Starting phenix.real_space_refine
on Sat Mar 23 06:45:43 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c97_16504/03_2024/8c97_16504.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c97_16504/03_2024/8c97_16504.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c97_16504/03_2024/8c97_16504.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c97_16504/03_2024/8c97_16504.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c97_16504/03_2024/8c97_16504.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c97_16504/03_2024/8c97_16504.pdb"
  }
  resolution = 4.07
  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=   0.017 sd=   0.096
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    1292      5.49       5
     S      25      5.16       5
     C   17639      2.51       5
     N    6738      2.21       5
     O   10469      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "T GLU    4": "OE1" <-> "OE2"
    Residue "T GLU    5": "OE1" <-> "OE2"
    Residue "U PHE   72": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 36163
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "0"
      Number of atoms: 263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 263
          Classifications: {'peptide': 33}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 32}
    Chain: "2"
      Number of atoms: 262
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 262
          Classifications: {'peptide': 32}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 31}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 27767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1292, 27767
          Classifications: {'RNA': 1292}
          Modifications used: {'rna2p_pur': 119, 'rna2p_pyr': 70, 'rna3p_pur': 641, 'rna3p_pyr': 462}
          Link IDs: {'rna2p': 189, 'rna3p': 1102}
          Chain breaks: 6
    Chain: "D"
      Number of atoms: 1200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1200
          Classifications: {'peptide': 161}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 156}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1129
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 143}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 938
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
    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: "S"
      Number of atoms: 717
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 717
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 91}
          Chain breaks: 1
    Chain: "T"
      Number of atoms: 722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 722
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 1, 'TRANS': 89}
    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}
  Time building chain proxies: 18.30, per 1000 atoms: 0.51
  Number of scatterers: 36163
  At special positions: 0
  Unit cell: (150, 175, 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      25     16.00
     P    1292     15.00
     O   10469      8.00
     N    6738      7.00
     C   17639      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  - 3.50
        Amino acid           : False - 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: 21.13
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2006

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 15 sheets defined
      31.6% alpha, 21.4% beta
      404 base pairs and 629 stacking pairs defined.
    Time for finding SS restraints: 16.74
  Creating SS restraints...
    Processing helix  chain '2' and resid 11 through 16
    Processing helix  chain '2' and resid 17 through 24
    Processing helix  chain '2' and resid 24 through 36
    Processing helix  chain 'D' and resid 39 through 44
    Processing helix  chain 'D' and resid 61 through 72
      removed outlier: 3.774A  pdb=" N   LYS D  70 " --> pdb=" O   GLY D  66 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   ALA D  71 " --> pdb=" O   HIS D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 97 through 103
      removed outlier: 4.326A  pdb=" N   ASP D 103 " --> pdb=" O   LEU D 100 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 15 through 20
    Processing helix  chain 'E' and resid 24 through 39
    Processing helix  chain 'E' and resid 97 through 115
    Processing helix  chain 'E' and resid 130 through 142
      removed outlier: 3.513A  pdb=" N   LEU E 134 " --> pdb=" O   LYS E 130 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 154 through 160
      removed outlier: 3.541A  pdb=" N   PHE E 158 " --> pdb=" O   ASP E 154 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 176 through 183
      removed outlier: 3.680A  pdb=" N   PHE E 183 " --> pdb=" O   SER E 179 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 191 through 201
      removed outlier: 4.122A  pdb=" N   GLN E 195 " --> pdb=" O   ASP E 191 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 109 through 113
      removed outlier: 3.800A  pdb=" N   MET K 113 " --> pdb=" O   GLU K 110 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 13 through 32
      removed outlier: 3.542A  pdb=" N   GLN N  18 " --> pdb=" O   SER N  14 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 37 through 56
      removed outlier: 3.712A  pdb=" N   ARG N  46 " --> pdb=" O   LYS N  42 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL N  47 " --> pdb=" O   GLU N  43 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLU N  49 " --> pdb=" O   ARG N  45 " (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 88
    Processing helix  chain 'P' and resid 2 through 10
    Processing helix  chain 'P' and resid 52 through 55
    Processing helix  chain 'P' and resid 96 through 101
    Processing helix  chain 'P' and resid 103 through 108
    Processing helix  chain 'S' and resid 15 through 23
    Processing helix  chain 'S' and resid 28 through 39
    Processing helix  chain 'S' and resid 42 through 62
      removed outlier: 3.981A  pdb=" N   LEU S  46 " --> pdb=" O   LYS S  42 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 17 through 28
    Processing helix  chain 'T' and resid 39 through 52
    Processing helix  chain 'U' and resid 65 through 67
      No H-bonds generated for 'chain 'U' and resid 65 through 67'
    Processing helix  chain 'Y' and resid 2 through 7
    Processing helix  chain 'Y' and resid 9 through 33
      removed outlier: 4.069A  pdb=" N   GLN Y  25 " --> pdb=" O   LEU Y  21 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   PHE Y  26 " --> pdb=" O   LEU Y  22 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   GLN Y  31 " --> pdb=" O   ASN Y  27 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 46 through 56
    Processing sheet with id=AA1, first strand: chain '0' and resid 28 through 29
    Processing sheet with id=AA2, first strand: chain '0' and resid 47 through 48
    Processing sheet with id=AA3, first strand: chain 'D' and resid 170 through 176
      removed outlier: 5.059A  pdb=" N   THR D 171 " --> pdb=" O   GLY D 111 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   GLY D 111 " --> pdb=" O   THR D 171 " (cutoff:3.500A)
      removed outlier: 5.344A  pdb=" N   GLN D 173 " --> pdb=" O   VAL D 109 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   VAL D 109 " --> pdb=" O   GLN D 173 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ILE D  27 " --> pdb=" O   LEU D 187 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU D 187 " --> pdb=" O   ILE D  27 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 12 through 15
    Processing sheet with id=AA5, first strand: chain 'D' and resid 34 through 38
      removed outlier: 5.653A  pdb=" N   VAL D  34 " --> pdb=" O   THR D  51 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   THR D  51 " --> pdb=" O   VAL D  34 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 121
      removed outlier: 3.707A  pdb=" N   ASP E 168 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'K' and resid 6 through 10
      removed outlier: 3.704A  pdb=" N   VAL K  10 " --> pdb=" O   ARG K  17 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ARG K  17 " --> pdb=" O   VAL K  10 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ALA K  16 " --> pdb=" O   ALA K  46 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ALA K  46 " --> pdb=" O   ALA K  16 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ARG K  18 " --> pdb=" O   LYS K  44 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   LYS K  40 " --> pdb=" O   ILE K  22 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   VAL K  24 " --> pdb=" O   ILE K  38 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   ILE K  38 " --> pdb=" O   VAL K  24 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   VAL K  62 " --> pdb=" O   VAL K  85 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   VAL K  85 " --> pdb=" O   VAL K  62 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   CYS K  84 " --> pdb=" O   MET K   7 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   ASN K   9 " --> pdb=" O   CYS K  84 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   LEU K  86 " --> pdb=" O   ASN K   9 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 69 through 70
      removed outlier: 3.907A  pdb=" N   VAL K  69 " --> pdb=" O   ILE K  77 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE K  77 " --> pdb=" O   VAL K  69 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   VAL K  76 " --> pdb=" O   VAL P  72 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA P  48 " --> pdb=" O   THR P  59 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   ARG P  61 " --> pdb=" O   VAL P  46 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   VAL P  46 " --> pdb=" O   ARG P  61 " (cutoff:3.500A)
      removed outlier: 8.324A  pdb=" N   ILE P  63 " --> pdb=" O   GLY P  44 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   GLY P  44 " --> pdb=" O   ILE P  63 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL P  46 " --> pdb=" O   ASP P  23 " (cutoff:3.500A)
      removed outlier: 5.181A  pdb=" N   ASP P  23 " --> pdb=" O   VAL P  46 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   GLU P  26 " --> pdb=" O   VAL P  85 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   VAL P  85 " --> pdb=" O   GLU P  26 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   LYS P  28 " --> pdb=" O   ILE P  83 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   ILE P  83 " --> pdb=" O   LYS P  28 " (cutoff:3.500A)
      removed outlier: 7.559A  pdb=" N   TRP P  30 " --> pdb=" O   ASP P  81 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   ASP P  81 " --> pdb=" O   TRP P  30 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 33 through 36
      removed outlier: 6.649A  pdb=" N   MET N 110 " --> pdb=" O   CYS N 100 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 2 through 10
      removed outlier: 5.176A  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: 5.321A  pdb=" N   LYS S   6 " --> pdb=" O   VAL S 105 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   VAL S 105 " --> pdb=" O   LYS S   6 " (cutoff:3.500A)
      removed outlier: 5.427A  pdb=" N   ARG S   8 " --> pdb=" O   ILE S 103 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ILE S 103 " --> pdb=" O   ARG S   8 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   HIS S 102 " --> pdb=" O   VAL S  76 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   VAL S  76 " --> pdb=" O   HIS S 102 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   THR S 104 " --> pdb=" O   ILE S  74 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   ILE S  74 " --> pdb=" O   THR S 104 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   VAL S 106 " --> pdb=" O   THR S  72 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'T' and resid 13 through 14
      removed outlier: 3.811A  pdb=" N   LYS T  81 " --> pdb=" O   VAL T  34 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   TRP T  80 " --> pdb=" O   VAL T  62 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   VAL T  62 " --> pdb=" O   TRP T  80 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   LYS T  82 " --> pdb=" O   THR T  60 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   THR T  60 " --> pdb=" O   LYS T  82 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   TYR T  84 " --> pdb=" O   VAL T  58 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   VAL T  58 " --> pdb=" O   TYR T  84 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   THR T  86 " --> pdb=" O   GLU T  56 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'T' and resid 67 through 68
    Processing sheet with id=AB4, first strand: chain 'U' and resid 33 through 35
      removed outlier: 3.827A  pdb=" N   ASN U  26 " --> pdb=" O   ILE U  34 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   GLU U   9 " --> pdb=" O   PHE U  72 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   PHE U  72 " --> pdb=" O   GLU U   9 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ASN U  73 " --> pdb=" O   LYS U  78 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LYS U  78 " --> pdb=" O   ASN U  73 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'U' and resid 40 through 41
      removed outlier: 3.520A  pdb=" N   LYS U  60 " --> pdb=" O   VAL U  41 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'U' and resid 82 through 86

    311 hydrogen bonds defined for protein.
    858 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      1029 hydrogen bonds
      1648 hydrogen bond angles
      0 basepair planarities
      404 basepair parallelities
      629 stacking parallelities
  Total time for adding SS restraints: 26.85

  Time building geometry restraints manager: 22.23 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 5958
        1.33 -     1.45: 16665
        1.45 -     1.57: 14330
        1.57 -     1.69: 2578
        1.69 -     1.81: 47
  Bond restraints: 39578
  Sorted by residual:
  bond pdb=" C1'   U A 138 "
       pdb=" N1    U A 138 "
    ideal  model  delta    sigma   weight residual
    1.480  1.573 -0.093 1.50e-02 4.44e+03 3.83e+01
  bond pdb=" O5'   A A2733 "
       pdb=" C5'   A A2733 "
    ideal  model  delta    sigma   weight residual
    1.420  1.457 -0.037 1.50e-02 4.44e+03 5.93e+00
  bond pdb=" N   GLU T   4 "
       pdb=" CA  GLU T   4 "
    ideal  model  delta    sigma   weight residual
    1.453  1.484 -0.031 1.37e-02 5.33e+03 4.97e+00
  bond pdb=" N   GLU T   5 "
       pdb=" CA  GLU T   5 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.29e-02 6.01e+03 4.92e+00
  bond pdb=" O5'   A A2734 "
       pdb=" C5'   A A2734 "
    ideal  model  delta    sigma   weight residual
    1.420  1.448 -0.028 1.50e-02 4.44e+03 3.49e+00
  ... (remaining 39573 not shown)

  Histogram of bond angle deviations from ideal:
       98.46 -   105.56: 6249
      105.56 -   112.66: 23321
      112.66 -   119.76: 13816
      119.76 -   126.85: 13075
      126.85 -   133.95: 3406
  Bond angle restraints: 59867
  Sorted by residual:
  angle pdb=" C3'   A A2733 "
        pdb=" O3'   A A2733 "
        pdb=" P     A A2734 "
      ideal   model   delta    sigma   weight residual
     120.20  106.05   14.15 1.50e+00 4.44e-01 8.89e+01
  angle pdb=" N   GLU T   4 "
        pdb=" CA  GLU T   4 "
        pdb=" C   GLU T   4 "
      ideal   model   delta    sigma   weight residual
     110.41  104.28    6.13 1.23e+00 6.61e-01 2.48e+01
  angle pdb=" C3'   G A2732 "
        pdb=" O3'   G A2732 "
        pdb=" P     A A2733 "
      ideal   model   delta    sigma   weight residual
     120.20  112.76    7.44 1.50e+00 4.44e-01 2.46e+01
  angle pdb=" CA  GLU T   4 "
        pdb=" C   GLU T   4 "
        pdb=" O   GLU T   4 "
      ideal   model   delta    sigma   weight residual
     121.99  116.68    5.31 1.14e+00 7.69e-01 2.17e+01
  angle pdb=" O2'   A A2733 "
        pdb=" C2'   A A2733 "
        pdb=" C1'   A A2733 "
      ideal   model   delta    sigma   weight residual
     108.40  114.33   -5.93 1.50e+00 4.44e-01 1.57e+01
  ... (remaining 59862 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.91: 22201
       35.91 -    71.82: 2787
       71.82 -   107.73: 346
      107.73 -   143.64: 14
      143.64 -   179.54: 4
  Dihedral angle restraints: 25352
    sinusoidal: 22272
      harmonic: 3080
  Sorted by residual:
  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   42.32 -170.32     1      1.70e+01 3.46e-03 6.60e+01
  dihedral pdb=" O4'   U A1313 "
           pdb=" C1'   U A1313 "
           pdb=" N1    U A1313 "
           pdb=" C2    U A1313 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   95.41  104.59     1      1.50e+01 4.44e-03 5.34e+01
  dihedral pdb=" O4'   C A 323 "
           pdb=" C1'   C A 323 "
           pdb=" N1    C A 323 "
           pdb=" C2    C A 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -18.41 -109.59     1      1.70e+01 3.46e-03 4.44e+01
  ... (remaining 25349 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 7660
       0.092 -    0.184: 126
       0.184 -    0.276: 1
       0.276 -    0.368: 1
       0.368 -    0.460: 2
  Chirality restraints: 7790
  Sorted by residual:
  chirality pdb=" P     G A2732 "
            pdb=" OP1   G A2732 "
            pdb=" OP2   G A2732 "
            pdb=" O5'   G A2732 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.87   -0.46 2.00e-01 2.50e+01 5.29e+00
  chirality pdb=" P     A A2733 "
            pdb=" OP1   A A2733 "
            pdb=" OP2   A A2733 "
            pdb=" O5'   A A2733 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.87   -0.46 2.00e-01 2.50e+01 5.18e+00
  chirality pdb=" P     A A2734 "
            pdb=" OP1   A A2734 "
            pdb=" OP2   A A2734 "
            pdb=" O5'   A A2734 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.75   -0.34 2.00e-01 2.50e+01 2.92e+00
  ... (remaining 7787 not shown)

  Planarity restraints: 2745
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A1575 "    0.003 2.00e-02 2.50e+03   1.94e-02 8.44e+00
        pdb=" N1    C A1575 "   -0.006 2.00e-02 2.50e+03
        pdb=" C2    C A1575 "   -0.047 2.00e-02 2.50e+03
        pdb=" O2    C A1575 "    0.031 2.00e-02 2.50e+03
        pdb=" N3    C A1575 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    C A1575 "   -0.002 2.00e-02 2.50e+03
        pdb=" N4    C A1575 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    C A1575 "    0.007 2.00e-02 2.50e+03
        pdb=" C6    C A1575 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A 305 "   -0.005 2.00e-02 2.50e+03   1.55e-02 5.42e+00
        pdb=" N1    C A 305 "    0.010 2.00e-02 2.50e+03
        pdb=" C2    C A 305 "   -0.038 2.00e-02 2.50e+03
        pdb=" O2    C A 305 "    0.023 2.00e-02 2.50e+03
        pdb=" N3    C A 305 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    C A 305 "   -0.006 2.00e-02 2.50e+03
        pdb=" N4    C A 305 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    C A 305 "    0.004 2.00e-02 2.50e+03
        pdb=" C6    C A 305 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 363 "   -0.004 2.00e-02 2.50e+03   1.14e-02 3.92e+00
        pdb=" N9    G A 363 "    0.004 2.00e-02 2.50e+03
        pdb=" C8    G A 363 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    G A 363 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5    G A 363 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    G A 363 "   -0.005 2.00e-02 2.50e+03
        pdb=" O6    G A 363 "    0.001 2.00e-02 2.50e+03
        pdb=" N1    G A 363 "    0.004 2.00e-02 2.50e+03
        pdb=" C2    G A 363 "    0.030 2.00e-02 2.50e+03
        pdb=" N2    G A 363 "   -0.024 2.00e-02 2.50e+03
        pdb=" N3    G A 363 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    G A 363 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 2742 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 256
        2.50 -     3.10: 25207
        3.10 -     3.70: 68095
        3.70 -     4.30: 95019
        4.30 -     4.90: 129330
  Nonbonded interactions: 317907
  Sorted by model distance:
  nonbonded pdb=" O2'   G A1734 "
            pdb=" OP1   A A1735 "
     model   vdw
     1.904 2.440
  nonbonded pdb=" O2'   G A2692 "
            pdb=" O2'   U A2847 "
     model   vdw
     1.926 2.440
  nonbonded pdb=" O2'   C A1351 "
            pdb=" O2'   A A1571 "
     model   vdw
     1.931 2.440
  nonbonded pdb=" O2'   G A2859 "
            pdb=" O4'   A A2860 "
     model   vdw
     1.943 2.440
  nonbonded pdb=" OP2   G A1521 "
            pdb=" O2'   A A1522 "
     model   vdw
     1.976 2.440
  ... (remaining 317902 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             1.500
  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:             0.040
  Extract box with map and model:          7.510
  Check model and map are aligned:         0.510
  Set scattering table:                    0.320
  Process input model:                     118.450
  Find NCS groups from input model:        0.680
  Set up NCS constraints:                  0.100
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  132.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.093  39578  Z= 0.095
  Angle     :  0.391  14.146  59867  Z= 0.205
  Chirality :  0.027   0.460   7790
  Planarity :  0.002   0.025   2745
  Dihedral  : 23.091 179.544  23346
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.58 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  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:  0.72 (0.28), residues: 1047
  helix:  2.05 (0.34), residues: 301
  sheet:  0.67 (0.36), residues: 233
  loop : -0.57 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP T  80 
 HIS   0.002   0.000   HIS S   7 
 PHE   0.008   0.001   PHE U  95 
 TYR   0.004   0.001   TYR N 112 
 ARG   0.002   0.000   ARG U  85 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 2.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   11 MET cc_start: 0.7337 (ptm) cc_final: 0.7043 (ppp)
REVERT: E    1 MET cc_start: 0.9193 (tmm) cc_final: 0.8787 (tmm)
REVERT: K    4 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7523 (mp0)
REVERT: K   20 MET cc_start: 0.8023 (ttt) cc_final: 0.7681 (tpp)
REVERT: K  109 SER cc_start: 0.8242 (t) cc_final: 0.7994 (p)
REVERT: K  113 MET cc_start: 0.8764 (mmp) cc_final: 0.8478 (mmm)
REVERT: S   68 ASP cc_start: 0.8803 (t0) cc_final: 0.8233 (t0)
REVERT: S  110 ARG cc_start: 0.8923 (tmm-80) cc_final: 0.8481 (ttp80)
REVERT: U   38 ILE cc_start: 0.9062 (mm) cc_final: 0.8835 (mm)
REVERT: Y   30 MET cc_start: 0.8937 (mmp) cc_final: 0.8426 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.4943
  time to fit residues: 50.0435
Evaluate side-chains
  40 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 1.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 197 optimal weight:   10.0000
   chunk 177 optimal weight:   50.0000
   chunk 98 optimal weight:   30.0000
   chunk 60 optimal weight:   50.0000
   chunk 119 optimal weight:   20.0000
   chunk 94 optimal weight:   20.0000
   chunk 183 optimal weight:   10.0000
   chunk 70 optimal weight:   20.0000
   chunk 111 optimal weight:   30.0000
   chunk 136 optimal weight:    5.9990
   chunk 212 optimal weight:   20.0000
   overall best weight:   13.1998

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

Flipped N/Q/H residues before XYZ refinement:
0  41 HIS
D  36 GLN
E 115 GLN
** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  62 ASN
S  31 GLN
S  61 ASN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.091  39578  Z= 0.442
  Angle     :  0.838  10.936  59867  Z= 0.413
  Chirality :  0.041   0.262   7790
  Planarity :  0.006   0.059   2745
  Dihedral  : 24.506 179.801  21228
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 28.21
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.55 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  4.77 %
    Favored  : 94.89 %
  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: -0.85 (0.26), residues: 1047
  helix: -0.16 (0.29), residues: 322
  sheet: -0.23 (0.34), residues: 222
  loop : -0.89 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP P  30 
 HIS   0.007   0.002   HIS K  29 
 PHE   0.035   0.003   PHE N  87 
 TYR   0.011   0.002   TYR E 101 
 ARG   0.009   0.001   ARG 2  34 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 1.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.8973 (tmm) cc_final: 0.8584 (tmm)
REVERT: K   20 MET cc_start: 0.7715 (ttt) cc_final: 0.7264 (tpp)
REVERT: K  109 SER cc_start: 0.7476 (t) cc_final: 0.7101 (t)
REVERT: N    1 MET cc_start: 0.0846 (ttt) cc_final: 0.0576 (ttp)
REVERT: N  110 MET cc_start: 0.8773 (tpt) cc_final: 0.8552 (mmm)
REVERT: Y   30 MET cc_start: 0.8822 (mmp) cc_final: 0.8417 (mmp)
  outliers start: 3
  outliers final: 2
  residues processed: 43
  average time/residue: 0.4879
  time to fit residues: 36.3695
Evaluate side-chains
  36 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 1.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 118 optimal weight:   10.0000
   chunk 65 optimal weight:   50.0000
   chunk 176 optimal weight:    6.9990
   chunk 144 optimal weight:    9.9990
   chunk 58 optimal weight:   30.0000
   chunk 212 optimal weight:    5.9990
   chunk 229 optimal weight:    3.9990
   chunk 189 optimal weight:    0.7980
   chunk 211 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 170 optimal weight:    9.9990
   overall best weight:    4.9588

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

Flipped N/Q/H residues before XYZ refinement:
** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.3745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  39578  Z= 0.181
  Angle     :  0.529   9.327  59867  Z= 0.267
  Chirality :  0.030   0.250   7790
  Planarity :  0.004   0.033   2745
  Dihedral  : 24.281 177.846  21228
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.78 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  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: -0.52 (0.26), residues: 1047
  helix:  0.47 (0.30), residues: 309
  sheet: -0.06 (0.35), residues: 227
  loop : -0.94 (0.26), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  80 
 HIS   0.006   0.001   HIS S   7 
 PHE   0.012   0.001   PHE P  73 
 TYR   0.011   0.001   TYR S  38 
 ARG   0.005   0.001   ARG 2  34 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 1.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.9001 (tmm) cc_final: 0.8556 (tmm)
REVERT: K   20 MET cc_start: 0.7971 (ttt) cc_final: 0.7551 (tpp)
REVERT: K  109 SER cc_start: 0.7735 (t) cc_final: 0.7447 (p)
REVERT: Y   30 MET cc_start: 0.8863 (mmp) cc_final: 0.8302 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.4817
  time to fit residues: 32.5834
Evaluate side-chains
  35 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 1.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 210 optimal weight:    0.9990
   chunk 160 optimal weight:   10.0000
   chunk 110 optimal weight:   20.0000
   chunk 23 optimal weight:   20.0000
   chunk 101 optimal weight:   30.0000
   chunk 142 optimal weight:   20.0000
   chunk 213 optimal weight:    2.9990
   chunk 226 optimal weight:    9.9990
   chunk 111 optimal weight:   30.0000
   chunk 202 optimal weight:    1.9990
   chunk 60 optimal weight:   50.0000
   overall best weight:    5.1992

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

Flipped N/Q/H residues before XYZ refinement:
** 2  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  32 ASN
** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  29 HIS
S  31 GLN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.3953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  39578  Z= 0.195
  Angle     :  0.537   9.295  59867  Z= 0.271
  Chirality :  0.030   0.253   7790
  Planarity :  0.004   0.031   2745
  Dihedral  : 24.255 179.445  21228
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 17.10
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.26 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  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: -0.63 (0.26), residues: 1047
  helix:  0.45 (0.31), residues: 308
  sheet: -0.21 (0.34), residues: 226
  loop : -1.00 (0.26), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  80 
 HIS   0.005   0.001   HIS S   7 
 PHE   0.011   0.001   PHE P  73 
 TYR   0.010   0.001   TYR E 101 
 ARG   0.004   0.000   ARG 2  34 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 1.702 
Fit side-chains
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.9026 (tmm) cc_final: 0.8493 (tmm)
REVERT: K   20 MET cc_start: 0.8031 (ttt) cc_final: 0.7635 (tpp)
REVERT: K  113 MET cc_start: 0.8781 (mmp) cc_final: 0.8533 (mmm)
REVERT: N    1 MET cc_start: 0.0677 (ttt) cc_final: 0.0468 (ttp)
REVERT: N  110 MET cc_start: 0.8425 (mmm) cc_final: 0.7826 (mmm)
REVERT: Y   30 MET cc_start: 0.8844 (mmp) cc_final: 0.8252 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.5038
  time to fit residues: 34.7174
Evaluate side-chains
  35 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 1.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 188 optimal weight:    9.9990
   chunk 128 optimal weight:   10.0000
   chunk 3 optimal weight:   30.0000
   chunk 168 optimal weight:   30.0000
   chunk 93 optimal weight:   30.0000
   chunk 193 optimal weight:   20.0000
   chunk 156 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 115 optimal weight:   20.0000
   chunk 203 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   overall best weight:    8.5994

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

Flipped N/Q/H residues before XYZ refinement:
** 2  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.5438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.103  39578  Z= 0.308
  Angle     :  0.691  10.834  59867  Z= 0.346
  Chirality :  0.037   0.275   7790
  Planarity :  0.005   0.042   2745
  Dihedral  : 24.716 178.406  21228
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 26.31
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.02 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.77 %
    Favored  : 95.12 %
  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: -1.43 (0.25), residues: 1047
  helix: -0.45 (0.28), residues: 320
  sheet: -0.80 (0.32), residues: 245
  loop : -1.27 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  80 
 HIS   0.005   0.001   HIS S   7 
 PHE   0.015   0.002   PHE N  87 
 TYR   0.014   0.002   TYR N 112 
 ARG   0.010   0.001   ARG 2  34 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 35
  time to evaluate  : 1.842 
Fit side-chains
   revert: symmetry clash
REVERT: D  165 MET cc_start: 0.4252 (tmm) cc_final: 0.3960 (tmm)
REVERT: E    1 MET cc_start: 0.8991 (tmm) cc_final: 0.8700 (tmm)
REVERT: K   20 MET cc_start: 0.8011 (ttt) cc_final: 0.7652 (tpp)
REVERT: N    1 MET cc_start: 0.0689 (ttt) cc_final: 0.0467 (ttp)
REVERT: N  110 MET cc_start: 0.8438 (mmm) cc_final: 0.7863 (mmm)
REVERT: S   66 ILE cc_start: 0.9250 (pt) cc_final: 0.9006 (mp)
REVERT: Y   30 MET cc_start: 0.8939 (mmp) cc_final: 0.8610 (mmp)
  outliers start: 1
  outliers final: 1
  residues processed: 36
  average time/residue: 0.4994
  time to fit residues: 30.9500
Evaluate side-chains
  34 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 33
  time to evaluate  : 2.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 76 optimal weight:   50.0000
   chunk 203 optimal weight:    5.9990
   chunk 44 optimal weight:   50.0000
   chunk 132 optimal weight:   10.0000
   chunk 55 optimal weight:   10.0000
   chunk 226 optimal weight:    6.9990
   chunk 187 optimal weight:    0.0050
   chunk 104 optimal weight:   20.0000
   chunk 18 optimal weight:   20.0000
   chunk 74 optimal weight:   10.0000
   chunk 118 optimal weight:   10.0000
   overall best weight:    6.6006

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

Flipped N/Q/H residues before XYZ refinement:
** 2  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.5394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  39578  Z= 0.234
  Angle     :  0.578   9.716  59867  Z= 0.291
  Chirality :  0.032   0.233   7790
  Planarity :  0.004   0.037   2745
  Dihedral  : 24.573 178.063  21228
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 20.79
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.97 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  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: -1.28 (0.25), residues: 1047
  helix: -0.08 (0.29), residues: 312
  sheet: -0.71 (0.33), residues: 235
  loop : -1.36 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  80 
 HIS   0.006   0.001   HIS 0  37 
 PHE   0.013   0.002   PHE Y  26 
 TYR   0.010   0.001   TYR N 112 
 ARG   0.005   0.001   ARG 2  34 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 1.644 
Fit side-chains
   revert: symmetry clash
REVERT: D  165 MET cc_start: 0.4167 (tmm) cc_final: 0.3937 (tmm)
REVERT: E    1 MET cc_start: 0.9023 (tmm) cc_final: 0.8538 (tmm)
REVERT: K   20 MET cc_start: 0.7974 (ttt) cc_final: 0.7610 (tpp)
REVERT: N    1 MET cc_start: 0.0696 (ttt) cc_final: 0.0449 (ttp)
REVERT: N  110 MET cc_start: 0.8511 (mmm) cc_final: 0.7926 (mmm)
REVERT: S   66 ILE cc_start: 0.9237 (pt) cc_final: 0.8976 (mp)
REVERT: S   68 ASP cc_start: 0.9423 (t0) cc_final: 0.9148 (t0)
REVERT: Y   30 MET cc_start: 0.8924 (mmp) cc_final: 0.8316 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.4969
  time to fit residues: 31.6492
Evaluate side-chains
  34 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 1.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 218 optimal weight:    9.9990
   chunk 25 optimal weight:   50.0000
   chunk 128 optimal weight:   10.0000
   chunk 165 optimal weight:   10.0000
   chunk 190 optimal weight:    4.9990
   chunk 126 optimal weight:   10.0000
   chunk 225 optimal weight:    4.9990
   chunk 141 optimal weight:    6.9990
   chunk 137 optimal weight:    0.3980
   chunk 104 optimal weight:   20.0000
   chunk 139 optimal weight:    7.9990
   overall best weight:    5.0788

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

Flipped N/Q/H residues before XYZ refinement:
** 2  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.5422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  39578  Z= 0.192
  Angle     :  0.554   9.984  59867  Z= 0.279
  Chirality :  0.031   0.221   7790
  Planarity :  0.004   0.041   2745
  Dihedral  : 24.495 177.857  21228
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 19.43
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.55 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  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: -1.24 (0.25), residues: 1047
  helix:  0.06 (0.30), residues: 311
  sheet: -0.70 (0.33), residues: 235
  loop : -1.40 (0.26), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  80 
 HIS   0.004   0.001   HIS S   7 
 PHE   0.026   0.001   PHE Y  26 
 TYR   0.008   0.001   TYR N 112 
 ARG   0.006   0.000   ARG 2  34 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 1.759 
Fit side-chains
   revert: symmetry clash
REVERT: D   11 MET cc_start: 0.6547 (ptm) cc_final: 0.5888 (ppp)
REVERT: E    1 MET cc_start: 0.9098 (tmm) cc_final: 0.8492 (tmm)
REVERT: K   20 MET cc_start: 0.8025 (ttt) cc_final: 0.7683 (tpp)
REVERT: N    1 MET cc_start: 0.0591 (ttt) cc_final: 0.0250 (ttp)
REVERT: N  110 MET cc_start: 0.8516 (mmm) cc_final: 0.7886 (mmm)
REVERT: S   66 ILE cc_start: 0.9288 (pt) cc_final: 0.9037 (mp)
REVERT: S   68 ASP cc_start: 0.9387 (t0) cc_final: 0.9089 (t0)
REVERT: Y   30 MET cc_start: 0.8885 (mmp) cc_final: 0.8343 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.5151
  time to fit residues: 32.5773
Evaluate side-chains
  34 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 1.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 90 optimal weight:   50.0000
   chunk 134 optimal weight:   40.0000
   chunk 67 optimal weight:   10.0000
   chunk 44 optimal weight:   50.0000
   chunk 43 optimal weight:   50.0000
   chunk 143 optimal weight:   20.0000
   chunk 153 optimal weight:   30.0000
   chunk 111 optimal weight:   30.0000
   chunk 21 optimal weight:   30.0000
   chunk 177 optimal weight:   50.0000
   chunk 205 optimal weight:    7.9990
   overall best weight:   19.5998

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

Flipped N/Q/H residues before XYZ refinement:
** 0  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 2  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  30 GLN
E 195 GLN
P  11 GLN
S  31 GLN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.7151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.108  39578  Z= 0.677
  Angle     :  1.067  12.075  59867  Z= 0.521
  Chirality :  0.053   0.310   7790
  Planarity :  0.007   0.073   2745
  Dihedral  : 25.431 178.509  21228
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 47.85
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  : 10.22 %
    Favored  : 89.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -2.48 (0.24), residues: 1047
  helix: -1.57 (0.26), residues: 314
  sheet: -1.40 (0.31), residues: 230
  loop : -1.73 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D  80 
 HIS   0.013   0.003   HIS 0  40 
 PHE   0.032   0.003   PHE N  80 
 TYR   0.021   0.003   TYR N 112 
 ARG   0.015   0.001   ARG Y  47 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 1.960 
Fit side-chains
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.8834 (tmm) cc_final: 0.8596 (tmm)
REVERT: K   20 MET cc_start: 0.7654 (ttt) cc_final: 0.7373 (tpp)
REVERT: K   32 TYR cc_start: 0.5093 (m-10) cc_final: 0.4810 (m-10)
REVERT: K  107 LEU cc_start: 0.5715 (mp) cc_final: 0.5439 (pt)
REVERT: N    1 MET cc_start: 0.1231 (ttt) cc_final: 0.0958 (ttp)
REVERT: S   66 ILE cc_start: 0.9240 (pt) cc_final: 0.9032 (mp)
REVERT: Y   30 MET cc_start: 0.8935 (mmp) cc_final: 0.8555 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.4996
  time to fit residues: 30.9756
Evaluate side-chains
  34 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 1.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 216 optimal weight:    6.9990
   chunk 197 optimal weight:   20.0000
   chunk 210 optimal weight:    6.9990
   chunk 126 optimal weight:    0.9990
   chunk 91 optimal weight:   10.0000
   chunk 165 optimal weight:   50.0000
   chunk 64 optimal weight:   50.0000
   chunk 189 optimal weight:   10.0000
   chunk 198 optimal weight:    1.9990
   chunk 209 optimal weight:    6.9990
   chunk 138 optimal weight:   20.0000
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
2  29 GLN
E  30 GLN
E 195 GLN
S  31 GLN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.6519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  39578  Z= 0.197
  Angle     :  0.622   9.550  59867  Z= 0.311
  Chirality :  0.034   0.249   7790
  Planarity :  0.004   0.039   2745
  Dihedral  : 24.943 177.118  21228
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 21.14
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  7.26 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  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: -1.74 (0.25), residues: 1047
  helix: -0.57 (0.29), residues: 305
  sheet: -1.08 (0.33), residues: 220
  loop : -1.49 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  80 
 HIS   0.005   0.001   HIS 0  37 
 PHE   0.015   0.001   PHE P  73 
 TYR   0.009   0.001   TYR S  38 
 ARG   0.007   0.001   ARG 0  39 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 1.820 
Fit side-chains
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.8913 (tmm) cc_final: 0.8460 (tmm)
REVERT: K   20 MET cc_start: 0.7779 (ttt) cc_final: 0.7505 (tpp)
REVERT: K   32 TYR cc_start: 0.5185 (m-10) cc_final: 0.4977 (m-10)
REVERT: K  107 LEU cc_start: 0.5790 (mp) cc_final: 0.5479 (pt)
REVERT: N    1 MET cc_start: 0.0862 (ttt) cc_final: 0.0519 (ttp)
REVERT: N  110 MET cc_start: 0.8490 (mmm) cc_final: 0.7933 (mmm)
REVERT: S   66 ILE cc_start: 0.9252 (pt) cc_final: 0.9020 (mp)
REVERT: Y   30 MET cc_start: 0.8994 (mmp) cc_final: 0.8532 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.4991
  time to fit residues: 33.4156
Evaluate side-chains
  34 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 1.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 222 optimal weight:    1.9990
   chunk 135 optimal weight:    4.9990
   chunk 105 optimal weight:   30.0000
   chunk 154 optimal weight:   30.0000
   chunk 233 optimal weight:    4.9990
   chunk 214 optimal weight:    2.9990
   chunk 185 optimal weight:    9.9990
   chunk 19 optimal weight:   30.0000
   chunk 143 optimal weight:    4.9990
   chunk 113 optimal weight:   50.0000
   chunk 147 optimal weight:    9.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
T  72 GLN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.6176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  39578  Z= 0.169
  Angle     :  0.544   9.719  59867  Z= 0.274
  Chirality :  0.031   0.218   7790
  Planarity :  0.004   0.036   2745
  Dihedral  : 24.577 179.230  21228
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 18.43
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.55 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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: -1.46 (0.25), residues: 1047
  helix: -0.09 (0.30), residues: 307
  sheet: -0.92 (0.33), residues: 222
  loop : -1.50 (0.26), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  80 
 HIS   0.005   0.001   HIS S   7 
 PHE   0.010   0.001   PHE Y  26 
 TYR   0.008   0.001   TYR N 112 
 ARG   0.006   0.000   ARG Y   7 

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 1.829 
Fit side-chains
   revert: symmetry clash
REVERT: D   11 MET cc_start: 0.6805 (ptm) cc_final: 0.6184 (ppp)
REVERT: E    1 MET cc_start: 0.9001 (tmm) cc_final: 0.8467 (tmm)
REVERT: K   20 MET cc_start: 0.7953 (ttt) cc_final: 0.7610 (tpp)
REVERT: K  107 LEU cc_start: 0.5720 (mp) cc_final: 0.5290 (pt)
REVERT: N    1 MET cc_start: 0.0773 (ttt) cc_final: 0.0476 (ttp)
REVERT: N   20 MET cc_start: 0.8808 (tmm) cc_final: 0.8602 (tmm)
REVERT: N  110 MET cc_start: 0.8528 (mmm) cc_final: 0.7930 (mmm)
REVERT: S   66 ILE cc_start: 0.9281 (pt) cc_final: 0.9031 (mp)
REVERT: T   24 MET cc_start: 0.9214 (ttt) cc_final: 0.8923 (tmm)
REVERT: Y   30 MET cc_start: 0.8944 (mmp) cc_final: 0.8450 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.4701
  time to fit residues: 32.0523
Evaluate side-chains
  33 residues out of total 901 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 1.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 197 optimal weight:    8.9990
   chunk 56 optimal weight:   10.0000
   chunk 171 optimal weight:    0.0870
   chunk 27 optimal weight:   20.0000
   chunk 51 optimal weight:   20.0000
   chunk 185 optimal weight:    8.9990
   chunk 77 optimal weight:   40.0000
   chunk 190 optimal weight:   10.0000
   chunk 23 optimal weight:   20.0000
   chunk 34 optimal weight:   30.0000
   chunk 163 optimal weight:    7.9990
   overall best weight:    7.2168

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.044356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 102)---------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.031241 restraints weight = 476619.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.031793 restraints weight = 214624.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.032014 restraints weight = 147792.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.6344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  39578  Z= 0.262
  Angle     :  0.604   9.451  59867  Z= 0.303
  Chirality :  0.033   0.232   7790
  Planarity :  0.004   0.036   2745
  Dihedral  : 24.633 178.953  21228
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 22.26
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  8.40 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -1.48 (0.25), residues: 1047
  helix: -0.11 (0.30), residues: 307
  sheet: -0.93 (0.34), residues: 217
  loop : -1.51 (0.26), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  80 
 HIS   0.004   0.001   HIS S   7 
 PHE   0.014   0.002   PHE Y  26 
 TYR   0.008   0.002   TYR N 112 
 ARG   0.006   0.001   ARG 2  34 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3864.44 seconds
wall clock time: 74 minutes 28.83 seconds (4468.83 seconds total)