Starting phenix.real_space_refine
on Sat Jul  4 13:17:18 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7e9c_31029/07_2026/7e9c_31029.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e9c_31029/07_2026/7e9c_31029.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e9c_31029/07_2026/7e9c_31029.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e9c_31029/07_2026/7e9c_31029.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7e9c_31029/07_2026/7e9c_31029.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7e9c_31029/07_2026/7e9c_31029.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e9c_31029/07_2026/7e9c_31029.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e9c_31029/07_2026/7e9c_31029.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 sd=   0.079
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 11439 atoms to isotropic.
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     260      5.49       5
     S       3      5.16       5
     C    6945      2.51       5
     N    2302      2.21       5
     O    2828      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12338
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 770
          Classifications: {'peptide': 94}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 690
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 1, 'TRANS': 83}
    Chain: "C"
      Number of atoms: 776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 776
          Classifications: {'peptide': 101}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 96}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 714
          Classifications: {'peptide': 93}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "E"
      Number of atoms: 710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 710
          Classifications: {'peptide': 87}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 85}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "F"
      Number of atoms: 649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 649
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "G"
      Number of atoms: 781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 781
          Classifications: {'peptide': 102}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 97}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "H"
      Number of atoms: 714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 714
          Classifications: {'peptide': 93}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "I"
      Number of atoms: 2652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 2652
          Classifications: {'DNA': 130}
          Link IDs: {'rna3p': 129}
    Chain: "J"
      Number of atoms: 2678
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 2678
          Classifications: {'DNA': 130}
          Link IDs: {'rna3p': 129}
    Chain: "K"
      Number of atoms: 1204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 1204
          Classifications: {'peptide': 162}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 2, 'TRANS': 159}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 126
          Unresolved non-hydrogen angles: 156
          Unresolved non-hydrogen dihedrals: 106
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'AYA:plan-2': 1, 'GLN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 75
  Time building chain proxies: 2.56, per 1000 atoms: 0.21
  Number of scatterers: 12338
  At special positions: 0
  Unit cell: (116, 117, 111, 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       3     16.00
     P     260     15.00
     O    2828      8.00
     N    2302      7.00
     C    6945      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: 0.89
  Conformation dependent library (CDL) restraints added in 404.0 milliseconds
  

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1688

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      61.6% alpha, 6.1% beta
      116 base pairs and 176 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 57
      removed outlier: 3.976A  pdb=" N   ARG A  49 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 77
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 130
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 4.513A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 53 through 76
      removed outlier: 3.656A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 93
    Processing helix  chain 'C' and resid 17 through 23
      removed outlier: 3.661A  pdb=" N   ALA C  22 " --> pdb=" O   ARG C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 4.176A  pdb=" N   VAL C  50 " --> pdb=" O   SER C  46 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ASP C  73 " --> pdb=" O   ASN C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 91
    Processing helix  chain 'C' and resid 91 through 98
      removed outlier: 3.522A  pdb=" N   LYS C  96 " --> pdb=" O   ASP C  92 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LEU C  97 " --> pdb=" O   GLU C  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 52
      removed outlier: 4.037A  pdb=" N   THR D  51 " --> pdb=" O   VAL D  47 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   HIS D  52 " --> pdb=" O   LEU D  48 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 87
      removed outlier: 3.673A  pdb=" N   ASN D  87 " --> pdb=" O   LEU D  83 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 93 through 105
    Processing helix  chain 'D' and resid 107 through 126
      removed outlier: 3.964A  pdb=" N   LYS D 111 " --> pdb=" O   GLY D 107 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ARG D 119 " --> pdb=" O   SER D 115 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ALA D 120 " --> pdb=" O   GLU D 116 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER D 126 " --> pdb=" O   THR D 122 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 47 through 55
      removed outlier: 4.130A  pdb=" N   ARG E  52 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.879A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.506A  pdb=" N   GLY E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.563A  pdb=" N   ILE E 124 " --> pdb=" O   GLN E 120 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG E 131 " --> pdb=" O   ALA E 127 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 4.086A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.420A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.917A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 22
    Processing helix  chain 'G' and resid 27 through 38
    Processing helix  chain 'G' and resid 46 through 74
      removed outlier: 4.383A  pdb=" N   VAL G  50 " --> pdb=" O   SER G  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 91
      removed outlier: 3.552A  pdb=" N   LEU G  84 " --> pdb=" O   ILE G  80 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ASP G  91 " --> pdb=" O   ALA G  87 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 93 through 98
      removed outlier: 3.898A  pdb=" N   LEU G  97 " --> pdb=" O   GLU G  93 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   LEU G  98 " --> pdb=" O   LEU G  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 93 through 98'
    Processing helix  chain 'H' and resid 40 through 52
      removed outlier: 3.881A  pdb=" N   THR H  51 " --> pdb=" O   VAL H  47 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 58 through 87
      removed outlier: 3.608A  pdb=" N   ASN H  87 " --> pdb=" O   LEU H  83 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 93 through 105
    Processing helix  chain 'H' and resid 107 through 125
      removed outlier: 3.810A  pdb=" N   LYS H 111 " --> pdb=" O   GLY H 107 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   ARG H 119 " --> pdb=" O   SER H 115 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ALA H 120 " --> pdb=" O   GLU H 116 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL H 121 " --> pdb=" O   GLY H 117 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 189 through 199
      removed outlier: 4.219A  pdb=" N   ALA K 194 " --> pdb=" O   GLU K 190 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   TYR K 195 " --> pdb=" O   ASP K 191 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 200 through 212
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.332A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 4.112A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102
    Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.251A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.853A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 43 through 44
      removed outlier: 7.463A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H  92 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'K' and resid 14 through 16
      removed outlier: 4.257A  pdb=" N   LEU K  41 " --> pdb=" O   LEU K  50 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'K' and resid 138 through 141
      removed outlier: 4.187A  pdb=" N   LEU K  85 " --> pdb=" O   LEU K 141 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   GLU K  84 " --> pdb=" O   LEU K  74 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   LEU K  74 " --> pdb=" O   GLU K  84 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   TRP K  86 " --> pdb=" O   GLN K  72 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL K  57 " --> pdb=" O   ARG K 148 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   ARG K 148 " --> pdb=" O   VAL K  57 " (cutoff:3.500A)
      removed outlier: 7.903A  pdb=" N   HIS K  59 " --> pdb=" O   PHE K 146 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   PHE K 146 " --> pdb=" O   HIS K  59 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'K' and resid 131 through 134
      removed outlier: 7.524A  pdb=" N   LEU K 132 " --> pdb=" O   ARG K 174 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   ILE K 176 " --> pdb=" O   LEU K 132 " (cutoff:3.500A)
      removed outlier: 5.558A  pdb=" N   LEU K 134 " --> pdb=" O   ILE K 176 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   MET K 153 " --> pdb=" O   VAL K 173 " (cutoff:3.500A)
      removed outlier: 9.199A  pdb=" N   TYR K 175 " --> pdb=" O   MET K 153 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    389 hydrogen bonds defined for protein.
    1155 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      301 hydrogen bonds
      598 hydrogen bond angles
      0 basepair planarities
      116 basepair parallelities
      176 stacking parallelities
  Total time for adding SS restraints: 2.09

  Time building geometry restraints manager: 1.17 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: 2508
        1.33 -     1.45: 4019
        1.45 -     1.57: 6024
        1.57 -     1.69: 518
        1.69 -     1.81: 5
  Bond restraints: 13074
  Sorted by residual:
  bond pdb=" C3'  DA I  52 "
       pdb=" C2'  DA I  52 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.23e+01
  bond pdb=" C3'  DG I  63 "
       pdb=" C2'  DG I  63 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.20e+01
  bond pdb=" C3'  DA J 117 "
       pdb=" C2'  DA J 117 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.19e+01
  bond pdb=" C3'  DT J  45 "
       pdb=" C2'  DT J  45 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.10e+01
  bond pdb=" C3'  DG I  71 "
       pdb=" C2'  DG I  71 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.69e+00
  ... (remaining 13069 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 17778
        1.64 -     3.29: 933
        3.29 -     4.93: 59
        4.93 -     6.57: 12
        6.57 -     8.22: 2
  Bond angle restraints: 18784
  Sorted by residual:
  angle pdb=" O4'  DG I  34 "
        pdb=" C4'  DG I  34 "
        pdb=" C3'  DG I  34 "
      ideal   model   delta    sigma   weight residual
     106.00  103.19    2.81 6.00e-01 2.78e+00 2.20e+01
  angle pdb=" O4'  DA I   5 "
        pdb=" C4'  DA I   5 "
        pdb=" C3'  DA I   5 "
      ideal   model   delta    sigma   weight residual
     106.00  103.21    2.79 6.00e-01 2.78e+00 2.17e+01
  angle pdb=" N3   DT I 105 "
        pdb=" C4   DT I 105 "
        pdb=" O4   DT I 105 "
      ideal   model   delta    sigma   weight residual
     119.90  122.67   -2.77 6.00e-01 2.78e+00 2.14e+01
  angle pdb=" O4'  DA J 113 "
        pdb=" C4'  DA J 113 "
        pdb=" C3'  DA J 113 "
      ideal   model   delta    sigma   weight residual
     106.00  103.37    2.63 6.00e-01 2.78e+00 1.92e+01
  angle pdb=" O4   DT I 105 "
        pdb=" C4   DT I 105 "
        pdb=" C5   DT I 105 "
      ideal   model   delta    sigma   weight residual
     124.90  121.85    3.05 7.00e-01 2.04e+00 1.90e+01
  ... (remaining 18779 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.14: 5644
       29.14 -    58.29: 1366
       58.29 -    87.43: 144
       87.43 -   116.57: 3
      116.57 -   145.72: 2
  Dihedral angle restraints: 7159
    sinusoidal: 4551
      harmonic: 2608
  Sorted by residual:
  dihedral pdb=" C4'  DC I  24 "
           pdb=" C3'  DC I  24 "
           pdb=" O3'  DC I  24 "
           pdb=" P    DG I  25 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   74.28  145.72     1      3.50e+01 8.16e-04 1.43e+01
  dihedral pdb=" C4'  DG I  63 "
           pdb=" C3'  DG I  63 "
           pdb=" O3'  DG I  63 "
           pdb=" P    DC I  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   75.24  144.76     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" CA  ILE B  29 "
           pdb=" C   ILE B  29 "
           pdb=" N   THR B  30 "
           pdb=" CA  THR B  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.20  -16.80     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 7156 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1670
       0.047 -    0.094: 417
       0.094 -    0.141: 73
       0.141 -    0.189: 3
       0.189 -    0.236: 1
  Chirality restraints: 2164
  Sorted by residual:
  chirality pdb=" CB  ILE F  29 "
            pdb=" CA  ILE F  29 "
            pdb=" CG1 ILE F  29 "
            pdb=" CG2 ILE F  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CG  LEU A  48 "
            pdb=" CB  LEU A  48 "
            pdb=" CD1 LEU A  48 "
            pdb=" CD2 LEU A  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 7.82e-01
  chirality pdb=" CA  GLN K 205 "
            pdb=" N   GLN K 205 "
            pdb=" C   GLN K 205 "
            pdb=" CB  GLN K 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.92e-01
  ... (remaining 2161 not shown)

  Planarity restraints: 1475
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J 136 "   -0.005 2.00e-02 2.50e+03   1.17e-02 4.10e+00
        pdb=" N9   DG J 136 "    0.004 2.00e-02 2.50e+03
        pdb=" C8   DG J 136 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7   DG J 136 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DG J 136 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DG J 136 "    0.029 2.00e-02 2.50e+03
        pdb=" O6   DG J 136 "   -0.026 2.00e-02 2.50e+03
        pdb=" N1   DG J 136 "    0.005 2.00e-02 2.50e+03
        pdb=" C2   DG J 136 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2   DG J 136 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DG J 136 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DG J 136 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  31 "    0.029 5.00e-02 4.00e+02   4.32e-02 2.98e+00
        pdb=" N   PRO B  32 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I 105 "   -0.020 2.00e-02 2.50e+03   1.03e-02 2.63e+00
        pdb=" N1   DT I 105 "    0.022 2.00e-02 2.50e+03
        pdb=" C2   DT I 105 "    0.001 2.00e-02 2.50e+03
        pdb=" O2   DT I 105 "    0.006 2.00e-02 2.50e+03
        pdb=" N3   DT I 105 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DT I 105 "   -0.004 2.00e-02 2.50e+03
        pdb=" O4   DT I 105 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5   DT I 105 "   -0.002 2.00e-02 2.50e+03
        pdb=" C7   DT I 105 "    0.007 2.00e-02 2.50e+03
        pdb=" C6   DT I 105 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1472 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1614
        2.76 -     3.29: 11701
        3.29 -     3.83: 23832
        3.83 -     4.36: 25834
        4.36 -     4.90: 38608
  Nonbonded interactions: 101589
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN K  21 "
            pdb=" OH  TYR K  40 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   ILE E  62 "
            pdb=" NE2 GLN E  93 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" OG1 THR K  78 "
            pdb=" O   ASN K  81 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" N4   DC I  64 "
            pdb=" N6   DA I  65 "
     model   vdw
     2.236 3.200
  nonbonded pdb=" O   ILE A 119 "
            pdb=" OG  SER B  47 "
     model   vdw
     2.280 3.040
  ... (remaining 101584 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 46 through 49 or (resid 50 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 51 through 132))
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 21 through 101)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and (resid 16 through 74 or (resid 75 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 76 through 99 or (resid 100 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 101 through 116))
  selection = (chain 'G' and (resid 16 through 113 or (resid 114 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 115 through 116))
}
ncs_group {
  reference = (chain 'D' and (resid 35 through 37 or (resid 38 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 39 through 127))
  selection = (chain 'H' and (resid 35 through 107 or (resid 108 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 109 through 127))
}

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:             0.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.720
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6920
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      :  0.005   0.047  13074  Z= 0.468
  Angle     :  0.734   8.215  18784  Z= 0.639
  Chirality :  0.042   0.236   2164
  Planarity :  0.003   0.043   1475
  Dihedral  : 26.936 145.718   5471
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.41 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.28), residues: 875
  helix:  1.26 (0.23), residues: 518
  sheet: -0.56 (0.99), residues: 29
  loop : -1.76 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A  52 
 TYR   0.016   0.001   TYR D  45 
 PHE   0.025   0.001   PHE H  73 
 TRP   0.003   0.001   TRP K  86 
 HIS   0.007   0.001   HIS G 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00512 /  0.47 (13074)
  covalent geometry    : angle       0.73416 /  0.64 (18784)
  hydrogen bonds       : bond        0.11540 /  7.80 (  690)
  hydrogen bonds       : angle       4.89669 /  3.59 ( 1753)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 201
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   27 GLN cc_start: 0.7910 (pm20) cc_final: 0.7512 (pm20)
REVERT: B   83 SER cc_start: 0.8215 (t) cc_final: 0.7960 (t)
REVERT: B   98 TYR cc_start: 0.7617 (m-10) cc_final: 0.7384 (m-10)
REVERT: C   34 LEU cc_start: 0.8841 (tp) cc_final: 0.8631 (tp)
REVERT: C   82 ARG cc_start: 0.8508 (tpt90) cc_final: 0.7864 (tpt90)
REVERT: D   46 LYS cc_start: 0.8399 (mtpp) cc_final: 0.8013 (mtpt)
REVERT: D   71 ASP cc_start: 0.8258 (t70) cc_final: 0.7830 (t0)
REVERT: E  130 LEU cc_start: 0.8284 (tp) cc_final: 0.7943 (tp)
REVERT: F   52 GLU cc_start: 0.7666 (tp30) cc_final: 0.7422 (mm-30)
REVERT: G   37 ARG cc_start: 0.7496 (mmp80) cc_final: 0.6440 (mtm-85)
REVERT: G   57 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7529 (tm-30)
REVERT: G   65 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7389 (tm-30)
REVERT: H   71 ASP cc_start: 0.7979 (t70) cc_final: 0.7486 (t0)
REVERT: H   79 GLU cc_start: 0.8357 (tp30) cc_final: 0.7946 (tp30)
REVERT: H  111 LYS cc_start: 0.8181 (tmmt) cc_final: 0.7913 (tmtt)
REVERT: K   13 ILE cc_start: 0.4961 (mt) cc_final: 0.4726 (pt)
REVERT: K   52 ARG cc_start: 0.7312 (ttp-170) cc_final: 0.6795 (ttp-170)
REVERT: K   75 ARG cc_start: 0.7257 (ttp-170) cc_final: 0.6642 (mtm180)
  outliers start: 1
  outliers final: 0
  residues processed: 201
  average time/residue: 0.1170
  time to fit residues: 32.1489
Evaluate side-chains
  160 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:   40.0000
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:   30.0000
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:   10.0000
   chunk 106 optimal weight:   50.0000
   overall best weight:    1.7786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  90 ASN
E  55 GLN
** G  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  90 ASN
G 115 ASN
** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.138335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.100717 restraints weight = 37117.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.104016 restraints weight = 17663.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.106098 restraints weight = 11639.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.107312 restraints weight = 9327.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.107852 restraints weight = 8339.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.1279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13074  Z= 0.160
  Angle     :  0.616   6.979  18784  Z= 0.364
  Chirality :  0.044   0.220   2164
  Planarity :  0.004   0.038   1475
  Dihedral  : 30.508 150.088   3811
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 13.97 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.28), residues: 875
  helix:  1.35 (0.23), residues: 512
  sheet: -0.77 (0.91), residues: 33
  loop : -1.58 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  72 
 TYR   0.021   0.002   TYR K  40 
 PHE   0.014   0.001   PHE A  54 
 TRP   0.011   0.002   TRP K  11 
 HIS   0.009   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.16 (13074)
  covalent geometry    : angle       0.61635 /  0.36 (18784)
  hydrogen bonds       : bond        0.05702 /  3.79 (  690)
  hydrogen bonds       : angle       3.79053 /  2.76 ( 1753)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 184
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8413 (tm-30)
REVERT: B   27 GLN cc_start: 0.8160 (pm20) cc_final: 0.7635 (pm20)
REVERT: B   98 TYR cc_start: 0.8659 (m-10) cc_final: 0.8337 (m-10)
REVERT: C   82 ARG cc_start: 0.8609 (tpt90) cc_final: 0.7832 (tpt90)
REVERT: C   90 ASN cc_start: 0.9107 (m110) cc_final: 0.8773 (m110)
REVERT: C   93 GLU cc_start: 0.7744 (pm20) cc_final: 0.7534 (pm20)
REVERT: D   62 MET cc_start: 0.8992 (tpt) cc_final: 0.8767 (tpt)
REVERT: D   71 ASP cc_start: 0.8776 (t70) cc_final: 0.8258 (t0)
REVERT: E   94 GLU cc_start: 0.8291 (tp30) cc_final: 0.8046 (tp30)
REVERT: F   52 GLU cc_start: 0.7740 (tp30) cc_final: 0.7318 (tp30)
REVERT: F   75 HIS cc_start: 0.8020 (t-170) cc_final: 0.7601 (t-170)
REVERT: G   37 ARG cc_start: 0.7869 (mmp80) cc_final: 0.6972 (mtm-85)
REVERT: G   57 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7684 (tm-30)
REVERT: G   65 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7550 (tm-30)
REVERT: G   86 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8437 (mp)
REVERT: H   71 ASP cc_start: 0.8580 (t70) cc_final: 0.7786 (t0)
REVERT: H   79 GLU cc_start: 0.8497 (tp30) cc_final: 0.8068 (tp30)
REVERT: K   13 ILE cc_start: 0.4979 (mt) cc_final: 0.4719 (pt)
REVERT: K   52 ARG cc_start: 0.7318 (ttp-170) cc_final: 0.6717 (ttp-170)
REVERT: K   92 ARG cc_start: 0.6947 (mmt180) cc_final: 0.6695 (mmt180)
  outliers start: 25
  outliers final: 15
  residues processed: 193
  average time/residue: 0.1186
  time to fit residues: 31.1219
Evaluate side-chains
  171 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 155
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   44 ILE
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   86 LEU
Chi-restraints excluded: chain H residue   65 LEU
Chi-restraints excluded: chain K residue   55 SER
Chi-restraints excluded: chain K residue   89 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 109 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 73 optimal weight:   30.0000
   chunk 94 optimal weight:   30.0000
   chunk 110 optimal weight:   40.0000
   chunk 58 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 105 optimal weight:   30.0000
   overall best weight:    3.7588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  85 GLN
A  93 GLN
D  98 GLN
** G  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 115 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.131227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.090631 restraints weight = 36376.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.093763 restraints weight = 17353.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.095707 restraints weight = 11561.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.096813 restraints weight = 9367.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.097374 restraints weight = 8422.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  13074  Z= 0.221
  Angle     :  0.670   8.681  18784  Z= 0.388
  Chirality :  0.045   0.319   2164
  Planarity :  0.006   0.059   1475
  Dihedral  : 30.780 153.343   3811
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 17.43 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.28), residues: 875
  helix:  0.96 (0.22), residues: 530
  sheet: -1.23 (0.85), residues: 33
  loop : -1.60 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG F  45 
 TYR   0.022   0.002   TYR H  40 
 PHE   0.012   0.002   PHE F 100 
 TRP   0.005   0.001   TRP K  86 
 HIS   0.006   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00456 /  0.22 (13074)
  covalent geometry    : angle       0.67045 /  0.39 (18784)
  hydrogen bonds       : bond        0.05733 /  3.74 (  690)
  hydrogen bonds       : angle       3.79662 /  2.77 ( 1753)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 187
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8297 (tm-30)
REVERT: A   59 GLU cc_start: 0.8161 (pm20) cc_final: 0.7944 (pm20)
REVERT: B   27 GLN cc_start: 0.8316 (pm20) cc_final: 0.7814 (pm20)
REVERT: B   52 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7277 (tm-30)
REVERT: B   98 TYR cc_start: 0.8882 (m-10) cc_final: 0.8487 (m-10)
REVERT: C   33 ARG cc_start: 0.8468 (ptm-80) cc_final: 0.7999 (ptm-80)
REVERT: C   57 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7903 (tm-30)
REVERT: C   82 ARG cc_start: 0.8699 (tpt90) cc_final: 0.7847 (tpt90)
REVERT: C   90 ASN cc_start: 0.9101 (m110) cc_final: 0.8773 (m-40)
REVERT: C   93 GLU cc_start: 0.7850 (pm20) cc_final: 0.7384 (pm20)
REVERT: D   46 LYS cc_start: 0.8813 (mtpp) cc_final: 0.8356 (mttt)
REVERT: D   71 ASP cc_start: 0.8795 (t70) cc_final: 0.8214 (t0)
REVERT: E   94 GLU cc_start: 0.8375 (tp30) cc_final: 0.8073 (tp30)
REVERT: F   52 GLU cc_start: 0.7946 (tp30) cc_final: 0.7500 (tp30)
REVERT: G   37 ARG cc_start: 0.8067 (mmp80) cc_final: 0.7006 (mtm-85)
REVERT: G   57 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7902 (tm-30)
REVERT: G   65 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7421 (tm-30)
REVERT: H   62 MET cc_start: 0.8826 (tpp) cc_final: 0.8604 (tpp)
REVERT: H   71 ASP cc_start: 0.8642 (t70) cc_final: 0.7771 (t0)
REVERT: H   79 GLU cc_start: 0.8550 (tp30) cc_final: 0.8142 (tp30)
REVERT: K   52 ARG cc_start: 0.7370 (ttp-170) cc_final: 0.6719 (ttp-170)
REVERT: K   92 ARG cc_start: 0.6800 (mmt180) cc_final: 0.6496 (mmt180)
  outliers start: 41
  outliers final: 31
  residues processed: 211
  average time/residue: 0.1217
  time to fit residues: 35.1218
Evaluate side-chains
  191 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 159
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   29 ILE
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue   83 SER
Chi-restraints excluded: chain G residue   25 THR
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   53 THR
Chi-restraints excluded: chain G residue   56 LEU
Chi-restraints excluded: chain H residue   65 LEU
Chi-restraints excluded: chain H residue   69 VAL
Chi-restraints excluded: chain K residue   43 ARG
Chi-restraints excluded: chain K residue   55 SER
Chi-restraints excluded: chain K residue   89 THR
Chi-restraints excluded: chain K residue  152 VAL
Chi-restraints excluded: chain K residue  176 ILE
Chi-restraints excluded: chain K residue  185 VAL
Chi-restraints excluded: chain K residue  205 GLN
Chi-restraints excluded: chain K residue  206 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 23 optimal weight:    0.2980
   chunk 41 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 40 optimal weight:    0.1980
   chunk 97 optimal weight:   30.0000
   chunk 28 optimal weight:    0.9990
   chunk 98 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   chunk 96 optimal weight:   50.0000
   chunk 36 optimal weight:    0.0470
   chunk 89 optimal weight:   40.0000
   overall best weight:    0.4880

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** G  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  42 GLN
** G  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 115 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.135436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.095389 restraints weight = 33892.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.098391 restraints weight = 15896.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.100301 restraints weight = 10514.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.101424 restraints weight = 8454.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.101979 restraints weight = 7586.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  13074  Z= 0.136
  Angle     :  0.585   8.293  18784  Z= 0.346
  Chirality :  0.042   0.227   2164
  Planarity :  0.004   0.042   1475
  Dihedral  : 30.754 153.104   3811
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 22.27 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.28), residues: 875
  helix:  1.38 (0.22), residues: 520
  sheet: -0.95 (0.86), residues: 33
  loop : -1.56 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 102 
 TYR   0.027   0.002   TYR D  86 
 PHE   0.009   0.001   PHE A  54 
 TRP   0.014   0.001   TRP K  86 
 HIS   0.011   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00225 /  0.14 (13074)
  covalent geometry    : angle       0.58537 /  0.35 (18784)
  hydrogen bonds       : bond        0.05040 /  3.34 (  690)
  hydrogen bonds       : angle       3.56944 /  2.58 ( 1753)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 192
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8215 (tm-30)
REVERT: A   59 GLU cc_start: 0.8025 (pm20) cc_final: 0.7801 (pm20)
REVERT: B   27 GLN cc_start: 0.8219 (pm20) cc_final: 0.7687 (pm20)
REVERT: B   52 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7236 (tm-30)
REVERT: C   57 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8070 (tm-30)
REVERT: C   82 ARG cc_start: 0.8603 (tpt90) cc_final: 0.7748 (tpt90)
REVERT: C   90 ASN cc_start: 0.9156 (m110) cc_final: 0.8824 (m-40)
REVERT: C   93 GLU cc_start: 0.7829 (pm20) cc_final: 0.7410 (pm20)
REVERT: D   46 LYS cc_start: 0.8729 (mtpp) cc_final: 0.8375 (mtmm)
REVERT: D   62 MET cc_start: 0.8997 (tpt) cc_final: 0.8648 (tpp)
REVERT: D   71 ASP cc_start: 0.8687 (t70) cc_final: 0.8083 (t0)
REVERT: E   55 GLN cc_start: 0.8712 (mt0) cc_final: 0.8472 (mt0)
REVERT: E   94 GLU cc_start: 0.8293 (tp30) cc_final: 0.8031 (tp30)
REVERT: E   95 SER cc_start: 0.8800 (t) cc_final: 0.8419 (p)
REVERT: F   52 GLU cc_start: 0.7719 (tp30) cc_final: 0.7263 (tp30)
REVERT: G   57 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7242 (tm-30)
REVERT: G   65 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7429 (tm-30)
REVERT: H   62 MET cc_start: 0.8844 (tpp) cc_final: 0.8554 (tpp)
REVERT: H   79 GLU cc_start: 0.8492 (tp30) cc_final: 0.8095 (tp30)
REVERT: K   43 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7784 (ptp-110)
REVERT: K   52 ARG cc_start: 0.7363 (ttp-170) cc_final: 0.6725 (ttp-170)
REVERT: K   75 ARG cc_start: 0.7883 (ttm170) cc_final: 0.7663 (ttm170)
REVERT: K   92 ARG cc_start: 0.6831 (mmt180) cc_final: 0.6535 (mmt180)
  outliers start: 26
  outliers final: 16
  residues processed: 202
  average time/residue: 0.1204
  time to fit residues: 33.1969
Evaluate side-chains
  196 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 178
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   83 SER
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain H residue   65 LEU
Chi-restraints excluded: chain H residue  109 LEU
Chi-restraints excluded: chain K residue   43 ARG
Chi-restraints excluded: chain K residue   55 SER
Chi-restraints excluded: chain K residue   68 VAL
Chi-restraints excluded: chain K residue   89 THR
Chi-restraints excluded: chain K residue  176 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 38 optimal weight:    0.0770
   chunk 72 optimal weight:   40.0000
   chunk 17 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 83 optimal weight:   50.0000
   chunk 95 optimal weight:   50.0000
   chunk 6 optimal weight:    0.8980
   chunk 78 optimal weight:   40.0000
   chunk 74 optimal weight:   30.0000
   chunk 89 optimal weight:   30.0000
   overall best weight:    3.5944

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
** G  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 115 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.129791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.089890 restraints weight = 34165.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.092557 restraints weight = 16888.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.094257 restraints weight = 11431.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.095217 restraints weight = 9268.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.095653 restraints weight = 8336.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.2928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  13074  Z= 0.216
  Angle     :  0.648   8.074  18784  Z= 0.376
  Chirality :  0.044   0.223   2164
  Planarity :  0.005   0.059   1475
  Dihedral  : 30.887 154.779   3811
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 14.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 23.10 %
    Favored  : 71.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.27), residues: 875
  helix:  1.08 (0.22), residues: 526
  sheet: -0.84 (0.86), residues: 33
  loop : -1.65 (0.32), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG G  33 
 TYR   0.034   0.003   TYR H  86 
 PHE   0.013   0.002   PHE D  73 
 TRP   0.006   0.001   TRP K  86 
 HIS   0.014   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00447 /  0.22 (13074)
  covalent geometry    : angle       0.64791 /  0.38 (18784)
  hydrogen bonds       : bond        0.05672 /  3.75 (  690)
  hydrogen bonds       : angle       3.73930 /  2.70 ( 1753)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 191
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8352 (tm-30)
REVERT: A   59 GLU cc_start: 0.8175 (pm20) cc_final: 0.7960 (pm20)
REVERT: B   27 GLN cc_start: 0.8391 (pm20) cc_final: 0.7881 (pm20)
REVERT: B   39 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7798 (mmm-85)
REVERT: B   52 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7263 (tm-30)
REVERT: B   77 LYS cc_start: 0.8670 (mmtm) cc_final: 0.8420 (mmtm)
REVERT: B   98 TYR cc_start: 0.8713 (m-10) cc_final: 0.8507 (m-80)
REVERT: C   82 ARG cc_start: 0.8719 (tpt90) cc_final: 0.7889 (tpt90)
REVERT: C   90 ASN cc_start: 0.9108 (m110) cc_final: 0.8790 (m-40)
REVERT: C   93 GLU cc_start: 0.7865 (pm20) cc_final: 0.7353 (pm20)
REVERT: D   62 MET cc_start: 0.9041 (tpt) cc_final: 0.8815 (tpt)
REVERT: D   71 ASP cc_start: 0.8773 (t70) cc_final: 0.8155 (t0)
REVERT: D  116 GLU cc_start: 0.8097 (tp30) cc_final: 0.7408 (tm-30)
REVERT: E   55 GLN cc_start: 0.8848 (mt0) cc_final: 0.8571 (mt0)
REVERT: E   64 LYS cc_start: 0.8434 (mmtp) cc_final: 0.8204 (mmtp)
REVERT: E   94 GLU cc_start: 0.8263 (tp30) cc_final: 0.7967 (tp30)
REVERT: F   52 GLU cc_start: 0.8051 (tp30) cc_final: 0.7604 (tp30)
REVERT: G   57 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7375 (tm-30)
REVERT: G   65 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7461 (tm-30)
REVERT: H   71 ASP cc_start: 0.8712 (t70) cc_final: 0.7729 (t0)
REVERT: H   79 GLU cc_start: 0.8528 (tp30) cc_final: 0.8170 (tp30)
REVERT: H  122 THR cc_start: 0.9108 (m) cc_final: 0.8903 (p)
REVERT: K   52 ARG cc_start: 0.7469 (ttp-170) cc_final: 0.6780 (ttp-170)
  outliers start: 42
  outliers final: 29
  residues processed: 213
  average time/residue: 0.1164
  time to fit residues: 33.6562
Evaluate side-chains
  212 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 181
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   39 ARG
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   79 LYS
Chi-restraints excluded: chain E residue   96 VAL
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   29 ILE
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   53 THR
Chi-restraints excluded: chain G residue   80 ILE
Chi-restraints excluded: chain H residue   65 LEU
Chi-restraints excluded: chain H residue  109 LEU
Chi-restraints excluded: chain K residue   55 SER
Chi-restraints excluded: chain K residue   89 THR
Chi-restraints excluded: chain K residue  152 VAL
Chi-restraints excluded: chain K residue  176 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 106 optimal weight:    5.9990
   chunk 79 optimal weight:   30.0000
   chunk 24 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 86 optimal weight:   30.0000
   chunk 48 optimal weight:    0.0980
   chunk 90 optimal weight:   30.0000
   chunk 10 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    2.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 115 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.129611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.090097 restraints weight = 33629.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.092762 restraints weight = 16344.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.094466 restraints weight = 10999.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.095319 restraints weight = 8915.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.095925 restraints weight = 8070.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13074  Z= 0.169
  Angle     :  0.616  10.435  18784  Z= 0.361
  Chirality :  0.043   0.230   2164
  Planarity :  0.005   0.052   1475
  Dihedral  : 30.966 154.768   3811
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 25.31 %
    Favored  : 69.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.27), residues: 875
  helix:  1.22 (0.22), residues: 519
  sheet: -0.81 (0.85), residues: 33
  loop : -1.78 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  33 
 TYR   0.038   0.002   TYR H  86 
 PHE   0.030   0.001   PHE F 100 
 TRP   0.011   0.001   TRP K  86 
 HIS   0.010   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.17 (13074)
  covalent geometry    : angle       0.61612 /  0.36 (18784)
  hydrogen bonds       : bond        0.05141 /  3.42 (  690)
  hydrogen bonds       : angle       3.68788 /  2.65 ( 1753)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 195
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8376 (tm-30)
REVERT: A   59 GLU cc_start: 0.8175 (pm20) cc_final: 0.7923 (pm20)
REVERT: B   27 GLN cc_start: 0.8483 (pm20) cc_final: 0.7982 (pm20)
REVERT: B   39 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7829 (mmm-85)
REVERT: B   52 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7243 (tm-30)
REVERT: B   77 LYS cc_start: 0.8696 (mmtm) cc_final: 0.8443 (mmtm)
REVERT: C   33 ARG cc_start: 0.8506 (ptm-80) cc_final: 0.8291 (ptm-80)
REVERT: C   57 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8089 (tm-30)
REVERT: C   82 ARG cc_start: 0.8708 (tpt90) cc_final: 0.7882 (tpt90)
REVERT: C   90 ASN cc_start: 0.9125 (m110) cc_final: 0.8832 (m-40)
REVERT: C   93 GLU cc_start: 0.7923 (pm20) cc_final: 0.7438 (pm20)
REVERT: D   62 MET cc_start: 0.9044 (tpt) cc_final: 0.8646 (tpp)
REVERT: D   66 ASN cc_start: 0.9339 (t0) cc_final: 0.9126 (t0)
REVERT: D   71 ASP cc_start: 0.8735 (t70) cc_final: 0.8098 (t0)
REVERT: D  116 GLU cc_start: 0.8102 (tp30) cc_final: 0.7438 (tm-30)
REVERT: E   94 GLU cc_start: 0.8282 (tp30) cc_final: 0.8001 (tp30)
REVERT: E   95 SER cc_start: 0.8870 (t) cc_final: 0.8494 (p)
REVERT: F   52 GLU cc_start: 0.7938 (tp30) cc_final: 0.7513 (tp30)
REVERT: G   40 TYR cc_start: 0.7608 (m-10) cc_final: 0.7397 (m-10)
REVERT: G   57 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7912 (tm-30)
REVERT: G   65 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7447 (tm-30)
REVERT: H   79 GLU cc_start: 0.8528 (tp30) cc_final: 0.8196 (tp30)
REVERT: K   52 ARG cc_start: 0.7471 (ttp-170) cc_final: 0.6792 (ttp-170)
REVERT: K   92 ARG cc_start: 0.6933 (mmt180) cc_final: 0.6643 (mmt180)
  outliers start: 34
  outliers final: 27
  residues processed: 215
  average time/residue: 0.1143
  time to fit residues: 33.4695
Evaluate side-chains
  217 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 188
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   39 ARG
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   79 LYS
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue   83 SER
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   80 ILE
Chi-restraints excluded: chain H residue   65 LEU
Chi-restraints excluded: chain K residue   55 SER
Chi-restraints excluded: chain K residue   89 THR
Chi-restraints excluded: chain K residue  152 VAL
Chi-restraints excluded: chain K residue  176 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 107 optimal weight:    5.9990
   chunk 87 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 63 optimal weight:    7.9990
   chunk 88 optimal weight:   30.0000
   chunk 97 optimal weight:   20.0000
   chunk 65 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 103 optimal weight:    8.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    2.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 115 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.129476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.089515 restraints weight = 33423.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.092229 restraints weight = 16098.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.093954 restraints weight = 10803.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.094936 restraints weight = 8751.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.095405 restraints weight = 7870.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13074  Z= 0.161
  Angle     :  0.609   8.684  18784  Z= 0.356
  Chirality :  0.043   0.229   2164
  Planarity :  0.005   0.049   1475
  Dihedral  : 30.975 154.868   3811
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 25.03 %
    Favored  : 69.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.27), residues: 875
  helix:  1.29 (0.22), residues: 517
  sheet: -0.92 (0.83), residues: 33
  loop : -1.81 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  52 
 TYR   0.027   0.002   TYR H  86 
 PHE   0.040   0.002   PHE F 100 
 TRP   0.012   0.002   TRP K  86 
 HIS   0.019   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.16 (13074)
  covalent geometry    : angle       0.60871 /  0.36 (18784)
  hydrogen bonds       : bond        0.05093 /  3.40 (  690)
  hydrogen bonds       : angle       3.65607 /  2.63 ( 1753)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 191
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8339 (tm-30)
REVERT: A   59 GLU cc_start: 0.8128 (pm20) cc_final: 0.7834 (pm20)
REVERT: B   27 GLN cc_start: 0.8506 (pm20) cc_final: 0.8004 (pm20)
REVERT: B   39 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7801 (mmm-85)
REVERT: B   52 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7281 (tm-30)
REVERT: B   77 LYS cc_start: 0.8761 (mmtm) cc_final: 0.8492 (mmtm)
REVERT: C   33 ARG cc_start: 0.8477 (ptm-80) cc_final: 0.8259 (ptm-80)
REVERT: C   57 GLU cc_start: 0.8261 (tm-30) cc_final: 0.8001 (tm-30)
REVERT: C   82 ARG cc_start: 0.8701 (tpt90) cc_final: 0.7858 (tpt90)
REVERT: C   90 ASN cc_start: 0.9133 (m110) cc_final: 0.8845 (m-40)
REVERT: C   93 GLU cc_start: 0.7933 (pm20) cc_final: 0.7407 (pm20)
REVERT: D   62 MET cc_start: 0.9015 (tpt) cc_final: 0.8754 (tpp)
REVERT: D   71 ASP cc_start: 0.8720 (t70) cc_final: 0.8070 (t0)
REVERT: D   95 ARG cc_start: 0.7597 (ttm-80) cc_final: 0.7338 (ttm-80)
REVERT: D  116 GLU cc_start: 0.8119 (tp30) cc_final: 0.7413 (tm-30)
REVERT: E   52 ARG cc_start: 0.9081 (ptp90) cc_final: 0.8879 (mtm-85)
REVERT: E   94 GLU cc_start: 0.8370 (tp30) cc_final: 0.8068 (tp30)
REVERT: E   95 SER cc_start: 0.8869 (t) cc_final: 0.8523 (p)
REVERT: F   52 GLU cc_start: 0.7920 (tp30) cc_final: 0.7491 (tp30)
REVERT: G   57 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7899 (tm-30)
REVERT: G   65 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7486 (tm-30)
REVERT: H   46 LYS cc_start: 0.8822 (mttp) cc_final: 0.8608 (mttp)
REVERT: H   71 ASP cc_start: 0.8630 (t70) cc_final: 0.7678 (t0)
REVERT: H   79 GLU cc_start: 0.8476 (tp30) cc_final: 0.8201 (tp30)
REVERT: K   23 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6792 (mm)
REVERT: K   52 ARG cc_start: 0.7491 (ttp-170) cc_final: 0.6827 (ttp-170)
REVERT: K   75 ARG cc_start: 0.7777 (ttm170) cc_final: 0.7516 (ttm170)
  outliers start: 39
  outliers final: 30
  residues processed: 214
  average time/residue: 0.1106
  time to fit residues: 32.3494
Evaluate side-chains
  214 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 182
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain B residue   39 ARG
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   38 GLU
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   79 LYS
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain F residue   29 ILE
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   54 VAL
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue   83 SER
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   80 ILE
Chi-restraints excluded: chain H residue   65 LEU
Chi-restraints excluded: chain K residue   23 ILE
Chi-restraints excluded: chain K residue   55 SER
Chi-restraints excluded: chain K residue   89 THR
Chi-restraints excluded: chain K residue  152 VAL
Chi-restraints excluded: chain K residue  176 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 98 optimal weight:   30.0000
   chunk 56 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 27 optimal weight:    0.3980
   chunk 93 optimal weight:   30.0000
   chunk 36 optimal weight:    0.0020
   chunk 84 optimal weight:   50.0000
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.8794

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 113 HIS
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  66 ASN
** G  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 115 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.128161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.088855 restraints weight = 35638.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.091760 restraints weight = 16939.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.093653 restraints weight = 11305.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.094603 restraints weight = 9113.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.094796 restraints weight = 8226.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13074  Z= 0.140
  Angle     :  0.604   9.880  18784  Z= 0.353
  Chirality :  0.043   0.237   2164
  Planarity :  0.004   0.045   1475
  Dihedral  : 30.946 154.389   3811
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 25.73 %
    Favored  : 69.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.28), residues: 875
  helix:  1.28 (0.22), residues: 524
  sheet: -0.86 (0.86), residues: 33
  loop : -1.82 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG K 148 
 TYR   0.023   0.002   TYR H  86 
 PHE   0.039   0.002   PHE F 100 
 TRP   0.012   0.002   TRP K  86 
 HIS   0.019   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.14 (13074)
  covalent geometry    : angle       0.60435 /  0.35 (18784)
  hydrogen bonds       : bond        0.04963 /  3.33 (  690)
  hydrogen bonds       : angle       3.64404 /  2.62 ( 1753)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 189
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8342 (tm-30)
REVERT: A   59 GLU cc_start: 0.8047 (pm20) cc_final: 0.7760 (pm20)
REVERT: B   27 GLN cc_start: 0.8389 (pm20) cc_final: 0.7902 (pm20)
REVERT: B   39 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7781 (mmm-85)
REVERT: B   52 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7209 (tm-30)
REVERT: B   77 LYS cc_start: 0.8712 (mmtm) cc_final: 0.8468 (mmtm)
REVERT: C   33 ARG cc_start: 0.8500 (ptm-80) cc_final: 0.8261 (ptm-80)
REVERT: C   57 GLU cc_start: 0.8293 (tm-30) cc_final: 0.8024 (tm-30)
REVERT: C   82 ARG cc_start: 0.8675 (tpt90) cc_final: 0.7885 (tpt90)
REVERT: C   90 ASN cc_start: 0.9126 (m110) cc_final: 0.8841 (m-40)
REVERT: C   93 GLU cc_start: 0.7942 (pm20) cc_final: 0.7421 (pm20)
REVERT: D   71 ASP cc_start: 0.8707 (t70) cc_final: 0.8120 (t0)
REVERT: D  116 GLU cc_start: 0.8090 (tp30) cc_final: 0.7404 (tm-30)
REVERT: E   79 LYS cc_start: 0.5322 (OUTLIER) cc_final: 0.4608 (ptmm)
REVERT: E   94 GLU cc_start: 0.8374 (tp30) cc_final: 0.8043 (tp30)
REVERT: E   95 SER cc_start: 0.8817 (t) cc_final: 0.8509 (p)
REVERT: F   52 GLU cc_start: 0.7799 (tp30) cc_final: 0.7347 (tp30)
REVERT: G   57 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7922 (tm-30)
REVERT: G   65 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7535 (tm-30)
REVERT: H   46 LYS cc_start: 0.8806 (mttp) cc_final: 0.8588 (mttp)
REVERT: H   71 ASP cc_start: 0.8650 (t70) cc_final: 0.7658 (t0)
REVERT: H   79 GLU cc_start: 0.8487 (tp30) cc_final: 0.8225 (tp30)
REVERT: K   23 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6806 (mm)
REVERT: K   52 ARG cc_start: 0.7429 (ttp-170) cc_final: 0.6761 (ttp-170)
REVERT: K   75 ARG cc_start: 0.7746 (ttm170) cc_final: 0.7497 (ttm170)
REVERT: K   92 ARG cc_start: 0.6933 (mmt180) cc_final: 0.6594 (mmt180)
  outliers start: 32
  outliers final: 25
  residues processed: 209
  average time/residue: 0.1233
  time to fit residues: 34.8712
Evaluate side-chains
  210 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 182
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain B residue   39 ARG
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   79 LYS
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue   83 SER
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   80 ILE
Chi-restraints excluded: chain H residue   65 LEU
Chi-restraints excluded: chain H residue  109 LEU
Chi-restraints excluded: chain K residue   23 ILE
Chi-restraints excluded: chain K residue   55 SER
Chi-restraints excluded: chain K residue   89 THR
Chi-restraints excluded: chain K residue  142 GLN
Chi-restraints excluded: chain K residue  152 VAL
Chi-restraints excluded: chain K residue  176 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 88 optimal weight:   30.0000
   chunk 103 optimal weight:   30.0000
   chunk 47 optimal weight:    0.7980
   chunk 19 optimal weight:    0.4980
   chunk 69 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   chunk 106 optimal weight:    0.2980
   chunk 37 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
** C  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  66 ASN
** G  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 115 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.128730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.089533 restraints weight = 35539.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.092494 restraints weight = 16865.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.094393 restraints weight = 11207.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.095493 restraints weight = 9036.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.095876 restraints weight = 8109.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.3441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  13074  Z= 0.135
  Angle     :  0.608   9.076  18784  Z= 0.352
  Chirality :  0.042   0.241   2164
  Planarity :  0.004   0.047   1475
  Dihedral  : 30.905 153.947   3811
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 26.83 %
    Favored  : 68.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.28), residues: 875
  helix:  1.27 (0.22), residues: 535
  sheet: -0.87 (0.87), residues: 33
  loop : -1.84 (0.32), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K 148 
 TYR   0.019   0.002   TYR H  86 
 PHE   0.038   0.002   PHE F 100 
 TRP   0.014   0.002   TRP K  86 
 HIS   0.019   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.13 (13074)
  covalent geometry    : angle       0.60822 /  0.35 (18784)
  hydrogen bonds       : bond        0.04950 /  3.33 (  690)
  hydrogen bonds       : angle       3.66824 /  2.62 ( 1753)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 193
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8343 (tm-30)
REVERT: A   59 GLU cc_start: 0.7954 (pm20) cc_final: 0.7697 (pm20)
REVERT: B   27 GLN cc_start: 0.8390 (pm20) cc_final: 0.8147 (pm20)
REVERT: B   39 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7787 (mmm-85)
REVERT: B   52 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7219 (tm-30)
REVERT: B   77 LYS cc_start: 0.8709 (mmtm) cc_final: 0.8465 (mmtm)
REVERT: C   33 ARG cc_start: 0.8426 (ptm-80) cc_final: 0.8184 (ptm-80)
REVERT: C   57 GLU cc_start: 0.8267 (tm-30) cc_final: 0.8011 (tm-30)
REVERT: C   82 ARG cc_start: 0.8658 (tpt90) cc_final: 0.7837 (tpt90)
REVERT: C   90 ASN cc_start: 0.9133 (m110) cc_final: 0.8864 (m-40)
REVERT: C   93 GLU cc_start: 0.7924 (pm20) cc_final: 0.7396 (pm20)
REVERT: D   71 ASP cc_start: 0.8709 (t70) cc_final: 0.8085 (t0)
REVERT: D  116 GLU cc_start: 0.8093 (tp30) cc_final: 0.7391 (tm-30)
REVERT: E   60 LEU cc_start: 0.8044 (mm) cc_final: 0.7615 (mt)
REVERT: E   79 LYS cc_start: 0.5283 (OUTLIER) cc_final: 0.4596 (ptmm)
REVERT: E   94 GLU cc_start: 0.8364 (tp30) cc_final: 0.7990 (tp30)
REVERT: E   95 SER cc_start: 0.8817 (t) cc_final: 0.8501 (p)
REVERT: F   52 GLU cc_start: 0.7657 (tp30) cc_final: 0.7198 (tp30)
REVERT: G   57 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7353 (tm-30)
REVERT: G   65 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7530 (tm-30)
REVERT: H   46 LYS cc_start: 0.8770 (mttp) cc_final: 0.8539 (mttp)
REVERT: H   71 ASP cc_start: 0.8604 (t70) cc_final: 0.7903 (t0)
REVERT: K   23 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6758 (mm)
REVERT: K   52 ARG cc_start: 0.7421 (ttp-170) cc_final: 0.6748 (ttp-170)
  outliers start: 33
  outliers final: 25
  residues processed: 209
  average time/residue: 0.1204
  time to fit residues: 34.1757
Evaluate side-chains
  214 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 186
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   39 ARG
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   79 LYS
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue   83 SER
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   80 ILE
Chi-restraints excluded: chain H residue   65 LEU
Chi-restraints excluded: chain H residue  109 LEU
Chi-restraints excluded: chain K residue   23 ILE
Chi-restraints excluded: chain K residue   55 SER
Chi-restraints excluded: chain K residue   89 THR
Chi-restraints excluded: chain K residue  152 VAL
Chi-restraints excluded: chain K residue  176 ILE
Chi-restraints excluded: chain K residue  205 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 85 optimal weight:   50.0000
   chunk 33 optimal weight:    0.8980
   chunk 93 optimal weight:   20.0000
   chunk 61 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 102 optimal weight:    9.9990
   chunk 95 optimal weight:   40.0000
   chunk 90 optimal weight:   30.0000
   overall best weight:    2.1584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  66 ASN
E  55 GLN
** G  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 115 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.127367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.088088 restraints weight = 35474.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.090970 restraints weight = 16805.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.092809 restraints weight = 11227.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.093876 restraints weight = 9091.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.094293 restraints weight = 8167.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  13074  Z= 0.166
  Angle     :  0.635   8.905  18784  Z= 0.365
  Chirality :  0.043   0.237   2164
  Planarity :  0.005   0.070   1475
  Dihedral  : 30.925 154.095   3811
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 27.80 %
    Favored  : 68.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.28), residues: 875
  helix:  1.21 (0.22), residues: 533
  sheet: -0.80 (0.88), residues: 33
  loop : -1.83 (0.32), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG E  83 
 TYR   0.040   0.003   TYR K  90 
 PHE   0.037   0.002   PHE F 100 
 TRP   0.016   0.003   TRP K  86 
 HIS   0.019   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.17 (13074)
  covalent geometry    : angle       0.63479 /  0.36 (18784)
  hydrogen bonds       : bond        0.05074 /  3.41 (  690)
  hydrogen bonds       : angle       3.72765 /  2.67 ( 1753)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 193
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8356 (tm-30)
REVERT: A   59 GLU cc_start: 0.7967 (pm20) cc_final: 0.7483 (pm20)
REVERT: B   27 GLN cc_start: 0.8484 (pm20) cc_final: 0.8239 (pm20)
REVERT: B   39 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7809 (mmm-85)
REVERT: B   52 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7263 (tm-30)
REVERT: B   77 LYS cc_start: 0.8759 (mmtm) cc_final: 0.8420 (mmtm)
REVERT: C   33 ARG cc_start: 0.8506 (ptm-80) cc_final: 0.8234 (ptm-80)
REVERT: C   57 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7983 (tm-30)
REVERT: C   82 ARG cc_start: 0.8709 (tpt90) cc_final: 0.7865 (tpt90)
REVERT: C   90 ASN cc_start: 0.9133 (m110) cc_final: 0.8864 (m-40)
REVERT: C   93 GLU cc_start: 0.7945 (pm20) cc_final: 0.7416 (pm20)
REVERT: D   71 ASP cc_start: 0.8718 (t70) cc_final: 0.8121 (t0)
REVERT: D   95 ARG cc_start: 0.7571 (ttm-80) cc_final: 0.7366 (ttm-80)
REVERT: D  116 GLU cc_start: 0.8102 (tp30) cc_final: 0.7446 (tm-30)
REVERT: E   94 GLU cc_start: 0.8381 (tp30) cc_final: 0.8085 (tp30)
REVERT: E   95 SER cc_start: 0.8827 (t) cc_final: 0.8532 (p)
REVERT: F   52 GLU cc_start: 0.7764 (tp30) cc_final: 0.7305 (tp30)
REVERT: G   57 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7443 (tm-30)
REVERT: G   65 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7475 (tm-30)
REVERT: H   36 ARG cc_start: 0.7560 (mmm160) cc_final: 0.7109 (mmm160)
REVERT: H   46 LYS cc_start: 0.8814 (mttp) cc_final: 0.8601 (mttp)
REVERT: H   71 ASP cc_start: 0.8675 (t70) cc_final: 0.7972 (t0)
REVERT: K   52 ARG cc_start: 0.7456 (ttp-170) cc_final: 0.6786 (ttp-170)
REVERT: K   75 ARG cc_start: 0.7690 (ttm110) cc_final: 0.7269 (ttm170)
REVERT: K   92 ARG cc_start: 0.6919 (mmt180) cc_final: 0.6673 (mmt180)
  outliers start: 29
  outliers final: 25
  residues processed: 208
  average time/residue: 0.1224
  time to fit residues: 34.5559
Evaluate side-chains
  215 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 189
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LYS
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   39 ARG
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue   86 TYR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   79 LYS
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   69 SER
Chi-restraints excluded: chain F residue   83 SER
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   80 ILE
Chi-restraints excluded: chain H residue   65 LEU
Chi-restraints excluded: chain H residue  109 LEU
Chi-restraints excluded: chain K residue   55 SER
Chi-restraints excluded: chain K residue   89 THR
Chi-restraints excluded: chain K residue  152 VAL
Chi-restraints excluded: chain K residue  176 ILE
Chi-restraints excluded: chain K residue  205 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 104 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 74 optimal weight:   30.0000
   chunk 11 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 79 optimal weight:   30.0000
   chunk 91 optimal weight:   30.0000
   chunk 14 optimal weight:    0.9990
   chunk 94 optimal weight:   30.0000
   chunk 108 optimal weight:   50.0000
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  66 ASN
** G  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 115 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.126972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.087423 restraints weight = 35397.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.090298 restraints weight = 16814.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.092159 restraints weight = 11269.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.093161 restraints weight = 9126.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.093724 restraints weight = 8234.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.3741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13074  Z= 0.152
  Angle     :  0.634   8.407  18784  Z= 0.363
  Chirality :  0.043   0.241   2164
  Planarity :  0.005   0.063   1475
  Dihedral  : 30.958 154.005   3811
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 28.49 %
    Favored  : 67.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.28), residues: 875
  helix:  1.25 (0.22), residues: 531
  sheet: -0.73 (0.89), residues: 33
  loop : -1.86 (0.32), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG E  83 
 TYR   0.028   0.002   TYR B  88 
 PHE   0.032   0.002   PHE F 100 
 TRP   0.013   0.002   TRP K  86 
 HIS   0.018   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.15 (13074)
  covalent geometry    : angle       0.63366 /  0.36 (18784)
  hydrogen bonds       : bond        0.04981 /  3.36 (  690)
  hydrogen bonds       : angle       3.72638 /  2.67 ( 1753)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2385.91 seconds
wall clock time: 41 minutes 35.05 seconds (2495.05 seconds total)