Starting phenix.real_space_refine
on Wed Feb  4 05:58:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vfp_31957/02_2026/7vfp_31957.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vfp_31957/02_2026/7vfp_31957.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vfp_31957/02_2026/7vfp_31957.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vfp_31957/02_2026/7vfp_31957.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vfp_31957/02_2026/7vfp_31957.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vfp_31957/02_2026/7vfp_31957.map"
  }
  resolution = 4.03
  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=   0.001 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     P       3      5.49       5
     Mg      1      5.21       5
     S      46      5.16       5
     C    5789      2.51       5
     N    1513      2.21       5
     O    1504      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8857
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1586
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 6, 'TRANS': 195}
    Chain: "B"
      Number of atoms: 1663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1663
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 16, 'TRANS': 203}
    Chain: "C"
      Number of atoms: 1848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1848
          Classifications: {'peptide': 231}
          Link IDs: {'PTRANS': 11, 'TRANS': 219}
    Chain: "D"
      Number of atoms: 434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 434
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 2, 'TRANS': 52}
    Chain: "E"
      Number of atoms: 1586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1586
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 6, 'TRANS': 195}
    Chain: "F"
      Number of atoms: 1663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1663
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 16, 'TRANS': 203}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 34
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2, 'water': 2}
          Link IDs: {None: 3}
  Time building chain proxies: 2.54, per 1000 atoms: 0.29
  Number of scatterers: 8857
  At special positions: 0
  Unit cell: (104.832, 98.176, 113.152, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Fe      1     26.01
     S      46     16.00
     P       3     15.00
     Mg      1     11.99
     O    1504      8.00
     N    1513      7.00
     C    5789      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: 0.88
  Conformation dependent library (CDL) restraints added in 564.9 milliseconds
  

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2084

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 6 sheets defined
      68.1% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 49
      removed outlier: 3.914A  pdb=" N   THR A  42 " --> pdb=" O   ALA A  38 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU A  44 " --> pdb=" O   LYS A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 69
    Processing helix  chain 'A' and resid 90 through 99
      removed outlier: 3.688A  pdb=" N   PHE A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   TYR A  98 " --> pdb=" O   ASN A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 114
    Processing helix  chain 'A' and resid 123 through 127
    Processing helix  chain 'A' and resid 130 through 138
    Processing helix  chain 'A' and resid 139 through 142
    Processing helix  chain 'A' and resid 158 through 176
      removed outlier: 3.503A  pdb=" N   GLN A 171 " --> pdb=" O   GLN A 167 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   HIS A 172 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLN A 175 " --> pdb=" O   GLN A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 194
    Processing helix  chain 'B' and resid 2 through 15
      removed outlier: 3.611A  pdb=" N   ALA B  14 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   PHE B  15 " --> pdb=" O   LEU B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 21
      No H-bonds generated for 'chain 'B' and resid 19 through 21'
    Processing helix  chain 'B' and resid 22 through 39
      removed outlier: 4.170A  pdb=" N   PHE B  35 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      Proline residue:  B  36  - end of helix
    Processing helix  chain 'B' and resid 42 through 49
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.629A  pdb=" N   GLU B  67 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ARG B  68 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE B  70 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   ASP B  72 " --> pdb=" O   ARG B  68 " (cutoff:3.500A)
      removed outlier: 5.410A  pdb=" N   ASP B  73 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLN B  75 " --> pdb=" O   ARG B  71 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASP B  76 " --> pdb=" O   ASP B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 119
      removed outlier: 3.534A  pdb=" N   VAL B  92 " --> pdb=" O   PRO B  88 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   LEU B 106 " --> pdb=" O   MET B 102 " (cutoff:3.500A)
      Proline residue:  B 107  - end of helix
      Proline residue:  B 113  - end of helix
      removed outlier: 3.580A  pdb=" N   MET B 117 " --> pdb=" O   PRO B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 154
      Proline residue:  B 138  - end of helix
      removed outlier: 3.868A  pdb=" N   GLY B 141 " --> pdb=" O   THR B 137 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   PHE B 142 " --> pdb=" O   PRO B 138 " (cutoff:3.500A)
      Proline residue:  B 146  - end of helix
      removed outlier: 3.517A  pdb=" N   LEU B 150 " --> pdb=" O   PRO B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 165
    Processing helix  chain 'B' and resid 166 through 168
      No H-bonds generated for 'chain 'B' and resid 166 through 168'
    Processing helix  chain 'B' and resid 169 through 185
    Processing helix  chain 'B' and resid 189 through 220
      removed outlier: 4.021A  pdb=" N   THR B 205 " --> pdb=" O   ALA B 201 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU B 206 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      Proline residue:  B 208  - end of helix
      removed outlier: 3.841A  pdb=" N   GLN B 220 " --> pdb=" O   ARG B 216 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 20
    Processing helix  chain 'C' and resid 21 through 40
    Processing helix  chain 'C' and resid 50 through 55
      removed outlier: 3.821A  pdb=" N   SER C  53 " --> pdb=" O   GLN C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 84
      Proline residue:  C  62  - end of helix
      removed outlier: 3.588A  pdb=" N   VAL C  83 " --> pdb=" O   PHE C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 115
      removed outlier: 3.504A  pdb=" N   ASN C  90 " --> pdb=" O   MET C  86 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   VAL C  93 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   ALA C  94 " --> pdb=" O   ASN C  90 " (cutoff:3.500A)
      Proline residue:  C  98  - end of helix
    Processing helix  chain 'C' and resid 115 through 120
    Processing helix  chain 'C' and resid 126 through 149
      removed outlier: 3.712A  pdb=" N   PHE C 149 " --> pdb=" O   LEU C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 157 through 185
      Proline residue:  C 171  - end of helix
      removed outlier: 3.591A  pdb=" N   HIS C 184 " --> pdb=" O   TRP C 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 198
    Processing helix  chain 'C' and resid 199 through 229
    Processing helix  chain 'C' and resid 230 through 231
      No H-bonds generated for 'chain 'C' and resid 230 through 231'
    Processing helix  chain 'C' and resid 232 through 236
    Processing helix  chain 'D' and resid 17 through 54
      Proline residue:  D  31  - end of helix
      removed outlier: 4.080A  pdb=" N   ALA D  51 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLN D  52 " --> pdb=" O   ARG D  48 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLN D  53 " --> pdb=" O   GLY D  49 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 39 through 48
    Processing helix  chain 'E' and resid 68 through 73
      removed outlier: 3.840A  pdb=" N   HIS E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 97
      removed outlier: 3.744A  pdb=" N   PHE E  97 " --> pdb=" O   GLU E  93 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 106 through 115
      removed outlier: 3.942A  pdb=" N   ALA E 110 " --> pdb=" O   GLN E 106 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 123 through 127
    Processing helix  chain 'E' and resid 128 through 138
      removed outlier: 3.919A  pdb=" N   ALA E 136 " --> pdb=" O   GLN E 132 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 139 through 142
    Processing helix  chain 'E' and resid 158 through 171
    Processing helix  chain 'E' and resid 172 through 176
      removed outlier: 3.564A  pdb=" N   GLN E 175 " --> pdb=" O   HIS E 172 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 194
      removed outlier: 3.582A  pdb=" N   ILE E 194 " --> pdb=" O   GLU E 191 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 17
    Processing helix  chain 'F' and resid 21 through 39
      removed outlier: 3.914A  pdb=" N   LEU F  25 " --> pdb=" O   ILE F  21 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   PHE F  35 " --> pdb=" O   VAL F  31 " (cutoff:3.500A)
      Proline residue:  F  36  - end of helix
    Processing helix  chain 'F' and resid 42 through 67
      removed outlier: 3.758A  pdb=" N   LEU F  46 " --> pdb=" O   GLU F  42 " (cutoff:3.500A)
      Proline residue:  F  51  - end of helix
    Processing helix  chain 'F' and resid 88 through 120
      removed outlier: 4.148A  pdb=" N   LEU F 106 " --> pdb=" O   MET F 102 " (cutoff:3.500A)
      Proline residue:  F 107  - end of helix
      Proline residue:  F 113  - end of helix
    Processing helix  chain 'F' and resid 122 through 152
      Proline residue:  F 138  - end of helix
      Proline residue:  F 146  - end of helix
    Processing helix  chain 'F' and resid 158 through 165
      removed outlier: 3.610A  pdb=" N   SER F 162 " --> pdb=" O   GLY F 158 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU F 164 " --> pdb=" O   LEU F 160 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL F 165 " --> pdb=" O   LEU F 161 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 166 through 168
      No H-bonds generated for 'chain 'F' and resid 166 through 168'
    Processing helix  chain 'F' and resid 169 through 185
      removed outlier: 3.665A  pdb=" N   MET F 185 " --> pdb=" O   ASP F 181 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 189 through 220
      removed outlier: 3.772A  pdb=" N   THR F 205 " --> pdb=" O   ALA F 201 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LEU F 206 " --> pdb=" O   GLY F 202 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER F 207 " --> pdb=" O   THR F 203 " (cutoff:3.500A)
      Proline residue:  F 208  - end of helix
      removed outlier: 3.774A  pdb=" N   GLN F 220 " --> pdb=" O   ARG F 216 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8
      removed outlier: 6.026A  pdb=" N   ALA A   4 " --> pdb=" O   LEU A  59 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   LEU A  59 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   GLU A   6 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 5.438A  pdb=" N   GLU A  57 " --> pdb=" O   GLU A   6 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11
    Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79
      removed outlier: 5.915A  pdb=" N   ILE A  79 " --> pdb=" O   ASP A 151 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU A 150 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 14 through 20
      removed outlier: 6.246A  pdb=" N   LEU E  16 " --> pdb=" O   ARG E  11 " (cutoff:3.500A)
      removed outlier: 8.842A  pdb=" N   ARG E  11 " --> pdb=" O   LEU E  16 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   SER E  18 " --> pdb=" O   CYS E   9 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   CYS E   9 " --> pdb=" O   SER E  18 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 14 through 20
      removed outlier: 6.246A  pdb=" N   LEU E  16 " --> pdb=" O   ARG E  11 " (cutoff:3.500A)
      removed outlier: 8.842A  pdb=" N   ARG E  11 " --> pdb=" O   LEU E  16 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   SER E  18 " --> pdb=" O   CYS E   9 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   CYS E   9 " --> pdb=" O   SER E  18 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   LEU E   7 " --> pdb=" O   ALA E  55 " (cutoff:3.500A)
      removed outlier: 7.319A  pdb=" N   ALA E  55 " --> pdb=" O   LEU E   7 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 77 through 79
      removed outlier: 6.121A  pdb=" N   LEU E  77 " --> pdb=" O   ILE E 149 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   ASP E 151 " --> pdb=" O   LEU E  77 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ILE E  79 " --> pdb=" O   ASP E 151 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   VAL E  30 " --> pdb=" O   LEU E 181 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   TRP E  29 " --> pdb=" O   ARG E 195 " (cutoff:3.500A)
      removed outlier: 8.328A  pdb=" N   ILE E 197 " --> pdb=" O   TRP E  29 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   GLN E  31 " --> pdb=" O   ILE E 197 " (cutoff:3.500A)

    502 hydrogen bonds defined for protein.
    1428 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.33

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.22 -     1.39: 3509
        1.39 -     1.56: 5472
        1.56 -     1.73: 5
        1.73 -     1.90: 87
        1.90 -     2.07: 4
  Bond restraints: 9077
  Sorted by residual:
  bond pdb=" C4  ATP E 301 "
       pdb=" C5  ATP E 301 "
    ideal  model  delta    sigma   weight residual
    1.388  1.470 -0.082 1.00e-02 1.00e+04 6.78e+01
  bond pdb=" C5  ATP E 301 "
       pdb=" C6  ATP E 301 "
    ideal  model  delta    sigma   weight residual
    1.409  1.482 -0.073 1.00e-02 1.00e+04 5.28e+01
  bond pdb=" C8  ATP E 301 "
       pdb=" N7  ATP E 301 "
    ideal  model  delta    sigma   weight residual
    1.310  1.356 -0.046 1.00e-02 1.00e+04 2.15e+01
  bond pdb=" C5  ATP E 301 "
       pdb=" N7  ATP E 301 "
    ideal  model  delta    sigma   weight residual
    1.387  1.343  0.044 1.00e-02 1.00e+04 1.92e+01
  bond pdb=" C4  ATP E 301 "
       pdb=" N9  ATP E 301 "
    ideal  model  delta    sigma   weight residual
    1.374  1.338  0.036 1.00e-02 1.00e+04 1.27e+01
  ... (remaining 9072 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.06: 12307
        4.06 -     8.13: 95
        8.13 -    12.19: 3
       12.19 -    16.26: 0
       16.26 -    20.32: 2
  Bond angle restraints: 12407
  Sorted by residual:
  angle pdb=" PB  ATP E 301 "
        pdb=" O3B ATP E 301 "
        pdb=" PG  ATP E 301 "
      ideal   model   delta    sigma   weight residual
     139.87  119.55   20.32 1.00e+00 1.00e+00 4.13e+02
  angle pdb=" PA  ATP E 301 "
        pdb=" O3A ATP E 301 "
        pdb=" PB  ATP E 301 "
      ideal   model   delta    sigma   weight residual
     136.83  118.86   17.97 1.00e+00 1.00e+00 3.23e+02
  angle pdb=" C5  ATP E 301 "
        pdb=" C4  ATP E 301 "
        pdb=" N3  ATP E 301 "
      ideal   model   delta    sigma   weight residual
     126.80  118.32    8.48 1.00e+00 1.00e+00 7.19e+01
  angle pdb=" N3  ATP E 301 "
        pdb=" C4  ATP E 301 "
        pdb=" N9  ATP E 301 "
      ideal   model   delta    sigma   weight residual
     127.04  135.44   -8.40 1.15e+00 7.59e-01 5.36e+01
  angle pdb=" N1  ATP E 301 "
        pdb=" C2  ATP E 301 "
        pdb=" N3  ATP E 301 "
      ideal   model   delta    sigma   weight residual
     128.69  123.66    5.03 1.00e+00 1.00e+00 2.53e+01
  ... (remaining 12402 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 4769
       17.41 -    34.81: 447
       34.81 -    52.22: 80
       52.22 -    69.63: 8
       69.63 -    87.03: 8
  Dihedral angle restraints: 5312
    sinusoidal: 2088
      harmonic: 3224
  Sorted by residual:
  dihedral pdb=" CA  TRP C  39 "
           pdb=" C   TRP C  39 "
           pdb=" N   GLY C  40 "
           pdb=" CA  GLY C  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.71   20.29     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" CA  LEU A 127 "
           pdb=" C   LEU A 127 "
           pdb=" N   SER A 128 "
           pdb=" CA  SER A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.61  -18.39     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  ASP F  76 "
           pdb=" C   ASP F  76 "
           pdb=" N   GLY F  77 "
           pdb=" CA  GLY F  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.36  -17.64     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 5309 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1195
       0.058 -    0.116: 234
       0.116 -    0.174: 25
       0.174 -    0.232: 3
       0.232 -    0.290: 1
  Chirality restraints: 1458
  Sorted by residual:
  chirality pdb=" CB  ILE A 149 "
            pdb=" CA  ILE A 149 "
            pdb=" CG1 ILE A 149 "
            pdb=" CG2 ILE A 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" CB  ILE A 180 "
            pdb=" CA  ILE A 180 "
            pdb=" CG1 ILE A 180 "
            pdb=" CG2 ILE A 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CB  ILE C  10 "
            pdb=" CA  ILE C  10 "
            pdb=" CG1 ILE C  10 "
            pdb=" CG2 ILE C  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 1455 not shown)

  Planarity restraints: 1526
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B   6 "   -0.014 2.00e-02 2.50e+03   2.74e-02 7.50e+00
        pdb=" C   ILE B   6 "    0.047 2.00e-02 2.50e+03
        pdb=" O   ILE B   6 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   PHE B   7 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C  97 "   -0.035 5.00e-02 4.00e+02   5.21e-02 4.34e+00
        pdb=" N   PRO C  98 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO C  98 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C  98 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU F 106 "    0.026 5.00e-02 4.00e+02   3.90e-02 2.43e+00
        pdb=" N   PRO F 107 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO F 107 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO F 107 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1523 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.53: 64
        2.53 -     3.12: 7128
        3.12 -     3.71: 14804
        3.71 -     4.31: 18987
        4.31 -     4.90: 30992
  Nonbonded interactions: 71975
  Sorted by model distance:
  nonbonded pdb="MG    MG E 300 "
            pdb=" O2B ATP E 301 "
     model   vdw
     1.933 2.170
  nonbonded pdb=" OG1 THR E  41 "
            pdb="MG    MG E 300 "
     model   vdw
     2.036 2.170
  nonbonded pdb="MG    MG E 300 "
            pdb=" O   HOH E 402 "
     model   vdw
     2.050 2.170
  nonbonded pdb="MG    MG E 300 "
            pdb=" O   HOH E 401 "
     model   vdw
     2.052 2.170
  nonbonded pdb="MG    MG E 300 "
            pdb=" O3G ATP E 301 "
     model   vdw
     2.082 2.170
  ... (remaining 71970 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'
  selection = (chain 'E' and resid -1 through 200)
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}

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:             3.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.840
  Find NCS groups from input model:        0.130
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
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      :  0.004   0.082   9077  Z= 0.220
  Angle     :  0.841  20.325  12407  Z= 0.481
  Chirality :  0.045   0.290   1458
  Planarity :  0.005   0.052   1526
  Dihedral  : 13.882  87.031   3228
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 18.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.08 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.05 (0.25), residues: 1118
  helix:  0.89 (0.21), residues: 642
  sheet: -2.00 (0.64), residues: 49
  loop : -0.97 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  48 
 TYR   0.011   0.002   TYR C  15 
 PHE   0.026   0.002   PHE B 175 
 TRP   0.025   0.002   TRP C 146 
 HIS   0.004   0.001   HIS F  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 9077)
  covalent geometry    : angle       0.84070 (12407)
  hydrogen bonds       : bond        0.20737 (  500)
  hydrogen bonds       : angle       6.78865 ( 1428)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 292
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8003 (ppp) cc_final: 0.7467 (ppp)
REVERT: A   99 HIS cc_start: 0.8130 (t-90) cc_final: 0.7803 (t-90)
REVERT: A  181 LEU cc_start: 0.8559 (mt) cc_final: 0.8264 (mt)
REVERT: B    5 ARG cc_start: 0.8925 (mtm180) cc_final: 0.8494 (mtp180)
REVERT: B   44 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8742 (tm-30)
REVERT: B   73 ASP cc_start: 0.8203 (m-30) cc_final: 0.7827 (m-30)
REVERT: B   83 MET cc_start: 0.7590 (tmm) cc_final: 0.6997 (tmm)
REVERT: B  133 LEU cc_start: 0.9593 (tp) cc_final: 0.9374 (tp)
REVERT: B  175 PHE cc_start: 0.8992 (m-80) cc_final: 0.8719 (m-80)
REVERT: C   88 MET cc_start: 0.8655 (mmp) cc_final: 0.8386 (mmt)
REVERT: C   90 ASN cc_start: 0.8851 (m-40) cc_final: 0.8540 (m-40)
REVERT: C  165 ILE cc_start: 0.9607 (mm) cc_final: 0.9353 (mm)
REVERT: C  169 ASN cc_start: 0.9103 (m110) cc_final: 0.8759 (m-40)
REVERT: C  215 THR cc_start: 0.9396 (p) cc_final: 0.8761 (p)
REVERT: C  219 MET cc_start: 0.8719 (mpp) cc_final: 0.8486 (mpp)
REVERT: C  228 MET cc_start: 0.8729 (ttm) cc_final: 0.8239 (tmm)
REVERT: E  113 GLN cc_start: 0.8485 (tp40) cc_final: 0.8197 (tp40)
REVERT: F   15 PHE cc_start: 0.7944 (m-80) cc_final: 0.7684 (m-80)
REVERT: F   68 ARG cc_start: 0.8488 (ppt170) cc_final: 0.8172 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 292
  average time/residue: 0.0833
  time to fit residues: 35.2919
Evaluate side-chains
  243 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    0.3980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  94 ASN
E  96 HIS
E 160 ASN
E 171 GLN
E 188 ASN
F 100 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.099973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.080971 restraints weight = 30861.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.083306 restraints weight = 17770.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.084961 restraints weight = 11921.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.086108 restraints weight = 8847.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.086923 restraints weight = 7156.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9077  Z= 0.149
  Angle     :  0.716   7.563  12407  Z= 0.354
  Chirality :  0.044   0.199   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  6.622  72.126   1248
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.74 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  5.23 %
    Favored  : 94.66 %
  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 (0.25), residues: 1118
  helix:  0.77 (0.20), residues: 694
  sheet: -1.46 (0.69), residues: 49
  loop : -0.92 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  48 
 TYR   0.016   0.001   TYR D  17 
 PHE   0.024   0.002   PHE F  15 
 TRP   0.020   0.002   TRP C  66 
 HIS   0.006   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9077)
  covalent geometry    : angle       0.71581 (12407)
  hydrogen bonds       : bond        0.05032 (  500)
  hydrogen bonds       : angle       5.08036 ( 1428)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 293
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7916 (ppp) cc_final: 0.7614 (ppp)
REVERT: A   99 HIS cc_start: 0.8157 (t-90) cc_final: 0.7902 (t-90)
REVERT: A  181 LEU cc_start: 0.8446 (mt) cc_final: 0.8191 (mt)
REVERT: B    5 ARG cc_start: 0.8920 (mtm180) cc_final: 0.8432 (mtp180)
REVERT: B   44 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8792 (tm-30)
REVERT: B   73 ASP cc_start: 0.7971 (m-30) cc_final: 0.7689 (m-30)
REVERT: B  133 LEU cc_start: 0.9658 (tp) cc_final: 0.9417 (tp)
REVERT: B  175 PHE cc_start: 0.8980 (m-10) cc_final: 0.8648 (m-80)
REVERT: C   86 MET cc_start: 0.8183 (mmm) cc_final: 0.7921 (mmm)
REVERT: C   90 ASN cc_start: 0.9012 (m-40) cc_final: 0.8640 (m-40)
REVERT: C  169 ASN cc_start: 0.9133 (m110) cc_final: 0.8896 (m-40)
REVERT: C  228 MET cc_start: 0.8787 (ttm) cc_final: 0.8212 (tmm)
REVERT: C  230 LYS cc_start: 0.8529 (pptt) cc_final: 0.8030 (pptt)
REVERT: D   20 PHE cc_start: 0.8934 (m-80) cc_final: 0.8669 (m-10)
REVERT: D   27 MET cc_start: 0.9061 (tpp) cc_final: 0.8703 (tpp)
REVERT: E    1 MET cc_start: 0.8024 (pmm) cc_final: 0.7790 (pmm)
REVERT: F   68 ARG cc_start: 0.8623 (ppt170) cc_final: 0.8259 (ttp80)
REVERT: F   71 ARG cc_start: 0.7663 (ttt180) cc_final: 0.7033 (ttm-80)
REVERT: F   73 ASP cc_start: 0.8813 (m-30) cc_final: 0.8418 (m-30)
REVERT: F  164 LEU cc_start: 0.9360 (mt) cc_final: 0.9122 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 294
  average time/residue: 0.0849
  time to fit residues: 36.0971
Evaluate side-chains
  238 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 1 optimal weight:    0.0270
   chunk 7 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 79 optimal weight:    7.9990
   chunk 64 optimal weight:    2.9990
   chunk 89 optimal weight:    0.6980
   chunk 81 optimal weight:    8.9990
   chunk 83 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0170
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.102066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.082513 restraints weight = 31149.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.084973 restraints weight = 18144.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.086625 restraints weight = 12263.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.087741 restraints weight = 9221.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.088603 restraints weight = 7530.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9077  Z= 0.135
  Angle     :  0.694   6.701  12407  Z= 0.338
  Chirality :  0.044   0.202   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  6.401  68.503   1248
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.83 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.36 %
    Favored  : 95.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.13 (0.25), residues: 1118
  helix:  0.83 (0.20), residues: 695
  sheet: -1.31 (0.71), residues: 48
  loop : -1.01 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  48 
 TYR   0.011   0.001   TYR D  17 
 PHE   0.022   0.002   PHE F  15 
 TRP   0.018   0.001   TRP B  55 
 HIS   0.004   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9077)
  covalent geometry    : angle       0.69404 (12407)
  hydrogen bonds       : bond        0.04377 (  500)
  hydrogen bonds       : angle       4.86323 ( 1428)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 298
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7864 (ppp) cc_final: 0.7570 (ppp)
REVERT: A   47 LEU cc_start: 0.8674 (mt) cc_final: 0.8462 (mt)
REVERT: A   76 LEU cc_start: 0.9101 (tt) cc_final: 0.8563 (tt)
REVERT: A   85 ILE cc_start: 0.5881 (pt) cc_final: 0.5579 (pt)
REVERT: A   99 HIS cc_start: 0.8187 (t-90) cc_final: 0.7938 (t-170)
REVERT: A  109 GLU cc_start: 0.9560 (tt0) cc_final: 0.9306 (tm-30)
REVERT: B    5 ARG cc_start: 0.8890 (mtm180) cc_final: 0.8418 (mtp180)
REVERT: B   44 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8780 (tm-30)
REVERT: B  122 ASP cc_start: 0.8626 (p0) cc_final: 0.8400 (p0)
REVERT: B  133 LEU cc_start: 0.9635 (tp) cc_final: 0.9386 (tp)
REVERT: B  175 PHE cc_start: 0.9044 (m-10) cc_final: 0.8738 (m-80)
REVERT: C   90 ASN cc_start: 0.9042 (m-40) cc_final: 0.8646 (m-40)
REVERT: C  118 MET cc_start: 0.8509 (ptp) cc_final: 0.6218 (ptp)
REVERT: C  151 ASP cc_start: 0.8315 (t0) cc_final: 0.8083 (t0)
REVERT: C  153 ARG cc_start: 0.7704 (ttp-170) cc_final: 0.7352 (ptt-90)
REVERT: C  169 ASN cc_start: 0.9152 (m110) cc_final: 0.8761 (m-40)
REVERT: C  228 MET cc_start: 0.8776 (ttm) cc_final: 0.8162 (tmm)
REVERT: D   20 PHE cc_start: 0.8878 (m-80) cc_final: 0.8522 (m-10)
REVERT: D   27 MET cc_start: 0.9163 (tpp) cc_final: 0.8674 (tpp)
REVERT: E    6 GLU cc_start: 0.8028 (pp20) cc_final: 0.7756 (pp20)
REVERT: F   15 PHE cc_start: 0.8006 (m-80) cc_final: 0.7711 (m-80)
REVERT: F   68 ARG cc_start: 0.8663 (ppt170) cc_final: 0.8308 (ttp80)
REVERT: F   71 ARG cc_start: 0.7508 (ttt180) cc_final: 0.6805 (ttm-80)
REVERT: F   73 ASP cc_start: 0.8675 (m-30) cc_final: 0.8305 (m-30)
REVERT: F  104 THR cc_start: 0.8947 (p) cc_final: 0.8685 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 299
  average time/residue: 0.0770
  time to fit residues: 33.4099
Evaluate side-chains
  236 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 91 optimal weight:   10.0000
   chunk 88 optimal weight:    6.9990
   chunk 43 optimal weight:    0.0060
   chunk 21 optimal weight:    9.9990
   chunk 57 optimal weight:    0.6980
   chunk 35 optimal weight:    0.2980
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  50 GLN
E 171 GLN
F  17 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.102055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.082498 restraints weight = 31652.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.084959 restraints weight = 18237.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.086654 restraints weight = 12315.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.087846 restraints weight = 9214.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.088700 restraints weight = 7477.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9077  Z= 0.132
  Angle     :  0.691   6.454  12407  Z= 0.336
  Chirality :  0.043   0.205   1458
  Planarity :  0.005   0.047   1526
  Dihedral  :  6.295  66.927   1248
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.47 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  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 (0.25), residues: 1118
  helix:  0.84 (0.20), residues: 700
  sheet: -1.50 (0.70), residues: 48
  loop : -0.98 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  68 
 TYR   0.011   0.001   TYR D  17 
 PHE   0.020   0.002   PHE F  15 
 TRP   0.018   0.001   TRP C  66 
 HIS   0.009   0.001   HIS F  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9077)
  covalent geometry    : angle       0.69073 (12407)
  hydrogen bonds       : bond        0.03941 (  500)
  hydrogen bonds       : angle       4.76297 ( 1428)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 296
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7853 (ppp) cc_final: 0.7556 (ppp)
REVERT: A   35 SER cc_start: 0.7647 (m) cc_final: 0.7403 (t)
REVERT: A   47 LEU cc_start: 0.8673 (mt) cc_final: 0.8462 (mt)
REVERT: A   85 ILE cc_start: 0.5967 (pt) cc_final: 0.5639 (pt)
REVERT: A   99 HIS cc_start: 0.8186 (t-90) cc_final: 0.7951 (t-170)
REVERT: A  109 GLU cc_start: 0.9539 (tt0) cc_final: 0.9304 (tm-30)
REVERT: A  141 TRP cc_start: 0.7516 (m100) cc_final: 0.7171 (m100)
REVERT: B    5 ARG cc_start: 0.8913 (mtm180) cc_final: 0.8383 (mtp180)
REVERT: B   44 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8796 (tm-30)
REVERT: B  122 ASP cc_start: 0.8611 (p0) cc_final: 0.8409 (p0)
REVERT: B  133 LEU cc_start: 0.9633 (tp) cc_final: 0.9397 (tp)
REVERT: B  175 PHE cc_start: 0.9045 (m-10) cc_final: 0.8717 (m-80)
REVERT: C   90 ASN cc_start: 0.8951 (m-40) cc_final: 0.8583 (m-40)
REVERT: C   91 LEU cc_start: 0.9318 (tp) cc_final: 0.9052 (tp)
REVERT: C  118 MET cc_start: 0.7934 (ptp) cc_final: 0.6651 (ptp)
REVERT: C  119 TRP cc_start: 0.7647 (m100) cc_final: 0.7200 (m100)
REVERT: C  153 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7299 (ptt-90)
REVERT: C  169 ASN cc_start: 0.9153 (m110) cc_final: 0.8764 (m110)
REVERT: C  228 MET cc_start: 0.8761 (ttm) cc_final: 0.8219 (tmm)
REVERT: D   20 PHE cc_start: 0.8871 (m-80) cc_final: 0.8603 (m-10)
REVERT: D   27 MET cc_start: 0.9194 (tpp) cc_final: 0.8673 (tpp)
REVERT: E    6 GLU cc_start: 0.8065 (pp20) cc_final: 0.7797 (pp20)
REVERT: F   15 PHE cc_start: 0.7916 (m-80) cc_final: 0.7608 (m-80)
REVERT: F   68 ARG cc_start: 0.8702 (ppt170) cc_final: 0.8320 (ttp80)
REVERT: F   73 ASP cc_start: 0.8622 (m-30) cc_final: 0.8267 (m-30)
REVERT: F  104 THR cc_start: 0.8948 (p) cc_final: 0.8703 (t)
REVERT: F  111 LEU cc_start: 0.9239 (tp) cc_final: 0.8980 (tt)
REVERT: F  143 LEU cc_start: 0.9406 (tp) cc_final: 0.9146 (tp)
REVERT: F  168 LEU cc_start: 0.9438 (mt) cc_final: 0.9105 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 296
  average time/residue: 0.0746
  time to fit residues: 32.4550
Evaluate side-chains
  246 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 26 optimal weight:    8.9990
   chunk 77 optimal weight:    7.9990
   chunk 68 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 110 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 GLN
F  17 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.099345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.080424 restraints weight = 31047.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.082739 restraints weight = 17709.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.084352 restraints weight = 11889.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.085416 restraints weight = 8882.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.086246 restraints weight = 7239.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9077  Z= 0.175
  Angle     :  0.740  10.092  12407  Z= 0.360
  Chirality :  0.045   0.216   1458
  Planarity :  0.005   0.044   1526
  Dihedral  :  6.311  65.121   1248
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.10 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  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:  0.23 (0.25), residues: 1118
  helix:  0.94 (0.20), residues: 695
  sheet: -1.56 (0.69), residues: 48
  loop : -1.02 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  48 
 TYR   0.016   0.002   TYR C  58 
 PHE   0.018   0.002   PHE F  15 
 TRP   0.031   0.002   TRP C  66 
 HIS   0.006   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 9077)
  covalent geometry    : angle       0.74019 (12407)
  hydrogen bonds       : bond        0.03927 (  500)
  hydrogen bonds       : angle       4.82065 ( 1428)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7828 (ppp) cc_final: 0.7482 (ppp)
REVERT: A   47 LEU cc_start: 0.8621 (mt) cc_final: 0.8416 (mt)
REVERT: A   85 ILE cc_start: 0.6084 (pt) cc_final: 0.5738 (pt)
REVERT: A   99 HIS cc_start: 0.8174 (t-90) cc_final: 0.7923 (t-170)
REVERT: A  109 GLU cc_start: 0.9553 (tt0) cc_final: 0.9313 (tm-30)
REVERT: A  141 TRP cc_start: 0.7620 (m100) cc_final: 0.7311 (m100)
REVERT: B    5 ARG cc_start: 0.8907 (mtm180) cc_final: 0.8293 (mtp180)
REVERT: B   10 GLU cc_start: 0.8869 (mp0) cc_final: 0.8661 (mp0)
REVERT: B   29 LEU cc_start: 0.9546 (tp) cc_final: 0.9323 (tp)
REVERT: B   44 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8823 (tm-30)
REVERT: B  133 LEU cc_start: 0.9654 (tp) cc_final: 0.9453 (tp)
REVERT: B  175 PHE cc_start: 0.9076 (m-10) cc_final: 0.8770 (m-80)
REVERT: C   90 ASN cc_start: 0.8947 (m-40) cc_final: 0.8418 (m-40)
REVERT: C   91 LEU cc_start: 0.9330 (tp) cc_final: 0.9053 (tp)
REVERT: C  118 MET cc_start: 0.8106 (ptp) cc_final: 0.6415 (ptp)
REVERT: C  119 TRP cc_start: 0.7823 (m100) cc_final: 0.7334 (m100)
REVERT: C  153 ARG cc_start: 0.7621 (ttp-170) cc_final: 0.7365 (tmm-80)
REVERT: C  169 ASN cc_start: 0.9218 (m110) cc_final: 0.8796 (m110)
REVERT: C  228 MET cc_start: 0.8739 (ttm) cc_final: 0.8216 (tmm)
REVERT: D   20 PHE cc_start: 0.8945 (m-80) cc_final: 0.8739 (m-10)
REVERT: D   27 MET cc_start: 0.9198 (tpp) cc_final: 0.8783 (tpp)
REVERT: E    1 MET cc_start: 0.8058 (pmm) cc_final: 0.7737 (pmm)
REVERT: E    6 GLU cc_start: 0.8051 (pp20) cc_final: 0.7747 (pp20)
REVERT: F   15 PHE cc_start: 0.7913 (m-80) cc_final: 0.7661 (m-80)
REVERT: F   68 ARG cc_start: 0.8767 (ppt170) cc_final: 0.8374 (ttp80)
REVERT: F   73 ASP cc_start: 0.8563 (m-30) cc_final: 0.8186 (m-30)
REVERT: F  143 LEU cc_start: 0.9441 (tp) cc_final: 0.9183 (tp)
REVERT: F  168 LEU cc_start: 0.9499 (mt) cc_final: 0.9160 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 289
  average time/residue: 0.0731
  time to fit residues: 30.8539
Evaluate side-chains
  237 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 1 optimal weight:    9.9990
   chunk 66 optimal weight:    7.9990
   chunk 79 optimal weight:    8.9990
   chunk 55 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 11 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   chunk 85 optimal weight:    0.2980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A  94 ASN
** E  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 GLN
F  17 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.100676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.081766 restraints weight = 30622.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.084147 restraints weight = 17519.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.085734 restraints weight = 11737.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.086930 restraints weight = 8814.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.087783 restraints weight = 7105.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9077  Z= 0.146
  Angle     :  0.731   8.835  12407  Z= 0.351
  Chirality :  0.044   0.204   1458
  Planarity :  0.005   0.044   1526
  Dihedral  :  6.283  66.314   1248
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.65 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  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:  0.35 (0.26), residues: 1118
  helix:  1.06 (0.21), residues: 682
  sheet: -1.67 (0.67), residues: 48
  loop : -0.93 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D  48 
 TYR   0.012   0.001   TYR C  58 
 PHE   0.035   0.002   PHE C 103 
 TRP   0.029   0.002   TRP C  66 
 HIS   0.005   0.001   HIS F  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9077)
  covalent geometry    : angle       0.73131 (12407)
  hydrogen bonds       : bond        0.03787 (  500)
  hydrogen bonds       : angle       4.71417 ( 1428)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7821 (ppp) cc_final: 0.7396 (ppp)
REVERT: A   47 LEU cc_start: 0.8655 (mt) cc_final: 0.8453 (mt)
REVERT: A   85 ILE cc_start: 0.5978 (pt) cc_final: 0.5656 (pt)
REVERT: A   99 HIS cc_start: 0.8185 (t-90) cc_final: 0.7963 (t-170)
REVERT: A  109 GLU cc_start: 0.9578 (tt0) cc_final: 0.9347 (tm-30)
REVERT: B    5 ARG cc_start: 0.8910 (mtm180) cc_final: 0.8235 (mtp180)
REVERT: B   44 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8743 (tm-30)
REVERT: B  122 ASP cc_start: 0.8618 (p0) cc_final: 0.8406 (p0)
REVERT: B  133 LEU cc_start: 0.9631 (tp) cc_final: 0.9426 (tp)
REVERT: B  175 PHE cc_start: 0.9092 (m-10) cc_final: 0.8788 (m-80)
REVERT: C   90 ASN cc_start: 0.8927 (m-40) cc_final: 0.8396 (m-40)
REVERT: C   91 LEU cc_start: 0.9286 (tp) cc_final: 0.9033 (tp)
REVERT: C  118 MET cc_start: 0.8053 (ptp) cc_final: 0.6507 (ptp)
REVERT: C  119 TRP cc_start: 0.7897 (m100) cc_final: 0.7347 (m100)
REVERT: C  169 ASN cc_start: 0.9194 (m110) cc_final: 0.8745 (m110)
REVERT: C  228 MET cc_start: 0.8753 (ttm) cc_final: 0.8238 (tmm)
REVERT: D   27 MET cc_start: 0.9216 (tpp) cc_final: 0.8635 (tpp)
REVERT: E    1 MET cc_start: 0.8110 (pmm) cc_final: 0.7825 (pmm)
REVERT: E    6 GLU cc_start: 0.8086 (pp20) cc_final: 0.7786 (pp20)
REVERT: F   11 LEU cc_start: 0.9208 (mt) cc_final: 0.8817 (mm)
REVERT: F   15 PHE cc_start: 0.7883 (m-80) cc_final: 0.7654 (m-80)
REVERT: F   73 ASP cc_start: 0.8556 (m-30) cc_final: 0.8135 (m-30)
REVERT: F  111 LEU cc_start: 0.9260 (tp) cc_final: 0.9012 (tt)
REVERT: F  143 LEU cc_start: 0.9412 (tp) cc_final: 0.9151 (tp)
REVERT: F  168 LEU cc_start: 0.9516 (mt) cc_final: 0.9141 (mt)
REVERT: F  209 PHE cc_start: 0.7264 (t80) cc_final: 0.6927 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 289
  average time/residue: 0.0686
  time to fit residues: 29.7144
Evaluate side-chains
  240 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 20 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9980
   chunk 108 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 86 optimal weight:    6.9990
   chunk 88 optimal weight:    0.0980
   chunk 74 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 109 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.098495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.079342 restraints weight = 31275.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.081662 restraints weight = 17883.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.083217 restraints weight = 12062.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.084358 restraints weight = 9078.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.085073 restraints weight = 7387.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   9077  Z= 0.202
  Angle     :  0.779   8.765  12407  Z= 0.378
  Chirality :  0.046   0.291   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  6.352  64.093   1248
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.37 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.26 (0.26), residues: 1118
  helix:  1.02 (0.20), residues: 691
  sheet: -1.83 (0.67), residues: 48
  loop : -1.05 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG F  68 
 TYR   0.012   0.002   TYR C  58 
 PHE   0.017   0.002   PHE F  15 
 TRP   0.021   0.002   TRP C  66 
 HIS   0.005   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 9077)
  covalent geometry    : angle       0.77930 (12407)
  hydrogen bonds       : bond        0.03964 (  500)
  hydrogen bonds       : angle       4.87594 ( 1428)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 277
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7868 (ppp) cc_final: 0.7514 (ppp)
REVERT: A   85 ILE cc_start: 0.6292 (pt) cc_final: 0.5967 (pt)
REVERT: A   99 HIS cc_start: 0.8182 (t-90) cc_final: 0.7960 (t-170)
REVERT: A  109 GLU cc_start: 0.9571 (tt0) cc_final: 0.9350 (tm-30)
REVERT: B    2 MET cc_start: 0.5685 (tpt) cc_final: 0.4555 (tpp)
REVERT: B    5 ARG cc_start: 0.8860 (mtm180) cc_final: 0.7993 (mtm180)
REVERT: B   29 LEU cc_start: 0.9563 (tp) cc_final: 0.9331 (tp)
REVERT: B   44 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8703 (tm-30)
REVERT: B   73 ASP cc_start: 0.8128 (m-30) cc_final: 0.7874 (m-30)
REVERT: B  175 PHE cc_start: 0.9098 (m-10) cc_final: 0.8805 (m-80)
REVERT: C   90 ASN cc_start: 0.8938 (m-40) cc_final: 0.8466 (m-40)
REVERT: C   91 LEU cc_start: 0.9316 (tp) cc_final: 0.9040 (tp)
REVERT: C  146 TRP cc_start: 0.8810 (t60) cc_final: 0.8567 (t60)
REVERT: C  169 ASN cc_start: 0.9205 (m110) cc_final: 0.8738 (m110)
REVERT: C  228 MET cc_start: 0.8733 (ttm) cc_final: 0.8226 (tmm)
REVERT: D   27 MET cc_start: 0.9204 (tpp) cc_final: 0.8778 (tpp)
REVERT: E    1 MET cc_start: 0.8239 (pmm) cc_final: 0.7797 (pmm)
REVERT: E    6 GLU cc_start: 0.8081 (pp20) cc_final: 0.7741 (pp20)
REVERT: E    8 LEU cc_start: 0.9275 (pt) cc_final: 0.9065 (pt)
REVERT: F   11 LEU cc_start: 0.9301 (mt) cc_final: 0.8839 (mm)
REVERT: F   15 PHE cc_start: 0.7937 (m-80) cc_final: 0.7712 (m-80)
REVERT: F   73 ASP cc_start: 0.8497 (m-30) cc_final: 0.8043 (m-30)
REVERT: F  143 LEU cc_start: 0.9432 (tp) cc_final: 0.9136 (tp)
REVERT: F  168 LEU cc_start: 0.9569 (mt) cc_final: 0.9178 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 277
  average time/residue: 0.0704
  time to fit residues: 28.8152
Evaluate side-chains
  237 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 3 optimal weight:    7.9990
   chunk 54 optimal weight:    0.7980
   chunk 76 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.100133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.080813 restraints weight = 31559.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.083123 restraints weight = 18245.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.084732 restraints weight = 12352.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.085880 restraints weight = 9310.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.086579 restraints weight = 7579.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9077  Z= 0.151
  Angle     :  0.768   8.261  12407  Z= 0.369
  Chirality :  0.046   0.238   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  6.320  66.841   1248
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.10 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  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:  0.19 (0.26), residues: 1118
  helix:  1.01 (0.20), residues: 688
  sheet: -1.90 (0.67), residues: 48
  loop : -1.16 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG D  48 
 TYR   0.012   0.001   TYR C  58 
 PHE   0.030   0.002   PHE C 103 
 TRP   0.031   0.002   TRP C 119 
 HIS   0.004   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 9077)
  covalent geometry    : angle       0.76785 (12407)
  hydrogen bonds       : bond        0.03866 (  500)
  hydrogen bonds       : angle       4.82029 ( 1428)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 278
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7842 (ppp) cc_final: 0.7502 (ppp)
REVERT: A   85 ILE cc_start: 0.6146 (pt) cc_final: 0.5840 (pt)
REVERT: A   99 HIS cc_start: 0.8191 (t-90) cc_final: 0.7955 (t-170)
REVERT: A  109 GLU cc_start: 0.9563 (tt0) cc_final: 0.9334 (tm-30)
REVERT: B    2 MET cc_start: 0.5798 (tpt) cc_final: 0.5001 (mmm)
REVERT: B   10 GLU cc_start: 0.8900 (mp0) cc_final: 0.8489 (mp0)
REVERT: B   44 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8634 (tm-30)
REVERT: B   73 ASP cc_start: 0.8072 (m-30) cc_final: 0.7857 (m-30)
REVERT: B  133 LEU cc_start: 0.9635 (tp) cc_final: 0.9426 (tp)
REVERT: B  175 PHE cc_start: 0.9131 (m-10) cc_final: 0.8822 (m-80)
REVERT: C   87 LYS cc_start: 0.9013 (mttm) cc_final: 0.6527 (tptt)
REVERT: C   90 ASN cc_start: 0.8967 (m-40) cc_final: 0.8565 (m-40)
REVERT: C   91 LEU cc_start: 0.9256 (tp) cc_final: 0.9015 (tp)
REVERT: C  118 MET cc_start: 0.8364 (ptp) cc_final: 0.7762 (ptp)
REVERT: C  146 TRP cc_start: 0.8790 (t60) cc_final: 0.8544 (t60)
REVERT: C  169 ASN cc_start: 0.9178 (m110) cc_final: 0.8706 (m110)
REVERT: C  228 MET cc_start: 0.8726 (ttm) cc_final: 0.8231 (tmm)
REVERT: D   27 MET cc_start: 0.9209 (tpp) cc_final: 0.8641 (tpp)
REVERT: E    1 MET cc_start: 0.8178 (pmm) cc_final: 0.7805 (pmm)
REVERT: E    6 GLU cc_start: 0.8067 (pp20) cc_final: 0.7739 (pp20)
REVERT: E    8 LEU cc_start: 0.9293 (pt) cc_final: 0.9084 (pt)
REVERT: F    1 MET cc_start: 0.6636 (ppp) cc_final: 0.6198 (pmm)
REVERT: F   11 LEU cc_start: 0.9252 (mt) cc_final: 0.8804 (mm)
REVERT: F   73 ASP cc_start: 0.8516 (m-30) cc_final: 0.8038 (m-30)
REVERT: F  111 LEU cc_start: 0.9304 (tp) cc_final: 0.9023 (tt)
REVERT: F  143 LEU cc_start: 0.9422 (tp) cc_final: 0.9128 (tp)
REVERT: F  168 LEU cc_start: 0.9551 (mt) cc_final: 0.9156 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 278
  average time/residue: 0.0682
  time to fit residues: 28.3163
Evaluate side-chains
  238 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   chunk 86 optimal weight:    9.9990
   chunk 76 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  94 ASN
** E  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.097924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.079057 restraints weight = 31149.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.081252 restraints weight = 17872.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.082837 restraints weight = 12059.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.083876 restraints weight = 9047.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.084671 restraints weight = 7390.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   9077  Z= 0.222
  Angle     :  0.839  12.032  12407  Z= 0.404
  Chirality :  0.047   0.204   1458
  Planarity :  0.005   0.061   1526
  Dihedral  :  6.438  63.243   1248
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 17.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.81 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  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:  0.01 (0.26), residues: 1118
  helix:  0.83 (0.20), residues: 693
  sheet: -1.91 (0.70), residues: 48
  loop : -1.19 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  48 
 TYR   0.013   0.002   TYR F 192 
 PHE   0.035   0.002   PHE F  15 
 TRP   0.024   0.002   TRP C  66 
 HIS   0.005   0.001   HIS F  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 9077)
  covalent geometry    : angle       0.83918 (12407)
  hydrogen bonds       : bond        0.04161 (  500)
  hydrogen bonds       : angle       4.97874 ( 1428)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7903 (ppp) cc_final: 0.7511 (ppp)
REVERT: A   99 HIS cc_start: 0.8255 (t-90) cc_final: 0.7999 (t-170)
REVERT: B    5 ARG cc_start: 0.8917 (mtp180) cc_final: 0.8407 (mtp180)
REVERT: B   10 GLU cc_start: 0.8915 (mp0) cc_final: 0.8499 (mp0)
REVERT: B   29 LEU cc_start: 0.9543 (tp) cc_final: 0.9327 (tp)
REVERT: B   44 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8577 (tm-30)
REVERT: B  175 PHE cc_start: 0.9148 (m-10) cc_final: 0.8826 (m-80)
REVERT: C   87 LYS cc_start: 0.9109 (mttm) cc_final: 0.8525 (mttp)
REVERT: C   90 ASN cc_start: 0.8918 (m-40) cc_final: 0.8505 (m-40)
REVERT: C   91 LEU cc_start: 0.9275 (tp) cc_final: 0.9013 (tp)
REVERT: C  118 MET cc_start: 0.8067 (ptp) cc_final: 0.6112 (ptp)
REVERT: C  119 TRP cc_start: 0.8067 (m100) cc_final: 0.7653 (m100)
REVERT: C  169 ASN cc_start: 0.9210 (m110) cc_final: 0.8998 (m110)
REVERT: C  228 MET cc_start: 0.8739 (ttm) cc_final: 0.8150 (tmm)
REVERT: D   27 MET cc_start: 0.9197 (tpp) cc_final: 0.8743 (tpp)
REVERT: E    6 GLU cc_start: 0.8094 (pp20) cc_final: 0.7739 (pp20)
REVERT: E    8 LEU cc_start: 0.9321 (pt) cc_final: 0.9105 (pt)
REVERT: E   24 LEU cc_start: 0.8994 (mt) cc_final: 0.8772 (mt)
REVERT: F    1 MET cc_start: 0.6722 (ppp) cc_final: 0.6221 (pmm)
REVERT: F   11 LEU cc_start: 0.9244 (mt) cc_final: 0.9005 (mm)
REVERT: F   15 PHE cc_start: 0.8034 (m-80) cc_final: 0.7710 (m-80)
REVERT: F   73 ASP cc_start: 0.8502 (m-30) cc_final: 0.8088 (m-30)
REVERT: F  143 LEU cc_start: 0.9433 (tp) cc_final: 0.9221 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 270
  average time/residue: 0.0759
  time to fit residues: 29.8341
Evaluate side-chains
  231 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 109 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 94 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0470
   chunk 43 optimal weight:    0.0050
   chunk 107 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 111 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.4492

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

Flipped N/Q/H residues before XYZ refinement:
A  94 ASN
E 171 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.101191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.082218 restraints weight = 30569.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.084601 restraints weight = 17593.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.086222 restraints weight = 11805.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.087352 restraints weight = 8833.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.088177 restraints weight = 7155.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9077  Z= 0.140
  Angle     :  0.790  11.420  12407  Z= 0.374
  Chirality :  0.046   0.203   1458
  Planarity :  0.005   0.047   1526
  Dihedral  :  6.320  66.999   1248
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.38 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.25), residues: 1118
  helix:  0.95 (0.20), residues: 690
  sheet: -1.88 (0.66), residues: 48
  loop : -1.10 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG F  68 
 TYR   0.012   0.001   TYR C  58 
 PHE   0.029   0.002   PHE C 103 
 TRP   0.021   0.002   TRP B  55 
 HIS   0.007   0.001   HIS F  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 9077)
  covalent geometry    : angle       0.78984 (12407)
  hydrogen bonds       : bond        0.03850 (  500)
  hydrogen bonds       : angle       4.74835 ( 1428)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 281
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7862 (ppp) cc_final: 0.7517 (ppp)
REVERT: A   99 HIS cc_start: 0.8246 (t-90) cc_final: 0.7992 (t-170)
REVERT: A  109 GLU cc_start: 0.9546 (tt0) cc_final: 0.9338 (tm-30)
REVERT: B    2 MET cc_start: 0.5735 (tpt) cc_final: 0.5220 (mmm)
REVERT: B    5 ARG cc_start: 0.8854 (mtp180) cc_final: 0.8011 (mmp-170)
REVERT: B   10 GLU cc_start: 0.8855 (mp0) cc_final: 0.8437 (mp0)
REVERT: B   44 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8565 (tm-30)
REVERT: B   68 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7512 (mmm160)
REVERT: B  122 ASP cc_start: 0.8600 (p0) cc_final: 0.8392 (p0)
REVERT: B  133 LEU cc_start: 0.9652 (tp) cc_final: 0.9444 (tp)
REVERT: B  175 PHE cc_start: 0.9128 (m-10) cc_final: 0.8816 (m-80)
REVERT: C   90 ASN cc_start: 0.8828 (m-40) cc_final: 0.8480 (m-40)
REVERT: C   91 LEU cc_start: 0.9222 (tp) cc_final: 0.8970 (tp)
REVERT: C  118 MET cc_start: 0.7973 (ptp) cc_final: 0.6190 (ptp)
REVERT: C  119 TRP cc_start: 0.8018 (m100) cc_final: 0.7603 (m100)
REVERT: C  169 ASN cc_start: 0.9142 (m110) cc_final: 0.8731 (m-40)
REVERT: C  228 MET cc_start: 0.8686 (ttm) cc_final: 0.8121 (tmm)
REVERT: D   27 MET cc_start: 0.9175 (tpp) cc_final: 0.8634 (tpp)
REVERT: E    1 MET cc_start: 0.8079 (pmm) cc_final: 0.7577 (pmm)
REVERT: E    6 GLU cc_start: 0.8037 (pp20) cc_final: 0.7787 (pp20)
REVERT: E   24 LEU cc_start: 0.8837 (mt) cc_final: 0.8452 (mp)
REVERT: F    1 MET cc_start: 0.6432 (ppp) cc_final: 0.5122 (ptp)
REVERT: F   11 LEU cc_start: 0.9220 (mt) cc_final: 0.8940 (mm)
REVERT: F   15 PHE cc_start: 0.7977 (m-80) cc_final: 0.7647 (m-80)
REVERT: F   55 TRP cc_start: 0.9080 (m100) cc_final: 0.8827 (m100)
REVERT: F   73 ASP cc_start: 0.8553 (m-30) cc_final: 0.8119 (m-30)
REVERT: F  111 LEU cc_start: 0.9264 (tp) cc_final: 0.8982 (tt)
REVERT: F  143 LEU cc_start: 0.9376 (tp) cc_final: 0.9073 (tp)
REVERT: F  168 LEU cc_start: 0.9523 (mt) cc_final: 0.9135 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 281
  average time/residue: 0.0797
  time to fit residues: 32.7480
Evaluate side-chains
  237 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 80 optimal weight:    6.9990
   chunk 105 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 3 optimal weight:    9.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A  94 ASN
E 171 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.099273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.080482 restraints weight = 30989.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.082734 restraints weight = 17905.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.084277 restraints weight = 12056.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.085325 restraints weight = 9075.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.086147 restraints weight = 7411.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9077  Z= 0.177
  Angle     :  0.784  10.599  12407  Z= 0.376
  Chirality :  0.046   0.195   1458
  Planarity :  0.005   0.046   1526
  Dihedral  :  6.289  63.570   1248
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 15.50
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.37 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.22 (0.26), residues: 1118
  helix:  1.04 (0.20), residues: 685
  sheet: -1.83 (0.68), residues: 48
  loop : -1.17 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG F  68 
 TYR   0.015   0.002   TYR C  71 
 PHE   0.025   0.002   PHE F  15 
 TRP   0.024   0.002   TRP C  66 
 HIS   0.004   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 9077)
  covalent geometry    : angle       0.78381 (12407)
  hydrogen bonds       : bond        0.03793 (  500)
  hydrogen bonds       : angle       4.82001 ( 1428)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1513.22 seconds
wall clock time: 26 minutes 48.85 seconds (1608.85 seconds total)