Starting phenix.real_space_refine
on Thu Mar 13 19:35:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vfp_31957/03_2025/7vfp_31957.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vfp_31957/03_2025/7vfp_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vfp_31957/03_2025/7vfp_31957.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vfp_31957/03_2025/7vfp_31957.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vfp_31957/03_2025/7vfp_31957.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vfp_31957/03_2025/7vfp_31957.cif"
  }
  resolution = 4.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.16, per 1000 atoms: 0.70
  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: 2.55
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.83
  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: 2.32

  Time building geometry restraints manager: 2.97 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:             31.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.900
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.040
  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:3.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.820
-------------------------------------------------------------------------------
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= 0.257
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (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
 TRP   0.025   0.002   TRP C 146 
 HIS   0.004   0.001   HIS F  17 
 PHE   0.026   0.002   PHE B 175 
 TYR   0.011   0.002   TYR C  15 
 ARG   0.008   0.001   ARG D  48 

*********************** 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  : 1.431 
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: 0.8560 (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: 0.8741 (tm-30)
REVERT: B   73 ASP cc_start: 0.8203 (m-30) cc_final: 0.7826 (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: 0.8760 (p)
REVERT: C  219 MET cc_start: 0.8718 (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: 0.8486 (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: 0.2080
  time to fit residues: 86.5956
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  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0870
   chunk 57 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   chunk 33 optimal weight:    9.9990
   chunk 53 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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
F 100 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.100465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.081425 restraints weight = 30413.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.083776 restraints weight = 17542.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.085278 restraints weight = 11807.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1387

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= 0.212
  Angle     :  0.717   8.026  12407  Z= 0.354
  Chirality :  0.044   0.197   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  6.589  71.954   1248
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.92 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  5.45 %
    Favored  : 94.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.25), residues: 1118
  helix:  0.77 (0.20), residues: 694
  sheet: -1.47 (0.69), residues: 49
  loop : -0.92 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C 119 
 HIS   0.006   0.001   HIS B 100 
 PHE   0.024   0.002   PHE F  15 
 TYR   0.016   0.001   TYR D  17 
 ARG   0.006   0.000   ARG D  48 

*********************** 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
  295 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 294
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8013 (ppp) cc_final: 0.7709 (ppp)
REVERT: A   47 LEU cc_start: 0.8677 (mt) cc_final: 0.8473 (mt)
REVERT: A   99 HIS cc_start: 0.8158 (t-90) cc_final: 0.7895 (t-90)
REVERT: B    1 MET cc_start: 0.8326 (tmm) cc_final: 0.8097 (tmm)
REVERT: B    5 ARG cc_start: 0.8940 (mtm180) cc_final: 0.8462 (mtp180)
REVERT: B   44 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8759 (tm-30)
REVERT: B   73 ASP cc_start: 0.8036 (m-30) cc_final: 0.7758 (m-30)
REVERT: B  133 LEU cc_start: 0.9655 (tp) cc_final: 0.9424 (tp)
REVERT: B  175 PHE cc_start: 0.8980 (m-10) cc_final: 0.8646 (m-80)
REVERT: C   86 MET cc_start: 0.8215 (mmm) cc_final: 0.7963 (mmm)
REVERT: C   90 ASN cc_start: 0.9045 (m-40) cc_final: 0.8677 (m-40)
REVERT: C  169 ASN cc_start: 0.9104 (m110) cc_final: 0.8882 (m-40)
REVERT: C  228 MET cc_start: 0.8856 (ttm) cc_final: 0.8262 (tmm)
REVERT: C  230 LYS cc_start: 0.8491 (pptt) cc_final: 0.8019 (pptt)
REVERT: D   20 PHE cc_start: 0.8938 (m-80) cc_final: 0.8689 (m-10)
REVERT: D   27 MET cc_start: 0.9074 (tpp) cc_final: 0.8718 (tpp)
REVERT: E    1 MET cc_start: 0.8063 (pmm) cc_final: 0.7827 (pmm)
REVERT: F   15 PHE cc_start: 0.8040 (m-80) cc_final: 0.7823 (m-80)
REVERT: F   68 ARG cc_start: 0.8616 (ppt170) cc_final: 0.8277 (ttp80)
REVERT: F   71 ARG cc_start: 0.7613 (ttt180) cc_final: 0.6966 (ttm-80)
REVERT: F   73 ASP cc_start: 0.8852 (m-30) cc_final: 0.8431 (m-30)
REVERT: F  164 LEU cc_start: 0.9311 (mt) cc_final: 0.9069 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 295
  average time/residue: 0.1801
  time to fit residues: 75.2939
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  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 105 optimal weight:    0.0970
   chunk 60 optimal weight:   10.0000
   chunk 1 optimal weight:    0.2980
   chunk 94 optimal weight:    0.9990
   chunk 101 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 79 optimal weight:    0.4980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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
E 188 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.102152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.082558 restraints weight = 31873.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.085061 restraints weight = 18496.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.086661 restraints weight = 12471.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1799

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= 0.201
  Angle     :  0.695   6.773  12407  Z= 0.338
  Chirality :  0.044   0.198   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  6.392  68.575   1248
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.92 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.14 %
    Favored  : 95.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.25), residues: 1118
  helix:  0.82 (0.20), residues: 695
  sheet: -1.55 (0.69), residues: 48
  loop : -1.01 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  55 
 HIS   0.004   0.001   HIS B 100 
 PHE   0.018   0.002   PHE F  15 
 TYR   0.011   0.001   TYR D  17 
 ARG   0.006   0.000   ARG D  48 

*********************** 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
  294 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 293
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7968 (ppp) cc_final: 0.7663 (ppp)
REVERT: A   47 LEU cc_start: 0.8681 (mt) cc_final: 0.8469 (mt)
REVERT: A   76 LEU cc_start: 0.9088 (tt) cc_final: 0.8569 (tt)
REVERT: A   85 ILE cc_start: 0.5964 (pt) cc_final: 0.5658 (pt)
REVERT: A   99 HIS cc_start: 0.8189 (t-90) cc_final: 0.7928 (t-170)
REVERT: A  109 GLU cc_start: 0.9560 (tt0) cc_final: 0.9304 (tm-30)
REVERT: B    5 ARG cc_start: 0.8920 (mtm180) cc_final: 0.8515 (mtp180)
REVERT: B   44 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8759 (tm-30)
REVERT: B  122 ASP cc_start: 0.8626 (p0) cc_final: 0.8391 (p0)
REVERT: B  133 LEU cc_start: 0.9633 (tp) cc_final: 0.9384 (tp)
REVERT: B  175 PHE cc_start: 0.9055 (m-10) cc_final: 0.8754 (m-80)
REVERT: C   90 ASN cc_start: 0.9063 (m-40) cc_final: 0.8681 (m-40)
REVERT: C  118 MET cc_start: 0.8525 (ptp) cc_final: 0.6250 (ptp)
REVERT: C  151 ASP cc_start: 0.8341 (t0) cc_final: 0.8077 (t0)
REVERT: C  153 ARG cc_start: 0.7655 (ttp-170) cc_final: 0.7293 (ptt-90)
REVERT: C  169 ASN cc_start: 0.9113 (m110) cc_final: 0.8888 (m-40)
REVERT: C  228 MET cc_start: 0.8839 (ttm) cc_final: 0.8211 (tmm)
REVERT: D   20 PHE cc_start: 0.8870 (m-80) cc_final: 0.8540 (m-10)
REVERT: D   27 MET cc_start: 0.9182 (tpp) cc_final: 0.8706 (tpp)
REVERT: E    6 GLU cc_start: 0.8134 (pp20) cc_final: 0.7845 (pp20)
REVERT: F   15 PHE cc_start: 0.8033 (m-80) cc_final: 0.7812 (m-80)
REVERT: F   68 ARG cc_start: 0.8692 (ppt170) cc_final: 0.8341 (ttp80)
REVERT: F   71 ARG cc_start: 0.7517 (ttt180) cc_final: 0.6817 (ttm-80)
REVERT: F   73 ASP cc_start: 0.8714 (m-30) cc_final: 0.8343 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 294
  average time/residue: 0.2051
  time to fit residues: 87.2269
Evaluate side-chains
  235 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 2.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 65 optimal weight:    0.0270
   chunk 82 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9990
   chunk 98 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 69 optimal weight:    7.9990
   chunk 104 optimal weight:    0.9980
   chunk 94 optimal weight:    6.9990
   chunk 101 optimal weight:    0.8980
   overall best weight:    0.7440

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.101950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.082367 restraints weight = 31335.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.084779 restraints weight = 18172.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.086491 restraints weight = 12278.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.2104

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= 0.198
  Angle     :  0.686   6.439  12407  Z= 0.334
  Chirality :  0.043   0.205   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  6.295  66.892   1248
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.47 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.25), residues: 1118
  helix:  0.85 (0.20), residues: 701
  sheet: -1.58 (0.69), residues: 48
  loop : -0.95 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  55 
 HIS   0.007   0.001   HIS B 100 
 PHE   0.015   0.001   PHE F  15 
 TYR   0.012   0.001   TYR D  17 
 ARG   0.008   0.000   ARG D  48 

*********************** 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
  298 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 298
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7975 (ppp) cc_final: 0.7659 (ppp)
REVERT: A   35 SER cc_start: 0.7640 (m) cc_final: 0.7417 (t)
REVERT: A   47 LEU cc_start: 0.8674 (mt) cc_final: 0.8466 (mt)
REVERT: A   85 ILE cc_start: 0.6034 (pt) cc_final: 0.5692 (pt)
REVERT: A   99 HIS cc_start: 0.8202 (t-90) cc_final: 0.7949 (t-170)
REVERT: A  109 GLU cc_start: 0.9550 (tt0) cc_final: 0.9307 (tm-30)
REVERT: A  141 TRP cc_start: 0.7532 (m100) cc_final: 0.7196 (m100)
REVERT: B    5 ARG cc_start: 0.8838 (mtm180) cc_final: 0.8335 (mtp180)
REVERT: B   44 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8789 (tm-30)
REVERT: B  122 ASP cc_start: 0.8619 (p0) cc_final: 0.8415 (p0)
REVERT: B  133 LEU cc_start: 0.9638 (tp) cc_final: 0.9398 (tp)
REVERT: B  175 PHE cc_start: 0.9071 (m-10) cc_final: 0.8746 (m-80)
REVERT: C   90 ASN cc_start: 0.8984 (m-40) cc_final: 0.8625 (m-40)
REVERT: C   91 LEU cc_start: 0.9326 (tp) cc_final: 0.9054 (tp)
REVERT: C  118 MET cc_start: 0.7932 (ptp) cc_final: 0.6623 (ptp)
REVERT: C  119 TRP cc_start: 0.7621 (m100) cc_final: 0.7182 (m100)
REVERT: C  153 ARG cc_start: 0.7709 (ttp-170) cc_final: 0.7432 (ptt-90)
REVERT: C  169 ASN cc_start: 0.9110 (m110) cc_final: 0.8874 (m-40)
REVERT: C  228 MET cc_start: 0.8844 (ttm) cc_final: 0.8284 (tmm)
REVERT: D   20 PHE cc_start: 0.8895 (m-80) cc_final: 0.8661 (m-10)
REVERT: D   27 MET cc_start: 0.9202 (tpp) cc_final: 0.8689 (tpp)
REVERT: D   42 GLN cc_start: 0.8783 (tp-100) cc_final: 0.8163 (tp-100)
REVERT: E    6 GLU cc_start: 0.8216 (pp20) cc_final: 0.7920 (pp20)
REVERT: F   68 ARG cc_start: 0.8737 (ppt170) cc_final: 0.8333 (ttp80)
REVERT: F   73 ASP cc_start: 0.8692 (m-30) cc_final: 0.8308 (m-30)
REVERT: F  111 LEU cc_start: 0.9271 (tp) cc_final: 0.8989 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 298
  average time/residue: 0.1831
  time to fit residues: 79.0050
Evaluate side-chains
  241 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 95 optimal weight:    0.1980
   chunk 8 optimal weight:    8.9990
   chunk 109 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   chunk 63 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   chunk 40 optimal weight:    0.5980
   chunk 56 optimal weight:    9.9990
   overall best weight:    2.3586

-------------------------------------------------------------------------------
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 = 0.3777 r_free = 0.3777 target = 0.099065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.079397 restraints weight = 31875.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.081720 restraints weight = 18755.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.083315 restraints weight = 12828.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9077  Z= 0.288
  Angle     :  0.760  10.195  12407  Z= 0.371
  Chirality :  0.045   0.202   1458
  Planarity :  0.005   0.044   1526
  Dihedral  :  6.369  64.523   1248
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 15.33
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.28 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.25), residues: 1118
  helix:  0.92 (0.20), residues: 691
  sheet: -1.54 (0.72), residues: 48
  loop : -1.17 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C  66 
 HIS   0.006   0.001   HIS B 100 
 PHE   0.036   0.002   PHE F  15 
 TYR   0.012   0.002   TYR D  17 
 ARG   0.011   0.001   ARG D  48 

*********************** 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
  285 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 285
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8053 (ppp) cc_final: 0.7657 (ppp)
REVERT: A   85 ILE cc_start: 0.6288 (pt) cc_final: 0.5956 (pt)
REVERT: A   99 HIS cc_start: 0.8199 (t-90) cc_final: 0.7914 (t-170)
REVERT: A  141 TRP cc_start: 0.7667 (m100) cc_final: 0.7438 (m100)
REVERT: B    5 ARG cc_start: 0.8913 (mtm180) cc_final: 0.8233 (mtp180)
REVERT: B   29 LEU cc_start: 0.9551 (tp) cc_final: 0.9315 (tp)
REVERT: B   44 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8849 (tm-30)
REVERT: B  175 PHE cc_start: 0.9114 (m-10) cc_final: 0.8808 (m-80)
REVERT: C   90 ASN cc_start: 0.8996 (m-40) cc_final: 0.8632 (m-40)
REVERT: C   91 LEU cc_start: 0.9330 (tp) cc_final: 0.9070 (tp)
REVERT: C  118 MET cc_start: 0.8079 (ptp) cc_final: 0.6477 (ptp)
REVERT: C  119 TRP cc_start: 0.7848 (m100) cc_final: 0.7331 (m100)
REVERT: C  153 ARG cc_start: 0.7604 (ttp-170) cc_final: 0.7398 (tmm-80)
REVERT: C  169 ASN cc_start: 0.9147 (m110) cc_final: 0.8518 (m-40)
REVERT: C  228 MET cc_start: 0.8822 (ttm) cc_final: 0.8288 (tmm)
REVERT: D   20 PHE cc_start: 0.8990 (m-80) cc_final: 0.8726 (m-10)
REVERT: D   27 MET cc_start: 0.9203 (tpp) cc_final: 0.8777 (tpp)
REVERT: E    1 MET cc_start: 0.8223 (pmm) cc_final: 0.7922 (pmm)
REVERT: E    6 GLU cc_start: 0.8212 (pp20) cc_final: 0.7858 (pp20)
REVERT: E    8 LEU cc_start: 0.9313 (pt) cc_final: 0.9096 (pt)
REVERT: F   15 PHE cc_start: 0.8145 (m-80) cc_final: 0.7736 (m-80)
REVERT: F   68 ARG cc_start: 0.8831 (ppt170) cc_final: 0.8407 (ttp80)
REVERT: F   73 ASP cc_start: 0.8602 (m-30) cc_final: 0.8220 (m-30)
REVERT: F  168 LEU cc_start: 0.9520 (mt) cc_final: 0.9142 (mt)
REVERT: F  209 PHE cc_start: 0.7416 (t80) cc_final: 0.7068 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 285
  average time/residue: 0.1709
  time to fit residues: 70.1381
Evaluate side-chains
  228 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 100 optimal weight:    6.9990
   chunk 6 optimal weight:    0.0870
   chunk 70 optimal weight:    9.9990
   chunk 58 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 101 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 83 optimal weight:    8.9990
   chunk 43 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   overall best weight:    3.2166

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

Flipped N/Q/H residues before XYZ refinement:
A  36 ASN
** A  94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.096059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.077199 restraints weight = 31274.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.079531 restraints weight = 17664.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.081101 restraints weight = 11739.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   9077  Z= 0.360
  Angle     :  0.822   8.897  12407  Z= 0.399
  Chirality :  0.047   0.224   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  6.508  64.308   1248
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 17.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.28 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.26), residues: 1118
  helix:  0.82 (0.20), residues: 693
  sheet: -1.46 (0.74), residues: 48
  loop : -1.15 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C  66 
 HIS   0.006   0.001   HIS A  73 
 PHE   0.025   0.002   PHE F  15 
 TYR   0.012   0.002   TYR D  17 
 ARG   0.016   0.001   ARG D  48 

*********************** 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
  267 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8062 (ppp) cc_final: 0.7573 (ppp)
REVERT: A   85 ILE cc_start: 0.6483 (pt) cc_final: 0.6273 (pt)
REVERT: A   99 HIS cc_start: 0.8210 (t-90) cc_final: 0.7942 (t-170)
REVERT: B    5 ARG cc_start: 0.8879 (mtm180) cc_final: 0.8279 (mtp180)
REVERT: B   10 GLU cc_start: 0.8970 (mp0) cc_final: 0.8623 (mp0)
REVERT: B   29 LEU cc_start: 0.9550 (tp) cc_final: 0.9304 (tp)
REVERT: B   44 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8790 (tm-30)
REVERT: B   73 ASP cc_start: 0.8181 (m-30) cc_final: 0.7948 (m-30)
REVERT: B  175 PHE cc_start: 0.9159 (m-10) cc_final: 0.8834 (m-80)
REVERT: C   90 ASN cc_start: 0.9029 (m-40) cc_final: 0.8618 (m-40)
REVERT: C   91 LEU cc_start: 0.9354 (tp) cc_final: 0.9097 (tp)
REVERT: C  119 TRP cc_start: 0.7943 (m100) cc_final: 0.7714 (m100)
REVERT: C  153 ARG cc_start: 0.7639 (ttp-170) cc_final: 0.7428 (tmm-80)
REVERT: C  169 ASN cc_start: 0.9153 (m110) cc_final: 0.8835 (m-40)
REVERT: C  228 MET cc_start: 0.8907 (ttm) cc_final: 0.8352 (tmm)
REVERT: D   27 MET cc_start: 0.9214 (tpp) cc_final: 0.8783 (tpp)
REVERT: E    1 MET cc_start: 0.8368 (pmm) cc_final: 0.7954 (pmm)
REVERT: E    6 GLU cc_start: 0.8325 (pp20) cc_final: 0.7958 (pp20)
REVERT: E    8 LEU cc_start: 0.9341 (pt) cc_final: 0.9122 (pt)
REVERT: F   15 PHE cc_start: 0.8120 (m-80) cc_final: 0.7822 (m-80)
REVERT: F   68 ARG cc_start: 0.8525 (ppt170) cc_final: 0.8298 (tmm160)
REVERT: F   73 ASP cc_start: 0.8635 (m-30) cc_final: 0.8185 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 267
  average time/residue: 0.1705
  time to fit residues: 65.9898
Evaluate side-chains
  232 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0040
   chunk 68 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 60 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0020
   chunk 66 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.5602

-------------------------------------------------------------------------------
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 = 0.3813 r_free = 0.3813 target = 0.101058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.082072 restraints weight = 30892.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.084464 restraints weight = 17574.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.086124 restraints weight = 11694.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2655

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= 0.200
  Angle     :  0.748   8.535  12407  Z= 0.357
  Chirality :  0.045   0.204   1458
  Planarity :  0.005   0.046   1526
  Dihedral  :  6.320  68.396   1248
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.83 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.26), residues: 1118
  helix:  1.04 (0.20), residues: 691
  sheet: -1.49 (0.70), residues: 48
  loop : -1.13 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C  66 
 HIS   0.008   0.001   HIS F  17 
 PHE   0.040   0.002   PHE C 103 
 TYR   0.015   0.001   TYR D  17 
 ARG   0.015   0.000   ARG D  48 

*********************** 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
  293 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 293
  time to evaluate  : 0.884 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7985 (ppp) cc_final: 0.7663 (ppp)
REVERT: A   85 ILE cc_start: 0.6147 (pt) cc_final: 0.5826 (pt)
REVERT: A   99 HIS cc_start: 0.8203 (t-90) cc_final: 0.7986 (t-170)
REVERT: B    5 ARG cc_start: 0.8849 (mtm180) cc_final: 0.8178 (mtp180)
REVERT: B   29 LEU cc_start: 0.9504 (tp) cc_final: 0.9296 (tp)
REVERT: B   44 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8694 (tm-30)
REVERT: B  133 LEU cc_start: 0.9630 (tp) cc_final: 0.9412 (tp)
REVERT: B  175 PHE cc_start: 0.9139 (m-10) cc_final: 0.8828 (m-80)
REVERT: C   90 ASN cc_start: 0.8966 (m-40) cc_final: 0.8568 (m-40)
REVERT: C   91 LEU cc_start: 0.9283 (tp) cc_final: 0.9011 (tp)
REVERT: C  118 MET cc_start: 0.8084 (ptp) cc_final: 0.6521 (ptp)
REVERT: C  119 TRP cc_start: 0.7930 (m100) cc_final: 0.7410 (m100)
REVERT: C  153 ARG cc_start: 0.7551 (ttp-170) cc_final: 0.7328 (tmm-80)
REVERT: C  169 ASN cc_start: 0.9100 (m110) cc_final: 0.8424 (m-40)
REVERT: C  228 MET cc_start: 0.8816 (ttm) cc_final: 0.8269 (tmm)
REVERT: D   20 PHE cc_start: 0.8949 (m-80) cc_final: 0.8718 (m-10)
REVERT: D   27 MET cc_start: 0.9201 (tpp) cc_final: 0.8668 (tpp)
REVERT: E    1 MET cc_start: 0.8268 (pmm) cc_final: 0.7927 (pmm)
REVERT: E    6 GLU cc_start: 0.8107 (pp20) cc_final: 0.7799 (pp20)
REVERT: F   15 PHE cc_start: 0.7994 (m-80) cc_final: 0.7605 (m-80)
REVERT: F   73 ASP cc_start: 0.8598 (m-30) cc_final: 0.8153 (m-30)
REVERT: F  168 LEU cc_start: 0.9498 (mt) cc_final: 0.9186 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 293
  average time/residue: 0.1665
  time to fit residues: 70.4657
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  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 80 optimal weight:    7.9990
   chunk 61 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 111 optimal weight:    0.6980
   chunk 102 optimal weight:    0.6980
   chunk 108 optimal weight:    4.9990
   chunk 89 optimal weight:    0.8980
   chunk 84 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3825 r_free = 0.3825 target = 0.101681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.082169 restraints weight = 31161.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.084597 restraints weight = 18131.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.086259 restraints weight = 12225.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2835

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= 0.199
  Angle     :  0.741   8.705  12407  Z= 0.351
  Chirality :  0.044   0.216   1458
  Planarity :  0.005   0.046   1526
  Dihedral  :  6.168  66.578   1248
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.83 %
    Favored  : 95.08 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.26), residues: 1118
  helix:  1.06 (0.20), residues: 691
  sheet: -1.48 (0.70), residues: 48
  loop : -1.09 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C 146 
 HIS   0.007   0.001   HIS F  17 
 PHE   0.018   0.002   PHE B  27 
 TYR   0.014   0.001   TYR C  71 
 ARG   0.009   0.000   ARG D  48 

*********************** 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
  291 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 291
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7971 (ppp) cc_final: 0.7661 (ppp)
REVERT: A   85 ILE cc_start: 0.6060 (pt) cc_final: 0.4459 (pt)
REVERT: A   99 HIS cc_start: 0.8204 (t-90) cc_final: 0.7969 (t-170)
REVERT: A  109 GLU cc_start: 0.9563 (tt0) cc_final: 0.9340 (tm-30)
REVERT: B    5 ARG cc_start: 0.8818 (mtm180) cc_final: 0.8154 (mtp180)
REVERT: B   10 GLU cc_start: 0.8966 (mp0) cc_final: 0.8604 (mp0)
REVERT: B   29 LEU cc_start: 0.9497 (tp) cc_final: 0.9281 (tp)
REVERT: B   44 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8655 (tm-30)
REVERT: B   68 ARG cc_start: 0.8401 (ttp80) cc_final: 0.8078 (tmm160)
REVERT: B   80 GLU cc_start: 0.8152 (tp30) cc_final: 0.7771 (tp30)
REVERT: B  122 ASP cc_start: 0.8618 (p0) cc_final: 0.8400 (p0)
REVERT: B  133 LEU cc_start: 0.9621 (tp) cc_final: 0.9419 (tp)
REVERT: B  175 PHE cc_start: 0.9167 (m-10) cc_final: 0.8843 (m-80)
REVERT: C   90 ASN cc_start: 0.8977 (m-40) cc_final: 0.8564 (m-40)
REVERT: C   91 LEU cc_start: 0.9307 (tp) cc_final: 0.9029 (tp)
REVERT: C  118 MET cc_start: 0.8060 (ptp) cc_final: 0.6340 (ptp)
REVERT: C  119 TRP cc_start: 0.7931 (m100) cc_final: 0.7416 (m100)
REVERT: C  153 ARG cc_start: 0.7625 (ttp-170) cc_final: 0.7414 (ptt-90)
REVERT: C  169 ASN cc_start: 0.9059 (m110) cc_final: 0.8841 (m-40)
REVERT: C  228 MET cc_start: 0.8855 (ttm) cc_final: 0.8314 (tmm)
REVERT: D   27 MET cc_start: 0.9216 (tpp) cc_final: 0.8714 (tpp)
REVERT: E    1 MET cc_start: 0.8335 (pmm) cc_final: 0.8078 (pmm)
REVERT: E    6 GLU cc_start: 0.8164 (pp20) cc_final: 0.7934 (pp20)
REVERT: E   24 LEU cc_start: 0.8747 (mt) cc_final: 0.7903 (mp)
REVERT: F   11 LEU cc_start: 0.9180 (mt) cc_final: 0.8797 (mm)
REVERT: F   15 PHE cc_start: 0.8020 (m-80) cc_final: 0.7677 (m-80)
REVERT: F   73 ASP cc_start: 0.8631 (m-30) cc_final: 0.8140 (m-30)
REVERT: F  111 LEU cc_start: 0.9283 (tp) cc_final: 0.9004 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 291
  average time/residue: 0.1755
  time to fit residues: 73.2550
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  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 85 optimal weight:    0.2980
   chunk 19 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9980
   chunk 75 optimal weight:    9.9990
   chunk 72 optimal weight:    9.9990
   chunk 93 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 7 optimal weight:    9.9990
   chunk 89 optimal weight:    0.0970
   chunk 29 optimal weight:   10.0000
   chunk 35 optimal weight:    0.3980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3817 r_free = 0.3817 target = 0.101382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.081993 restraints weight = 31825.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.084406 restraints weight = 18403.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.086097 restraints weight = 12368.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   9077  Z= 0.211
  Angle     :  0.756   9.017  12407  Z= 0.360
  Chirality :  0.045   0.224   1458
  Planarity :  0.005   0.060   1526
  Dihedral  :  6.136  66.097   1248
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.92 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.26), residues: 1118
  helix:  1.12 (0.20), residues: 685
  sheet: -1.41 (0.71), residues: 48
  loop : -1.11 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP C 146 
 HIS   0.008   0.001   HIS F  17 
 PHE   0.032   0.002   PHE C 103 
 TYR   0.013   0.001   TYR C  71 
 ARG   0.016   0.001   ARG D  48 

*********************** 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
  297 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 297
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7897 (ppp) cc_final: 0.7574 (ppp)
REVERT: A   85 ILE cc_start: 0.5683 (pt) cc_final: 0.4084 (pt)
REVERT: A   99 HIS cc_start: 0.8205 (t-90) cc_final: 0.7969 (t-170)
REVERT: A  109 GLU cc_start: 0.9561 (tt0) cc_final: 0.9325 (tm-30)
REVERT: B    5 ARG cc_start: 0.8850 (mtm180) cc_final: 0.8211 (mtp180)
REVERT: B   10 GLU cc_start: 0.8907 (mp0) cc_final: 0.8536 (mp0)
REVERT: B   29 LEU cc_start: 0.9490 (tp) cc_final: 0.9263 (tp)
REVERT: B   44 GLN cc_start: 0.8911 (tm-30) cc_final: 0.8608 (tm-30)
REVERT: B   80 GLU cc_start: 0.8073 (tp30) cc_final: 0.7659 (tp30)
REVERT: B  122 ASP cc_start: 0.8590 (p0) cc_final: 0.8380 (p0)
REVERT: B  133 LEU cc_start: 0.9609 (tp) cc_final: 0.9406 (tp)
REVERT: B  175 PHE cc_start: 0.9194 (m-10) cc_final: 0.8874 (m-80)
REVERT: C   90 ASN cc_start: 0.8983 (m-40) cc_final: 0.8559 (m-40)
REVERT: C   91 LEU cc_start: 0.9290 (tp) cc_final: 0.9011 (tp)
REVERT: C  118 MET cc_start: 0.8077 (ptp) cc_final: 0.6498 (ptp)
REVERT: C  119 TRP cc_start: 0.7951 (m100) cc_final: 0.7458 (m100)
REVERT: C  153 ARG cc_start: 0.7692 (ttp-170) cc_final: 0.7482 (ptt-90)
REVERT: C  228 MET cc_start: 0.8874 (ttm) cc_final: 0.8329 (tmm)
REVERT: D   27 MET cc_start: 0.9188 (tpp) cc_final: 0.8671 (tpp)
REVERT: E    1 MET cc_start: 0.8391 (pmm) cc_final: 0.8077 (pmm)
REVERT: E    6 GLU cc_start: 0.8203 (pp20) cc_final: 0.7919 (pp20)
REVERT: E   24 LEU cc_start: 0.8781 (mt) cc_final: 0.7774 (mp)
REVERT: F   11 LEU cc_start: 0.9173 (mt) cc_final: 0.8792 (mm)
REVERT: F   15 PHE cc_start: 0.8000 (m-80) cc_final: 0.7663 (m-80)
REVERT: F   73 ASP cc_start: 0.8634 (m-30) cc_final: 0.8178 (m-30)
REVERT: F  111 LEU cc_start: 0.9278 (tp) cc_final: 0.9004 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 297
  average time/residue: 0.1750
  time to fit residues: 74.9827
Evaluate side-chains
  247 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    0.0980
   chunk 100 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   chunk 70 optimal weight:    9.9990
   chunk 46 optimal weight:    0.0370
   chunk 110 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0030
   chunk 85 optimal weight:    0.0770
   chunk 57 optimal weight:    0.9990
   chunk 38 optimal weight:   10.0000
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.1826

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

Flipped N/Q/H residues before XYZ refinement:
A  94 ASN
C 169 ASN
E 171 GLN
F  17 HIS
F 100 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.104104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.084614 restraints weight = 31941.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.087077 restraints weight = 18599.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.088754 restraints weight = 12615.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9077  Z= 0.193
  Angle     :  0.746   9.067  12407  Z= 0.351
  Chirality :  0.044   0.226   1458
  Planarity :  0.005   0.050   1526
  Dihedral  :  6.048  66.605   1248
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.10 %
    Favored  : 94.81 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.26), residues: 1118
  helix:  1.18 (0.20), residues: 682
  sheet: -1.33 (0.71), residues: 48
  loop : -1.15 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP C 146 
 HIS   0.006   0.001   HIS F  17 
 PHE   0.022   0.002   PHE E  97 
 TYR   0.015   0.001   TYR C  71 
 ARG   0.012   0.000   ARG D  48 

********************** 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
  293 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 293
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7828 (ppp) cc_final: 0.7489 (ppp)
REVERT: A   85 ILE cc_start: 0.5584 (pt) cc_final: 0.5253 (pt)
REVERT: A   99 HIS cc_start: 0.8177 (t-90) cc_final: 0.7968 (t-170)
REVERT: A  109 GLU cc_start: 0.9536 (tt0) cc_final: 0.9298 (tm-30)
REVERT: B    5 ARG cc_start: 0.8802 (mtm180) cc_final: 0.8133 (mtp180)
REVERT: B    6 ILE cc_start: 0.9107 (mp) cc_final: 0.8862 (mp)
REVERT: B   10 GLU cc_start: 0.8877 (mp0) cc_final: 0.8549 (mp0)
REVERT: B   29 LEU cc_start: 0.9476 (tp) cc_final: 0.9274 (tp)
REVERT: B   44 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8555 (tm-30)
REVERT: B   68 ARG cc_start: 0.8468 (tmm160) cc_final: 0.7537 (mmm160)
REVERT: B  122 ASP cc_start: 0.8517 (p0) cc_final: 0.8282 (p0)
REVERT: B  133 LEU cc_start: 0.9593 (tp) cc_final: 0.9390 (tp)
REVERT: B  175 PHE cc_start: 0.9170 (m-10) cc_final: 0.8856 (m-80)
REVERT: B  193 LEU cc_start: 0.8815 (mt) cc_final: 0.8582 (pp)
REVERT: C   91 LEU cc_start: 0.9254 (tp) cc_final: 0.8986 (tp)
REVERT: C  118 MET cc_start: 0.8011 (ptp) cc_final: 0.6347 (ptp)
REVERT: C  119 TRP cc_start: 0.7985 (m100) cc_final: 0.7551 (m100)
REVERT: C  153 ARG cc_start: 0.7626 (ttp-170) cc_final: 0.7286 (tmm-80)
REVERT: C  228 MET cc_start: 0.8762 (ttm) cc_final: 0.8251 (tmm)
REVERT: D   27 MET cc_start: 0.9145 (tpp) cc_final: 0.8669 (tpp)
REVERT: E    1 MET cc_start: 0.8269 (pmm) cc_final: 0.7934 (pmm)
REVERT: E    6 GLU cc_start: 0.8090 (pp20) cc_final: 0.7831 (pp20)
REVERT: E   24 LEU cc_start: 0.8622 (mt) cc_final: 0.7620 (mp)
REVERT: F   11 LEU cc_start: 0.9190 (mt) cc_final: 0.8807 (mm)
REVERT: F   15 PHE cc_start: 0.7940 (m-80) cc_final: 0.7721 (m-80)
REVERT: F   55 TRP cc_start: 0.8997 (m100) cc_final: 0.8766 (m100)
REVERT: F   73 ASP cc_start: 0.8650 (m-30) cc_final: 0.8186 (m-30)
REVERT: F  111 LEU cc_start: 0.9231 (tp) cc_final: 0.8989 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 293
  average time/residue: 0.1695
  time to fit residues: 71.6125
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  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 88 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3828 r_free = 0.3828 target = 0.102189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.082590 restraints weight = 31726.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.085040 restraints weight = 18435.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.086742 restraints weight = 12495.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9077  Z= 0.206
  Angle     :  0.746   8.886  12407  Z= 0.354
  Chirality :  0.044   0.223   1458
  Planarity :  0.005   0.048   1526
  Dihedral  :  5.980  64.938   1248
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.92 %
    Favored  : 94.99 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.26), residues: 1118
  helix:  1.24 (0.20), residues: 684
  sheet: -1.25 (0.71), residues: 48
  loop : -1.08 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C 146 
 HIS   0.003   0.001   HIS B 100 
 PHE   0.029   0.002   PHE F  28 
 TYR   0.020   0.002   TYR C  58 
 ARG   0.011   0.000   ARG D  48 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2984.22 seconds
wall clock time: 53 minutes 2.66 seconds (3182.66 seconds total)