0.7427 (mmp)
REVERT: D  108 ASP cc_start: 0.8153 (m-30) cc_final: 0.7407 (p0)
REVERT: D  165 MET cc_start: 0.8744 (mtt) cc_final: 0.8529 (mtt)
REVERT: D  175 LEU cc_start: 0.8953 (mt) cc_final: 0.8700 (mt)
REVERT: D  176 ASP cc_start: 0.9286 (p0) cc_final: 0.9081 (p0)
REVERT: D  202 ILE cc_start: 0.9275 (mt) cc_final: 0.9002 (mm)
REVERT: J  109 LEU cc_start: 0.9482 (tp) cc_final: 0.8940 (tt)
REVERT: J  118 MET cc_start: 0.9096 (mtp) cc_final: 0.8652 (mtp)
REVERT: K   25 LEU cc_start: 0.9138 (tp) cc_final: 0.8878 (mp)
REVERT: K   67 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8487 (mtpt)
REVERT: L   29 LYS cc_start: 0.7546 (ttpt) cc_final: 0.7335 (ttpt)
REVERT: L   77 ILE cc_start: 0.2599 (mm) cc_final: 0.1994 (mm)
REVERT: N    1 MET cc_start: 0.7824 (tmm) cc_final: 0.7557 (tmm)
REVERT: N    5 LYS cc_start: 0.7991 (tptt) cc_final: 0.7410 (ttpp)
REVERT: N   72 ASP cc_start: 0.8946 (t0) cc_final: 0.8562 (t70)
REVERT: Q   44 TYR cc_start: 0.8173 (m-80) cc_final: 0.7694 (m-80)
REVERT: Q   48 ASP cc_start: 0.8730 (m-30) cc_final: 0.8425 (m-30)
REVERT: Q   96 ASP cc_start: 0.8602 (m-30) cc_final: 0.8226 (m-30)
REVERT: R   37 GLU cc_start: 0.8868 (mp0) cc_final: 0.8344 (tp30)
REVERT: R   43 ASN cc_start: 0.8850 (t0) cc_final: 0.8315 (t0)
REVERT: R   74 ILE cc_start: 0.8708 (mm) cc_final: 0.7996 (mm)
REVERT: R   87 GLN cc_start: 0.8227 (pp30) cc_final: 0.6922 (pm20)
REVERT: S   33 LEU cc_start: 0.9470 (mm) cc_final: 0.9231 (mm)
REVERT: S   65 ASP cc_start: 0.9099 (t0) cc_final: 0.8882 (t0)
REVERT: S   68 ASP cc_start: 0.8797 (t0) cc_final: 0.8240 (t0)
REVERT: S   82 MET cc_start: 0.5483 (pmm) cc_final: 0.4877 (ppp)
REVERT: T    4 GLU cc_start: 0.8755 (tp30) cc_final: 0.7976 (tp30)
REVERT: T    5 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8906 (mm-30)
REVERT: T   24 MET cc_start: 0.9310 (tpp) cc_final: 0.9012 (tpp)
REVERT: Y   18 LEU cc_start: 0.9740 (tt) cc_final: 0.9533 (pp)
REVERT: 0    9 ARG cc_start: 0.8604 (mmt90) cc_final: 0.8294 (mmt180)
REVERT: 2   33 ARG cc_start: 0.9558 (ttm110) cc_final: 0.9284 (ttm110)
REVERT: 2   39 ARG cc_start: 0.9160 (ttp-110) cc_final: 0.8559 (ttp-110)
REVERT: 2   41 ARG cc_start: 0.9120 (tmm-80) cc_final: 0.8411 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.6000
  time to fit residues: 266.1372
Evaluate side-chains
  215 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 2.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 387
   random chunks:
   chunk 347 optimal weight:   30.0000
   chunk 264 optimal weight:   20.0000
   chunk 182 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 168 optimal weight:    5.9990
   chunk 236 optimal weight:   20.0000
   chunk 353 optimal weight:   10.0000
   chunk 374 optimal weight:   20.0000
   chunk 184 optimal weight:   10.0000
   chunk 334 optimal weight:   20.0000
   chunk 100 optimal weight:    8.9990
   overall best weight:    8.9996

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

Flipped N/Q/H residues before XYZ refinement:
** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 142 ASN
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K   3 GLN
K  88 ASN
Q  19 GLN
Q  43 GLN
S   7 HIS
T  70 HIS
Y  20 ASN
** Y  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
0  18 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.6081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  64644  Z= 0.347
  Angle     :  0.730  12.576  97623  Z= 0.369
  Chirality :  0.038   0.256  12631
  Planarity :  0.006   0.178   4596
  Dihedral  : 24.289 178.601  34296
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 25.48
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.00 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.19), residues: 1812
  helix: -0.00 (0.22), residues: 510
  sheet: -0.99 (0.28), residues: 331
  loop : -1.41 (0.19), residues: 971

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP D  80 
 HIS   0.006   0.002   HIS J  77 
 PHE   0.034   0.003   PHE Z  52 
 TYR   0.024   0.003   TYR 0  47 
 ARG   0.009   0.001   ARG 2  35 

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 2.380 
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: D    1 MET cc_start: 0.8037 (ttp) cc_final: 0.7368 (mmp)
REVERT: D  165 MET cc_start: 0.9055 (mtt) cc_final: 0.8707 (mtt)
REVERT: D  175 LEU cc_start: 0.9089 (mt) cc_final: 0.8844 (mt)
REVERT: D  186 LEU cc_start: 0.9059 (mt) cc_final: 0.8791 (mt)
REVERT: D  202 ILE cc_start: 0.9347 (mt) cc_final: 0.9145 (mm)
REVERT: J   98 GLU cc_start: 0.8973 (pm20) cc_final: 0.8758 (pm20)
REVERT: J  109 LEU cc_start: 0.9536 (tp) cc_final: 0.9226 (tt)
REVERT: J  118 MET cc_start: 0.9111 (mtp) cc_final: 0.8691 (mtp)
REVERT: K  106 GLU cc_start: 0.8102 (mp0) cc_final: 0.7316 (mp0)
REVERT: K  112 PHE cc_start: 0.8743 (m-10) cc_final: 0.8506 (m-80)
REVERT: L   77 ILE cc_start: 0.2141 (mm) cc_final: 0.1433 (mm)
REVERT: N    5 LYS cc_start: 0.7866 (tptt) cc_final: 0.7369 (ttpp)
REVERT: N   72 ASP cc_start: 0.8981 (t0) cc_final: 0.8621 (t70)
REVERT: Q   44 TYR cc_start: 0.8256 (m-80) cc_final: 0.7817 (m-80)
REVERT: Q   48 ASP cc_start: 0.8785 (m-30) cc_final: 0.8476 (m-30)
REVERT: Q   61 ILE cc_start: 0.9408 (mm) cc_final: 0.9207 (mm)
REVERT: R   37 GLU cc_start: 0.8919 (mp0) cc_final: 0.8619 (pm20)
REVERT: R   39 LEU cc_start: 0.9075 (tp) cc_final: 0.8873 (tp)
REVERT: R   43 ASN cc_start: 0.8865 (t0) cc_final: 0.8490 (t0)
REVERT: R   74 ILE cc_start: 0.8852 (mm) cc_final: 0.8094 (mm)
REVERT: R   86 GLN cc_start: 0.9178 (mt0) cc_final: 0.8863 (mt0)
REVERT: R   87 GLN cc_start: 0.8448 (pp30) cc_final: 0.7247 (pm20)
REVERT: S   33 LEU cc_start: 0.9403 (mm) cc_final: 0.9170 (mm)
REVERT: S   52 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7458 (tm-30)
REVERT: S   65 ASP cc_start: 0.8963 (t0) cc_final: 0.8658 (t0)
REVERT: T    4 GLU cc_start: 0.8597 (tp30) cc_final: 0.7845 (tp30)
REVERT: T    5 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8802 (mm-30)
REVERT: Y    7 ARG cc_start: 0.9026 (ptp-170) cc_final: 0.8789 (ptp-170)
REVERT: 2   39 ARG cc_start: 0.9267 (ttp-110) cc_final: 0.8799 (ttp-110)
REVERT: 2   41 ARG cc_start: 0.9060 (tmm-80) cc_final: 0.8436 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 262
  average time/residue: 0.5973
  time to fit residues: 261.7365
Evaluate side-chains
  214 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 2.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 387
   random chunks:
   chunk 311 optimal weight:   10.0000
   chunk 212 optimal weight:   10.0000
   chunk 5 optimal weight:   30.0000
   chunk 278 optimal weight:   30.0000
   chunk 154 optimal weight:    4.9990
   chunk 319 optimal weight:   10.0000
   chunk 258 optimal weight:   40.0000
   chunk 0 optimal weight:   20.0000
   chunk 191 optimal weight:   10.0000
   chunk 335 optimal weight:   20.0000
   chunk 94 optimal weight:    9.9990
   overall best weight:    8.9996

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

Flipped N/Q/H residues before XYZ refinement:
** C  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 167 ASN
** E  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K   3 GLN
Q  19 GLN
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  70 HIS
** Y  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  41 HIS
0  18 HIS
** 2  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.6565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  64644  Z= 0.332
  Angle     :  0.688  12.072  97623  Z= 0.348
  Chirality :  0.037   0.259  12631
  Planarity :  0.006   0.163   4596
  Dihedral  : 24.374 178.753  34296
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 24.12
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.34 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  3.89 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.19), residues: 1812
  helix:  0.02 (0.22), residues: 510
  sheet: -1.20 (0.27), residues: 371
  loop : -1.49 (0.19), residues: 931

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D  80 
 HIS   0.015   0.002   HIS J  47 
 PHE   0.023   0.002   PHE T  51 
 TYR   0.016   0.002   TYR 0  47 
 ARG   0.010   0.001   ARG R  78 

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 258
  time to evaluate  : 2.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.8542 (ttm) cc_final: 0.7496 (mmp)
REVERT: D  108 ASP cc_start: 0.8318 (m-30) cc_final: 0.7394 (p0)
REVERT: D  165 MET cc_start: 0.8979 (mtt) cc_final: 0.8670 (mtt)
REVERT: D  175 LEU cc_start: 0.9104 (mt) cc_final: 0.8860 (mt)
REVERT: D  202 ILE cc_start: 0.9317 (mt) cc_final: 0.9089 (mm)
REVERT: J   92 MET cc_start: 0.8434 (ptp) cc_final: 0.8062 (ptp)
REVERT: J   98 GLU cc_start: 0.8941 (pm20) cc_final: 0.8700 (pm20)
REVERT: J  109 LEU cc_start: 0.9546 (tp) cc_final: 0.9098 (tt)
REVERT: J  118 MET cc_start: 0.9129 (mtp) cc_final: 0.8726 (mtp)
REVERT: K   20 MET cc_start: 0.4854 (mmp) cc_final: 0.4596 (tpp)
REVERT: K   67 LYS cc_start: 0.8994 (ttmt) cc_final: 0.8775 (mtpt)
REVERT: L   77 ILE cc_start: 0.1983 (mm) cc_final: 0.1274 (mm)
REVERT: N    1 MET cc_start: 0.7817 (tmm) cc_final: 0.7060 (ttp)
REVERT: N    5 LYS cc_start: 0.7863 (tptt) cc_final: 0.7575 (ttpp)
REVERT: N   72 ASP cc_start: 0.8939 (t0) cc_final: 0.8396 (t0)
REVERT: P    8 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8467 (tm-30)
REVERT: Q   44 TYR cc_start: 0.8316 (m-80) cc_final: 0.7899 (m-80)
REVERT: Q   48 ASP cc_start: 0.8780 (m-30) cc_final: 0.8573 (m-30)
REVERT: R   37 GLU cc_start: 0.9005 (mp0) cc_final: 0.8630 (pm20)
REVERT: R   43 ASN cc_start: 0.8839 (t0) cc_final: 0.8342 (t0)
REVERT: R   87 GLN cc_start: 0.8493 (pp30) cc_final: 0.8237 (pp30)
REVERT: S   65 ASP cc_start: 0.9017 (t0) cc_final: 0.8750 (t0)
REVERT: S   78 GLU cc_start: 0.8504 (pp20) cc_final: 0.8090 (pp20)
REVERT: S   82 MET cc_start: 0.6002 (pmm) cc_final: 0.5565 (ppp)
REVERT: T   24 MET cc_start: 0.9134 (tpp) cc_final: 0.8905 (tpp)
REVERT: U   14 THR cc_start: 0.7805 (p) cc_final: 0.7470 (t)
REVERT: 2   41 ARG cc_start: 0.9126 (tmm-80) cc_final: 0.8878 (ttp80)
  outliers start: 1
  outliers final: 0
  residues processed: 258
  average time/residue: 0.5875
  time to fit residues: 258.3960
Evaluate side-chains
  204 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 2.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 387
   random chunks:
   chunk 125 optimal weight:    2.9990
   chunk 336 optimal weight:   20.0000
   chunk 73 optimal weight:    7.9990
   chunk 219 optimal weight:   50.0000
   chunk 92 optimal weight:    0.6980
   chunk 374 optimal weight:   20.0000
   chunk 310 optimal weight:   10.0000
   chunk 173 optimal weight:    5.9990
   chunk 31 optimal weight:    0.4980
   chunk 123 optimal weight:   20.0000
   chunk 196 optimal weight:   30.0000
   overall best weight:    3.6386

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

Flipped N/Q/H residues before XYZ refinement:
D  32 ASN
E   9 GLN
** E  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  86 GLN
K   3 GLN
P  40 GLN
Q  43 GLN
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  86 GLN
Y  41 HIS
0  18 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.6262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  64644  Z= 0.169
  Angle     :  0.553  12.495  97623  Z= 0.280
  Chirality :  0.032   0.260  12631
  Planarity :  0.005   0.141   4596
  Dihedral  : 24.093 177.332  34296
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 15.76
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.24 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.37 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.19), residues: 1812
  helix:  0.46 (0.23), residues: 513
  sheet: -1.03 (0.27), residues: 376
  loop : -1.37 (0.19), residues: 923

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 125 
 HIS   0.013   0.001   HIS J  47 
 PHE   0.034   0.002   PHE Z  52 
 TYR   0.015   0.001   TYR E 101 
 ARG   0.012   0.001   ARG D 124 

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 280
  time to evaluate  : 2.374 
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: C  184 GLU cc_start: 0.8720 (pt0) cc_final: 0.8408 (pt0)
REVERT: D    1 MET cc_start: 0.8562 (ttm) cc_final: 0.7520 (mmp)
REVERT: D  108 ASP cc_start: 0.8155 (m-30) cc_final: 0.7156 (p0)
REVERT: D  161 MET cc_start: 0.8021 (tpt) cc_final: 0.7670 (tpt)
REVERT: D  165 MET cc_start: 0.9045 (mtt) cc_final: 0.8783 (mtt)
REVERT: D  175 LEU cc_start: 0.8968 (mt) cc_final: 0.8708 (mt)
REVERT: D  200 ASP cc_start: 0.7981 (m-30) cc_final: 0.7746 (m-30)
REVERT: D  202 ILE cc_start: 0.9324 (mt) cc_final: 0.9075 (mm)
REVERT: E    9 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7332 (mm-40)
REVERT: E  188 MET cc_start: 0.8398 (mmm) cc_final: 0.8130 (tpp)
REVERT: J   36 LEU cc_start: 0.8892 (mt) cc_final: 0.8642 (mm)
REVERT: J   98 GLU cc_start: 0.8890 (pm20) cc_final: 0.8687 (pm20)
REVERT: J  109 LEU cc_start: 0.9525 (tp) cc_final: 0.9133 (tt)
REVERT: J  140 LEU cc_start: 0.8798 (tt) cc_final: 0.8584 (tt)
REVERT: K   20 MET cc_start: 0.4607 (mmp) cc_final: 0.4367 (tpp)
REVERT: K   67 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8572 (mtpt)
REVERT: K  104 THR cc_start: 0.8370 (p) cc_final: 0.8164 (p)
REVERT: K  112 PHE cc_start: 0.8992 (m-10) cc_final: 0.8787 (m-80)
REVERT: L   77 ILE cc_start: 0.1627 (mm) cc_final: 0.1057 (mm)
REVERT: N    1 MET cc_start: 0.7765 (tmm) cc_final: 0.7395 (ttp)
REVERT: N   24 MET cc_start: 0.9354 (ttm) cc_final: 0.8817 (tpp)
REVERT: N   72 ASP cc_start: 0.8942 (t0) cc_final: 0.8469 (t0)
REVERT: N  107 ASN cc_start: 0.8334 (m110) cc_final: 0.8122 (m110)
REVERT: Q   44 TYR cc_start: 0.8039 (m-80) cc_final: 0.7250 (m-80)
REVERT: R   22 LEU cc_start: 0.8835 (tp) cc_final: 0.8621 (tp)
REVERT: R   37 GLU cc_start: 0.8911 (mp0) cc_final: 0.8624 (pm20)
REVERT: R   39 LEU cc_start: 0.8915 (tp) cc_final: 0.8574 (tp)
REVERT: R   43 ASN cc_start: 0.8831 (t0) cc_final: 0.8418 (t0)
REVERT: R   87 GLN cc_start: 0.8492 (pp30) cc_final: 0.8166 (pp30)
REVERT: S   65 ASP cc_start: 0.8840 (t0) cc_final: 0.8471 (t0)
REVERT: S   68 ASP cc_start: 0.8914 (t70) cc_final: 0.8666 (t0)
REVERT: S   78 GLU cc_start: 0.8468 (pp20) cc_final: 0.8060 (pp20)
REVERT: U   14 THR cc_start: 0.7706 (p) cc_final: 0.7377 (t)
REVERT: Y    1 MET cc_start: 0.8099 (tmm) cc_final: 0.7804 (tpt)
REVERT: 2   41 ARG cc_start: 0.9136 (tmm-80) cc_final: 0.8552 (ttp80)
REVERT: Z   15 ARG cc_start: 0.9045 (mmt-90) cc_final: 0.8690 (mmp80)
  outliers start: 2
  outliers final: 0
  residues processed: 281
  average time/residue: 0.5817
  time to fit residues: 275.5510
Evaluate side-chains
  218 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 217
  time to evaluate  : 2.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 387
   random chunks:
   chunk 361 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 213 optimal weight:   10.0000
   chunk 273 optimal weight:   10.0000
   chunk 211 optimal weight:   10.0000
   chunk 315 optimal weight:   30.0000
   chunk 209 optimal weight:   20.0000
   chunk 373 optimal weight:   40.0000
   chunk 233 optimal weight:   10.0000
   chunk 227 optimal weight:   10.0000
   chunk 172 optimal weight:   10.0000
   overall best weight:   10.0000

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

Flipped N/Q/H residues before XYZ refinement:
** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  32 ASN
D 167 ASN
E  30 GLN
** E  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  86 GLN
T  70 HIS
** Y  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  41 HIS
0  18 HIS
2  26 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.7096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  64644  Z= 0.370
  Angle     :  0.738  12.743  97623  Z= 0.371
  Chirality :  0.039   0.285  12631
  Planarity :  0.006   0.141   4596
  Dihedral  : 24.494 175.476  34296
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 27.31
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  9.05 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.57 %
    Favored  : 97.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.19), residues: 1812
  helix:  0.08 (0.23), residues: 520
  sheet: -1.32 (0.28), residues: 340
  loop : -1.61 (0.19), residues: 952

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP J  15 
 HIS   0.011   0.002   HIS 0  37 
 PHE   0.021   0.002   PHE Q 100 
 TYR   0.031   0.003   TYR 0  47 
 ARG   0.012   0.001   ARG D 124 

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 258
  time to evaluate  : 2.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 MET cc_start: 0.8529 (ttm) cc_final: 0.7506 (mmp)
REVERT: D  108 ASP cc_start: 0.8221 (m-30) cc_final: 0.7809 (m-30)
REVERT: D  161 MET cc_start: 0.8425 (tpt) cc_final: 0.7806 (tpt)
REVERT: D  165 MET cc_start: 0.8912 (mtt) cc_final: 0.8636 (mtt)
REVERT: D  175 LEU cc_start: 0.8924 (mt) cc_final: 0.8658 (mt)
REVERT: D  202 ILE cc_start: 0.9311 (mt) cc_final: 0.9059 (mm)
REVERT: J   75 TYR cc_start: 0.8033 (m-80) cc_final: 0.7717 (m-10)
REVERT: J   92 MET cc_start: 0.8304 (ptp) cc_final: 0.7864 (ptp)
REVERT: J  109 LEU cc_start: 0.9561 (tp) cc_final: 0.9165 (tt)
REVERT: J  118 MET cc_start: 0.9112 (mtp) cc_final: 0.8724 (mtp)
REVERT: K   20 MET cc_start: 0.5884 (mmp) cc_final: 0.5376 (tpp)
REVERT: L   77 ILE cc_start: 0.1469 (mm) cc_final: 0.0871 (mm)
REVERT: N   72 ASP cc_start: 0.9155 (t0) cc_final: 0.8645 (t70)
REVERT: Q   44 TYR cc_start: 0.8318 (m-80) cc_final: 0.7933 (m-80)
REVERT: R   37 GLU cc_start: 0.9041 (mp0) cc_final: 0.8671 (pm20)
REVERT: R   43 ASN cc_start: 0.8844 (t0) cc_final: 0.8353 (t0)
REVERT: R   79 ARG cc_start: 0.9387 (ptt180) cc_final: 0.8981 (ptm-80)
REVERT: R   87 GLN cc_start: 0.8565 (pp30) cc_final: 0.7458 (pm20)
REVERT: S   65 ASP cc_start: 0.9017 (t0) cc_final: 0.8763 (t0)
REVERT: S   78 GLU cc_start: 0.8615 (pp20) cc_final: 0.8199 (pp20)
REVERT: S   82 MET cc_start: 0.5825 (pmm) cc_final: 0.5438 (ppp)
REVERT: U   14 THR cc_start: 0.7798 (p) cc_final: 0.7458 (t)
REVERT: 2   41 ARG cc_start: 0.9139 (tmm-80) cc_final: 0.8521 (ttp80)
REVERT: Z   18 LYS cc_start: 0.8110 (ptpp) cc_final: 0.7200 (tptp)
  outliers start: 2
  outliers final: 0
  residues processed: 259
  average time/residue: 0.5953
  time to fit residues: 258.9471
Evaluate side-chains
  206 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 2.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 387
   random chunks:
   chunk 230 optimal weight:   10.0000
   chunk 148 optimal weight:   40.0000
   chunk 222 optimal weight:   40.0000
   chunk 112 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 72 optimal weight:    6.9990
   chunk 237 optimal weight:   20.0000
   chunk 254 optimal weight:   40.0000
   chunk 184 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 293 optimal weight:   10.0000
   overall best weight:    5.5992

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

Flipped N/Q/H residues before XYZ refinement:
D 167 ASN
E   9 GLN
** E  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  97 ASN
Q  43 GLN
** Q  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  86 GLN
** Y  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  41 HIS
0  18 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.6952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  64644  Z= 0.228
  Angle     :  0.601  12.125  97623  Z= 0.305
  Chirality :  0.034   0.267  12631
  Planarity :  0.005   0.137   4596
  Dihedral  : 24.333 179.894  34296
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 19.63
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.28 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.19 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.19), residues: 1812
  helix:  0.35 (0.23), residues: 515
  sheet: -1.28 (0.27), residues: 359
  loop : -1.50 (0.19), residues: 938

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 125 
 HIS   0.009   0.001   HIS J  47 
 PHE   0.019   0.002   PHE N  21 
 TYR   0.020   0.002   TYR 0  47 
 ARG   0.010   0.001   ARG D 124 

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 265
  time to evaluate  : 2.403 
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  184 GLU cc_start: 0.8931 (pt0) cc_final: 0.8689 (pt0)
REVERT: D    1 MET cc_start: 0.8421 (ttm) cc_final: 0.7458 (mmp)
REVERT: D  108 ASP cc_start: 0.8069 (m-30) cc_final: 0.7641 (m-30)
REVERT: D  161 MET cc_start: 0.8360 (tpt) cc_final: 0.7774 (tpt)
REVERT: D  165 MET cc_start: 0.8882 (mtt) cc_final: 0.8640 (mtt)
REVERT: D  175 LEU cc_start: 0.9012 (mt) cc_final: 0.8725 (mt)
REVERT: D  202 ILE cc_start: 0.9361 (mt) cc_final: 0.9073 (mm)
REVERT: J   92 MET cc_start: 0.8763 (ptp) cc_final: 0.8455 (ptp)
REVERT: J  109 LEU cc_start: 0.9511 (tp) cc_final: 0.9177 (tt)
REVERT: K   20 MET cc_start: 0.5308 (mmp) cc_final: 0.4918 (tpp)
REVERT: K  112 PHE cc_start: 0.8761 (m-10) cc_final: 0.8541 (m-10)
REVERT: L   77 ILE cc_start: 0.1403 (mm) cc_final: 0.0827 (mm)
REVERT: N    1 MET cc_start: 0.8010 (tmm) cc_final: 0.7402 (tmm)
REVERT: N   72 ASP cc_start: 0.9077 (t0) cc_final: 0.8613 (t70)
REVERT: Q   44 TYR cc_start: 0.8231 (m-80) cc_final: 0.7788 (m-80)
REVERT: Q   48 ASP cc_start: 0.8702 (m-30) cc_final: 0.8431 (m-30)
REVERT: R   37 GLU cc_start: 0.9075 (mp0) cc_final: 0.8647 (pm20)
REVERT: R   39 LEU cc_start: 0.9109 (tp) cc_final: 0.8822 (tp)
REVERT: R   43 ASN cc_start: 0.8816 (t0) cc_final: 0.8398 (t0)
REVERT: R   79 ARG cc_start: 0.9355 (ptt180) cc_final: 0.8916 (ptm-80)
REVERT: R   87 GLN cc_start: 0.8513 (pp30) cc_final: 0.8215 (pp30)
REVERT: S   65 ASP cc_start: 0.9012 (t0) cc_final: 0.8661 (t0)
REVERT: S   78 GLU cc_start: 0.8536 (pp20) cc_final: 0.8114 (pp20)
REVERT: S   82 MET cc_start: 0.5660 (pmm) cc_final: 0.5344 (ppp)
REVERT: U   14 THR cc_start: 0.7664 (p) cc_final: 0.7371 (t)
REVERT: 2   31 LEU cc_start: 0.9584 (tt) cc_final: 0.9227 (mm)
REVERT: 2   41 ARG cc_start: 0.9136 (tmm-80) cc_final: 0.8530 (ttp80)
REVERT: Z   18 LYS cc_start: 0.8069 (ptpp) cc_final: 0.7168 (tptp)
  outliers start: 2
  outliers final: 0
  residues processed: 265
  average time/residue: 0.5840
  time to fit residues: 261.6549
Evaluate side-chains
  221 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 2.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 387
   random chunks:
   chunk 339 optimal weight:   20.0000
   chunk 357 optimal weight:   20.0000
   chunk 326 optimal weight:   20.0000
   chunk 347 optimal weight:   40.0000
   chunk 209 optimal weight:   20.0000
   chunk 151 optimal weight:   10.0000
   chunk 272 optimal weight:   30.0000
   chunk 106 optimal weight:   10.0000
   chunk 314 optimal weight:   20.0000
   chunk 328 optimal weight:   20.0000
   chunk 346 optimal weight:   30.0000
   overall best weight:   16.0000

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

Flipped N/Q/H residues before XYZ refinement:
** C  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  67 HIS
D 167 ASN
** E  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  74 GLN
Q  58 GLN
R  86 GLN
S  40 ASN
** T  15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
T  70 HIS
** U  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  41 HIS
** 0   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.8176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.084  64644  Z= 0.578
  Angle     :  0.978  14.582  97623  Z= 0.484
  Chirality :  0.048   0.324  12631
  Planarity :  0.007   0.150   4596
  Dihedral  : 25.067 170.848  34296
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 41.21
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 10.87 %
    Favored  : 89.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.44 (0.18), residues: 1812
  helix: -0.66 (0.21), residues: 516
  sheet: -1.74 (0.27), residues: 327
  loop : -2.13 (0.18), residues: 969

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP J  15 
 HIS   0.017   0.003   HIS 0  37 
 PHE   0.028   0.003   PHE J   4 
 TYR   0.047   0.003   TYR 0  47 
 ARG   0.016   0.001   ARG D 124 

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 2.395 
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: C  134 ILE cc_start: 0.7741 (mt) cc_final: 0.7530 (tt)
REVERT: D  161 MET cc_start: 0.8548 (tpt) cc_final: 0.7977 (tpt)
REVERT: D  165 MET cc_start: 0.8958 (mtt) cc_final: 0.8656 (mtt)
REVERT: D  175 LEU cc_start: 0.8952 (mt) cc_final: 0.8645 (mt)
REVERT: D  202 ILE cc_start: 0.9308 (mt) cc_final: 0.9056 (mm)
REVERT: J   14 ASP cc_start: 0.8122 (p0) cc_final: 0.7310 (p0)
REVERT: J  109 LEU cc_start: 0.9587 (tp) cc_final: 0.9286 (tt)
REVERT: K  112 PHE cc_start: 0.8770 (m-10) cc_final: 0.8469 (m-10)
REVERT: N   72 ASP cc_start: 0.9211 (t0) cc_final: 0.8812 (t70)
REVERT: Q   48 ASP cc_start: 0.9010 (m-30) cc_final: 0.8774 (m-30)
REVERT: R   37 GLU cc_start: 0.9163 (mp0) cc_final: 0.8850 (pm20)
REVERT: R   39 LEU cc_start: 0.9182 (tp) cc_final: 0.8972 (tp)
REVERT: R   43 ASN cc_start: 0.8800 (t0) cc_final: 0.8421 (t0)
REVERT: R   87 GLN cc_start: 0.8714 (pp30) cc_final: 0.7636 (pm20)
REVERT: S   52 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7710 (tm-30)
REVERT: S   78 GLU cc_start: 0.8557 (pp20) cc_final: 0.8192 (pp20)
REVERT: S   82 MET cc_start: 0.6470 (pmm) cc_final: 0.5999 (ppp)
REVERT: T   24 MET cc_start: 0.9242 (tpt) cc_final: 0.8670 (tpp)
REVERT: T   32 LEU cc_start: 0.9389 (pp) cc_final: 0.9160 (pp)
REVERT: Y    1 MET cc_start: 0.8754 (tpt) cc_final: 0.8425 (tpp)
REVERT: 2   41 ARG cc_start: 0.9127 (tmm-80) cc_final: 0.8895 (tmm-80)
REVERT: Z   18 LYS cc_start: 0.8175 (ptpp) cc_final: 0.7322 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 231
  average time/residue: 0.5839
  time to fit residues: 228.1831
Evaluate side-chains
  180 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 2.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 387
   random chunks:
   chunk 228 optimal weight:    4.9990
   chunk 367 optimal weight:    7.9990
   chunk 224 optimal weight:    6.9990
   chunk 174 optimal weight:    5.9990
   chunk 255 optimal weight:   30.0000
   chunk 385 optimal weight:    5.9990
   chunk 354 optimal weight:   10.0000
   chunk 307 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 237 optimal weight:   10.0000
   chunk 188 optimal weight:    8.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
D  67 HIS
D 167 ASN
** E  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  86 GLN
** Y  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  41 HIS
0  18 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.7723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  64644  Z= 0.258
  Angle     :  0.654  12.226  97623  Z= 0.331
  Chirality :  0.036   0.296  12631
  Planarity :  0.005   0.149   4596
  Dihedral  : 24.635 178.791  34296
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 21.98
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.22 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.19), residues: 1812
  helix: -0.04 (0.22), residues: 514
  sheet: -1.60 (0.26), residues: 357
  loop : -1.85 (0.19), residues: 941

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D 125 
 HIS   0.014   0.002   HIS J  47 
 PHE   0.029   0.002   PHE N  21 
 TYR   0.024   0.002   TYR C 102 
 ARG   0.015   0.001   ARG P 108 

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

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

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3624 Ramachandran restraints generated.
    1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 2.406 
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  184 GLU cc_start: 0.8634 (pt0) cc_final: 0.8251 (pt0)
REVERT: D    1 MET cc_start: 0.8434 (ttm) cc_final: 0.7491 (mmp)
REVERT: D  108 ASP cc_start: 0.8163 (m-30) cc_final: 0.7366 (p0)
REVERT: D  161 MET cc_start: 0.8469 (tpt) cc_final: 0.7943 (tpt)
REVERT: D  165 MET cc_start: 0.8901 (mtt) cc_final: 0.8593 (mtt)
REVERT: D  175 LEU cc_start: 0.9091 (mt) cc_final: 0.8843 (mt)
REVERT: D  202 ILE cc_start: 0.9352 (mt) cc_final: 0.9070 (mm)
REVERT: J  109 LEU cc_start: 0.9533 (tp) cc_final: 0.9234 (tt)
REVERT: K    1 MET cc_start: 0.7784 (tpt) cc_final: 0.7539 (tpt)
REVERT: K   20 MET cc_start: 0.5928 (mmp) cc_final: 0.5250 (tpp)
REVERT: K  112 PHE cc_start: 0.8719 (m-10) cc_final: 0.8165 (m-10)
REVERT: N   43 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8710 (mm-30)
REVERT: N   72 ASP cc_start: 0.9057 (t0) cc_final: 0.8480 (t0)
REVERT: N  107 ASN cc_start: 0.9118 (t0) cc_final: 0.8762 (t0)
REVERT: Q   44 TYR cc_start: 0.8367 (m-80) cc_final: 0.7932 (m-80)
REVERT: Q   48 ASP cc_start: 0.8824 (m-30) cc_final: 0.8600 (m-30)
REVERT: R   37 GLU cc_start: 0.9120 (mp0) cc_final: 0.8724 (pm20)
REVERT: R   39 LEU cc_start: 0.9202 (tp) cc_final: 0.8885 (tp)
REVERT: R   43 ASN cc_start: 0.8833 (t0) cc_final: 0.8446 (t0)
REVERT: R   87 GLN cc_start: 0.8531 (pp30) cc_final: 0.8245 (pp30)
REVERT: S   78 GLU cc_start: 0.8529 (pp20) cc_final: 0.8174 (pp20)
REVERT: S   82 MET cc_start: 0.5914 (pmm) cc_final: 0.5498 (ppp)
REVERT: T   24 MET cc_start: 0.9203 (tpt) cc_final: 0.8724 (tpp)
REVERT: Y   18 LEU cc_start: 0.9809 (tp) cc_final: 0.9530 (pp)
REVERT: Y   30 MET cc_start: 0.8717 (mmm) cc_final: 0.8046 (mmm)
REVERT: 2   41 ARG cc_start: 0.9091 (tmm-80) cc_final: 0.8498 (ttp80)
REVERT: Z   18 LYS cc_start: 0.8077 (ptpp) cc_final: 0.7404 (mmtt)
REVERT: Z   35 VAL cc_start: 0.7591 (p) cc_final: 0.7376 (m)
REVERT: Z   36 GLU cc_start: 0.8425 (pp20) cc_final: 0.7746 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.5809
  time to fit residues: 259.7775
Evaluate side-chains
  213 residues out of total 1516 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 2.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 387
   random chunks:
   chunk 243 optimal weight:   30.0000
   chunk 327 optimal weight:   10.0000
   chunk 94 optimal weight:   10.0000
   chunk 283 optimal weight:   20.0000
   chunk 45 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 307 optimal weight:   20.0000
   chunk 128 optimal weight:    7.9990
   chunk 315 optimal weight:   30.0000
   chunk 38 optimal weight:    7.9990
   chunk 56 optimal weight:    9.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
D  32 ASN
D 167 ASN
** E  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  70 HIS
** Y  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
0  18 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.056357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.041817 restraints weight = 553357.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.042869 restraints weight = 239071.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.043505 restraints weight = 154804.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.7757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  64644  Z= 0.272
  Angle     :  0.654  11.603  97623  Z= 0.331
  Chirality :  0.036   0.296  12631
  Planarity :  0.005   0.136   4596
  Dihedral  : 24.588 178.404  34296
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 23.32
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.22 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.19), residues: 1812
  helix:  0.14 (0.23), residues: 516
  sheet: -1.61 (0.27), residues: 341
  loop : -1.84 (0.18), residues: 955

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D 125 
 HIS   0.015   0.002   HIS J  47 
 PHE   0.022   0.002   PHE Q 100 
 TYR   0.026   0.002   TYR S  38 
 ARG   0.012   0.001   ARG R  78 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6949.18 seconds
wall clock time: 136 minutes 28.66 seconds (8188.66 seconds total)