Starting phenix.real_space_refine
on Thu Feb 13 16:35:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vfp_31957/02_2025/7vfp_31957.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vfp_31957/02_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_31957/02_2025/7vfp_31957.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vfp_31957/02_2025/7vfp_31957.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vfp_31957/02_2025/7vfp_31957.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vfp_31957/02_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-5592/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: 6.94, per 1000 atoms: 0.78
  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: 2.65
  Conformation dependent library (CDL) restraints added in 2.2 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: 0.89
  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: 3.00

  Time building geometry restraints manager: 3.03 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:             1.620
  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:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.090
  Set scattering table:                    0.010
  Process input model:                     27.480
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  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:3.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.650
-------------------------------------------------------------------------------
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  : 1.406 
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: 0.2125
  time to fit residues: 90.2040
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  : 1.835 
-------------------------------------------------------------------------------
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 = 0.100463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.081425 restraints weight = 30412.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.083766 restraints weight = 17566.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.085412 restraints weight = 11825.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
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   8.024  12407  Z= 0.354
  Chirality :  0.044   0.197   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  6.589  71.957   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  : 0.922 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8016 (ppp) cc_final: 0.7711 (ppp)
REVERT: A   47 LEU cc_start: 0.8674 (mt) cc_final: 0.8470 (mt)
REVERT: A   99 HIS cc_start: 0.8157 (t-90) cc_final: 0.7897 (t-90)
REVERT: B    1 MET cc_start: 0.8323 (tmm) cc_final: 0.8093 (tmm)
REVERT: B    5 ARG cc_start: 0.8936 (mtm180) cc_final: 0.8455 (mtp180)
REVERT: B   44 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8762 (tm-30)
REVERT: B   73 ASP cc_start: 0.8034 (m-30) cc_final: 0.7755 (m-30)
REVERT: B  133 LEU cc_start: 0.9655 (tp) cc_final: 0.9423 (tp)
REVERT: B  175 PHE cc_start: 0.8978 (m-10) cc_final: 0.8644 (m-80)
REVERT: C   86 MET cc_start: 0.8210 (mmm) cc_final: 0.7960 (mmm)
REVERT: C   90 ASN cc_start: 0.9042 (m-40) cc_final: 0.8670 (m-40)
REVERT: C  169 ASN cc_start: 0.9110 (m110) cc_final: 0.8888 (m-40)
REVERT: C  228 MET cc_start: 0.8853 (ttm) cc_final: 0.8260 (tmm)
REVERT: C  230 LYS cc_start: 0.8490 (pptt) cc_final: 0.8019 (pptt)
REVERT: D   20 PHE cc_start: 0.8934 (m-80) cc_final: 0.8684 (m-10)
REVERT: D   27 MET cc_start: 0.9078 (tpp) cc_final: 0.8722 (tpp)
REVERT: E    1 MET cc_start: 0.8050 (pmm) cc_final: 0.7817 (pmm)
REVERT: F   15 PHE cc_start: 0.8040 (m-80) cc_final: 0.7823 (m-80)
REVERT: F   68 ARG cc_start: 0.8614 (ppt170) cc_final: 0.8277 (ttp80)
REVERT: F   71 ARG cc_start: 0.7616 (ttt180) cc_final: 0.6970 (ttm-80)
REVERT: F   73 ASP cc_start: 0.8851 (m-30) cc_final: 0.8433 (m-30)
REVERT: F  164 LEU cc_start: 0.9313 (mt) cc_final: 0.9070 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 295
  average time/residue: 0.1835
  time to fit residues: 76.5009
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  : 0.968 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 72 optimal weight:    6.9990
   chunk 105 optimal weight:    0.2980
   chunk 60 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 94 optimal weight:    0.1980
   chunk 101 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3814 r_free = 0.3814 target = 0.101335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.081794 restraints weight = 31996.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.084241 restraints weight = 18511.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.085855 restraints weight = 12505.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9077  Z= 0.214
  Angle     :  0.697   6.593  12407  Z= 0.340
  Chirality :  0.044   0.207   1458
  Planarity :  0.005   0.048   1526
  Dihedral  :  6.429  68.847   1248
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.74 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.03 %
    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:  0.09 (0.25), residues: 1118
  helix:  0.81 (0.20), residues: 695
  sheet: -1.56 (0.69), residues: 48
  loop : -1.02 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP F  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   0.005   0.000   ARG B  68 

*********************** 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
  286 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 285
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7983 (ppp) cc_final: 0.7673 (ppp)
REVERT: A   47 LEU cc_start: 0.8676 (mt) cc_final: 0.8462 (mt)
REVERT: A   76 LEU cc_start: 0.9088 (tt) cc_final: 0.8571 (tt)
REVERT: A   85 ILE cc_start: 0.6050 (pt) cc_final: 0.5755 (pt)
REVERT: A   99 HIS cc_start: 0.8195 (t-90) cc_final: 0.7933 (t-170)
REVERT: A  109 GLU cc_start: 0.9568 (tt0) cc_final: 0.9310 (tm-30)
REVERT: B    5 ARG cc_start: 0.8922 (mtm180) cc_final: 0.8492 (mtp180)
REVERT: B   44 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8774 (tm-30)
REVERT: B  122 ASP cc_start: 0.8643 (p0) cc_final: 0.8432 (p0)
REVERT: B  133 LEU cc_start: 0.9634 (tp) cc_final: 0.9384 (tp)
REVERT: B  175 PHE cc_start: 0.9059 (m-10) cc_final: 0.8761 (m-80)
REVERT: C   90 ASN cc_start: 0.9056 (m-40) cc_final: 0.8691 (m-40)
REVERT: C  118 MET cc_start: 0.8553 (ptp) cc_final: 0.6257 (ptp)
REVERT: C  169 ASN cc_start: 0.9119 (m110) cc_final: 0.8886 (m-40)
REVERT: C  228 MET cc_start: 0.8849 (ttm) cc_final: 0.8210 (tmm)
REVERT: D   20 PHE cc_start: 0.8887 (m-80) cc_final: 0.8670 (m-10)
REVERT: D   27 MET cc_start: 0.9166 (tpp) cc_final: 0.8717 (tpp)
REVERT: D   42 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8413 (tm-30)
REVERT: E    1 MET cc_start: 0.8170 (pmm) cc_final: 0.7957 (pmm)
REVERT: E    6 GLU cc_start: 0.8127 (pp20) cc_final: 0.7830 (pp20)
REVERT: F   15 PHE cc_start: 0.8069 (m-80) cc_final: 0.7850 (m-80)
REVERT: F   17 HIS cc_start: 0.8225 (m-70) cc_final: 0.8013 (m-70)
REVERT: F   67 GLU cc_start: 0.8913 (tt0) cc_final: 0.8637 (tt0)
REVERT: F   68 ARG cc_start: 0.8677 (ppt170) cc_final: 0.8330 (ttp80)
REVERT: F   73 ASP cc_start: 0.8723 (m-30) cc_final: 0.8350 (m-30)
REVERT: F  164 LEU cc_start: 0.9283 (mt) cc_final: 0.9065 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 286
  average time/residue: 0.1817
  time to fit residues: 74.1417
Evaluate side-chains
  239 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 82 optimal weight:    4.9990
   chunk 107 optimal weight:    0.7980
   chunk 98 optimal weight:    0.0470
   chunk 62 optimal weight:    4.9990
   chunk 84 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 104 optimal weight:    0.5980
   chunk 94 optimal weight:    8.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.6480

-------------------------------------------------------------------------------
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 = 0.3825 r_free = 0.3825 target = 0.101942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.082359 restraints weight = 31217.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.084834 restraints weight = 18022.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.086488 restraints weight = 12154.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9077  Z= 0.195
  Angle     :  0.692   6.454  12407  Z= 0.337
  Chirality :  0.043   0.208   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  6.269  66.854   1248
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.74 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.81 (0.20), residues: 699
  sheet: -1.60 (0.69), residues: 48
  loop : -0.96 (0.32), residues: 371

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   0.041   0.002   PHE C 103 
 TYR   0.012   0.001   TYR D  17 
 ARG   0.007   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
  299 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 299
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7970 (ppp) cc_final: 0.7643 (ppp)
REVERT: A   35 SER cc_start: 0.7656 (m) cc_final: 0.7439 (t)
REVERT: A   47 LEU cc_start: 0.8677 (mt) cc_final: 0.8471 (mt)
REVERT: A   85 ILE cc_start: 0.6041 (pt) cc_final: 0.5720 (pt)
REVERT: A   99 HIS cc_start: 0.8211 (t-90) cc_final: 0.7965 (t-170)
REVERT: A  109 GLU cc_start: 0.9545 (tt0) cc_final: 0.9306 (tm-30)
REVERT: A  141 TRP cc_start: 0.7502 (m100) cc_final: 0.7181 (m100)
REVERT: B    5 ARG cc_start: 0.8863 (mtm180) cc_final: 0.8363 (mtp180)
REVERT: B   44 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8784 (tm-30)
REVERT: B  122 ASP cc_start: 0.8666 (p0) cc_final: 0.8446 (p0)
REVERT: B  133 LEU cc_start: 0.9637 (tp) cc_final: 0.9402 (tp)
REVERT: B  175 PHE cc_start: 0.9064 (m-10) cc_final: 0.8751 (m-80)
REVERT: C   90 ASN cc_start: 0.8978 (m-40) cc_final: 0.8608 (m-40)
REVERT: C   91 LEU cc_start: 0.9316 (tp) cc_final: 0.9051 (tp)
REVERT: C  118 MET cc_start: 0.7919 (ptp) cc_final: 0.6558 (ptp)
REVERT: C  119 TRP cc_start: 0.7636 (m100) cc_final: 0.7192 (m100)
REVERT: C  169 ASN cc_start: 0.9115 (m110) cc_final: 0.8908 (m-40)
REVERT: C  228 MET cc_start: 0.8824 (ttm) cc_final: 0.8282 (tmm)
REVERT: D   20 PHE cc_start: 0.8895 (m-80) cc_final: 0.8662 (m-10)
REVERT: D   27 MET cc_start: 0.9199 (tpp) cc_final: 0.8688 (tpp)
REVERT: E    6 GLU cc_start: 0.8195 (pp20) cc_final: 0.7900 (pp20)
REVERT: E   93 GLU cc_start: 0.8735 (mp0) cc_final: 0.8525 (mp0)
REVERT: F   68 ARG cc_start: 0.8724 (ppt170) cc_final: 0.8326 (ttp80)
REVERT: F   73 ASP cc_start: 0.8646 (m-30) cc_final: 0.8272 (m-30)
REVERT: F  104 THR cc_start: 0.8944 (p) cc_final: 0.8684 (t)
REVERT: F  164 LEU cc_start: 0.9259 (mt) cc_final: 0.9006 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 299
  average time/residue: 0.1769
  time to fit residues: 76.1368
Evaluate side-chains
  242 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 8 optimal weight:   10.0000
   chunk 109 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 34 optimal weight:    7.9990
   chunk 86 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 63 optimal weight:    0.6980
   chunk 94 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 56 optimal weight:    0.3980
   overall best weight:    2.1384

-------------------------------------------------------------------------------
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 = 0.3788 r_free = 0.3788 target = 0.099543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.080418 restraints weight = 30985.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.082722 restraints weight = 17740.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.084346 restraints weight = 11901.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9077  Z= 0.273
  Angle     :  0.736   9.622  12407  Z= 0.359
  Chirality :  0.044   0.201   1458
  Planarity :  0.005   0.047   1526
  Dihedral  :  6.285  65.173   1248
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 15.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.01 %
    Favored  : 94.90 %
  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:  0.19 (0.25), residues: 1118
  helix:  0.93 (0.20), residues: 694
  sheet: -1.52 (0.70), residues: 48
  loop : -1.07 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C  66 
 HIS   0.008   0.001   HIS F  17 
 PHE   0.034   0.002   PHE F  15 
 TYR   0.010   0.001   TYR D  17 
 ARG   0.012   0.000   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
  290 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7970 (ppp) cc_final: 0.7592 (ppp)
REVERT: A   47 LEU cc_start: 0.8637 (mt) cc_final: 0.8436 (mt)
REVERT: A   85 ILE cc_start: 0.6148 (pt) cc_final: 0.5823 (pt)
REVERT: A   99 HIS cc_start: 0.8192 (t-90) cc_final: 0.7944 (t-170)
REVERT: A  141 TRP cc_start: 0.7601 (m100) cc_final: 0.7364 (m100)
REVERT: B    5 ARG cc_start: 0.8849 (mtm180) cc_final: 0.8359 (mtp180)
REVERT: B   29 LEU cc_start: 0.9542 (tp) cc_final: 0.9312 (tp)
REVERT: B   44 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8807 (tm-30)
REVERT: B  175 PHE cc_start: 0.9076 (m-10) cc_final: 0.8770 (m-80)
REVERT: C   86 MET cc_start: 0.8269 (mmm) cc_final: 0.8012 (mmm)
REVERT: C   87 LYS cc_start: 0.9068 (mtpp) cc_final: 0.8154 (tptt)
REVERT: C   90 ASN cc_start: 0.8984 (m-40) cc_final: 0.8629 (m-40)
REVERT: C   91 LEU cc_start: 0.9320 (tp) cc_final: 0.9082 (tp)
REVERT: C  118 MET cc_start: 0.8109 (ptp) cc_final: 0.6401 (ptp)
REVERT: C  119 TRP cc_start: 0.7790 (m100) cc_final: 0.7300 (m100)
REVERT: C  228 MET cc_start: 0.8817 (ttm) cc_final: 0.8303 (tmm)
REVERT: D   27 MET cc_start: 0.9192 (tpp) cc_final: 0.8776 (tpp)
REVERT: E    1 MET cc_start: 0.8158 (pmm) cc_final: 0.7800 (pmm)
REVERT: E    6 GLU cc_start: 0.8123 (pp20) cc_final: 0.7826 (pp20)
REVERT: E   93 GLU cc_start: 0.8801 (mp0) cc_final: 0.8506 (mp0)
REVERT: F   15 PHE cc_start: 0.8116 (m-80) cc_final: 0.7619 (m-80)
REVERT: F   68 ARG cc_start: 0.8777 (ppt170) cc_final: 0.8383 (ttp80)
REVERT: F   73 ASP cc_start: 0.8621 (m-30) cc_final: 0.8239 (m-30)
REVERT: F  164 LEU cc_start: 0.9384 (mt) cc_final: 0.9183 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 290
  average time/residue: 0.1846
  time to fit residues: 76.6921
Evaluate side-chains
  230 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 58 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    1.6162

-------------------------------------------------------------------------------
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
F  17 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.100024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.080955 restraints weight = 30702.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.083336 restraints weight = 17504.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.084931 restraints weight = 11704.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9077  Z= 0.244
  Angle     :  0.749   8.308  12407  Z= 0.359
  Chirality :  0.045   0.228   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  6.240  65.706   1248
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 15.05
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.10 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  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:  0.30 (0.26), residues: 1118
  helix:  1.03 (0.20), residues: 684
  sheet: -1.58 (0.70), residues: 48
  loop : -0.99 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  66 
 HIS   0.006   0.001   HIS A  73 
 PHE   0.025   0.002   PHE F  15 
 TYR   0.010   0.001   TYR D  17 
 ARG   0.015   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
  285 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 285
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8004 (ppp) cc_final: 0.7560 (ppp)
REVERT: A   47 LEU cc_start: 0.8655 (mt) cc_final: 0.8453 (mt)
REVERT: A   85 ILE cc_start: 0.6096 (pt) cc_final: 0.5770 (pt)
REVERT: A   99 HIS cc_start: 0.8229 (t-90) cc_final: 0.7973 (t-170)
REVERT: B    5 ARG cc_start: 0.8828 (mtm180) cc_final: 0.8308 (mtp180)
REVERT: B   29 LEU cc_start: 0.9511 (tp) cc_final: 0.9304 (tp)
REVERT: B   44 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8755 (tm-30)
REVERT: B   73 ASP cc_start: 0.8142 (m-30) cc_final: 0.7917 (m-30)
REVERT: B  175 PHE cc_start: 0.9109 (m-10) cc_final: 0.8800 (m-80)
REVERT: C   90 ASN cc_start: 0.8899 (m-40) cc_final: 0.8577 (m-40)
REVERT: C   91 LEU cc_start: 0.9250 (tp) cc_final: 0.9029 (tp)
REVERT: C  118 MET cc_start: 0.8046 (ptp) cc_final: 0.6355 (ptp)
REVERT: C  119 TRP cc_start: 0.7907 (m100) cc_final: 0.7361 (m100)
REVERT: C  228 MET cc_start: 0.8744 (ttm) cc_final: 0.8299 (tmm)
REVERT: D   27 MET cc_start: 0.9219 (tpp) cc_final: 0.8633 (tpp)
REVERT: E    1 MET cc_start: 0.8198 (pmm) cc_final: 0.7893 (pmm)
REVERT: E    6 GLU cc_start: 0.8205 (pp20) cc_final: 0.7889 (pp20)
REVERT: E   93 GLU cc_start: 0.8852 (mp0) cc_final: 0.8428 (mp0)
REVERT: F   11 LEU cc_start: 0.9208 (mt) cc_final: 0.8874 (mm)
REVERT: F   15 PHE cc_start: 0.8135 (m-80) cc_final: 0.7767 (m-80)
REVERT: F   73 ASP cc_start: 0.8602 (m-30) cc_final: 0.8167 (m-30)
REVERT: F  168 LEU cc_start: 0.9492 (mp) cc_final: 0.9242 (mt)
REVERT: F  209 PHE cc_start: 0.7315 (t80) cc_final: 0.6974 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 285
  average time/residue: 0.1677
  time to fit residues: 69.5035
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  : 1.069 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 107 optimal weight:    0.5980
   chunk 68 optimal weight:    0.4980
   chunk 75 optimal weight:    8.9990
   chunk 60 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 71 optimal weight:    5.9990
   overall best weight:    1.2184

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.100904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.081556 restraints weight = 31828.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.083883 restraints weight = 18568.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.085544 restraints weight = 12629.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9077  Z= 0.220
  Angle     :  0.735   8.495  12407  Z= 0.353
  Chirality :  0.045   0.222   1458
  Planarity :  0.005   0.044   1526
  Dihedral  :  6.181  66.084   1248
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.19 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  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:  0.30 (0.26), residues: 1118
  helix:  1.05 (0.20), residues: 690
  sheet: -1.57 (0.70), residues: 48
  loop : -1.08 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C  66 
 HIS   0.005   0.001   HIS F  17 
 PHE   0.037   0.002   PHE C 103 
 TYR   0.009   0.001   TYR D  17 
 ARG   0.008   0.000   ARG F  68 

*********************** 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
  291 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 291
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7999 (ppp) cc_final: 0.7696 (ppp)
REVERT: A   85 ILE cc_start: 0.5982 (pt) cc_final: 0.5657 (pt)
REVERT: A   99 HIS cc_start: 0.8240 (t-90) cc_final: 0.7999 (t-170)
REVERT: B    5 ARG cc_start: 0.8822 (mtm180) cc_final: 0.8157 (mtp180)
REVERT: B   10 GLU cc_start: 0.8938 (mp0) cc_final: 0.8619 (mp0)
REVERT: B   29 LEU cc_start: 0.9505 (tp) cc_final: 0.9295 (tp)
REVERT: B   44 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8766 (tm-30)
REVERT: B   84 LEU cc_start: 0.8396 (tp) cc_final: 0.8089 (tp)
REVERT: B  133 LEU cc_start: 0.9629 (tp) cc_final: 0.9429 (tp)
REVERT: B  175 PHE cc_start: 0.9142 (m-10) cc_final: 0.8843 (m-80)
REVERT: C   90 ASN cc_start: 0.8871 (m-40) cc_final: 0.8497 (m-40)
REVERT: C   91 LEU cc_start: 0.9266 (tp) cc_final: 0.8996 (tp)
REVERT: C  228 MET cc_start: 0.8845 (ttm) cc_final: 0.8315 (tmm)
REVERT: D   27 MET cc_start: 0.9224 (tpp) cc_final: 0.8679 (tpp)
REVERT: E    1 MET cc_start: 0.8258 (pmm) cc_final: 0.7958 (pmm)
REVERT: E    6 GLU cc_start: 0.8204 (pp20) cc_final: 0.7888 (pp20)
REVERT: E   93 GLU cc_start: 0.8830 (mp0) cc_final: 0.8407 (mp0)
REVERT: F   11 LEU cc_start: 0.9204 (mt) cc_final: 0.8885 (mm)
REVERT: F   15 PHE cc_start: 0.8068 (m-80) cc_final: 0.7750 (m-80)
REVERT: F   73 ASP cc_start: 0.8631 (m-30) cc_final: 0.8159 (m-30)
REVERT: F  111 LEU cc_start: 0.9327 (tp) cc_final: 0.9052 (tt)
REVERT: F  168 LEU cc_start: 0.9500 (mp) cc_final: 0.9248 (mt)
REVERT: F  209 PHE cc_start: 0.7341 (t80) cc_final: 0.7015 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 291
  average time/residue: 0.1743
  time to fit residues: 74.3445
Evaluate side-chains
  240 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 111 optimal weight:    0.7980
   chunk 102 optimal weight:    0.0000
   chunk 108 optimal weight:    0.0980
   chunk 89 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.5384

-------------------------------------------------------------------------------
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 = 0.3827 r_free = 0.3827 target = 0.102037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.083074 restraints weight = 31016.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.085431 restraints weight = 17484.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.087125 restraints weight = 11721.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
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   0.078   9077  Z= 0.210
  Angle     :  0.742   8.581  12407  Z= 0.353
  Chirality :  0.045   0.232   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  6.141  67.227   1248
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.01 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  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:  0.23 (0.25), residues: 1118
  helix:  1.02 (0.20), residues: 692
  sheet: -1.67 (0.69), residues: 48
  loop : -1.15 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C 119 
 HIS   0.004   0.001   HIS F  17 
 PHE   0.019   0.002   PHE F  15 
 TYR   0.013   0.001   TYR C  71 
 ARG   0.024   0.001   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
  289 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 0.954 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7947 (ppp) cc_final: 0.7631 (ppp)
REVERT: A   85 ILE cc_start: 0.5926 (pt) cc_final: 0.5604 (pt)
REVERT: A   99 HIS cc_start: 0.8186 (t-90) cc_final: 0.7966 (t-170)
REVERT: B    5 ARG cc_start: 0.8794 (mtm180) cc_final: 0.8131 (mtp180)
REVERT: B   10 GLU cc_start: 0.8873 (mp0) cc_final: 0.8621 (mp0)
REVERT: B   29 LEU cc_start: 0.9486 (tp) cc_final: 0.9273 (tp)
REVERT: B   44 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8699 (tm-30)
REVERT: B   68 ARG cc_start: 0.8401 (ttp80) cc_final: 0.8033 (tmm160)
REVERT: B  122 ASP cc_start: 0.8615 (p0) cc_final: 0.8407 (p0)
REVERT: B  175 PHE cc_start: 0.9113 (m-10) cc_final: 0.8799 (m-80)
REVERT: C   90 ASN cc_start: 0.8852 (m-40) cc_final: 0.8480 (m-40)
REVERT: C   91 LEU cc_start: 0.9253 (tp) cc_final: 0.8991 (tp)
REVERT: C  228 MET cc_start: 0.8819 (ttm) cc_final: 0.8303 (tmm)
REVERT: D   27 MET cc_start: 0.9197 (tpp) cc_final: 0.8690 (tpp)
REVERT: E    1 MET cc_start: 0.8204 (pmm) cc_final: 0.7860 (pmm)
REVERT: E    6 GLU cc_start: 0.8143 (pp20) cc_final: 0.7921 (pp20)
REVERT: E   93 GLU cc_start: 0.8817 (mp0) cc_final: 0.8592 (mt-10)
REVERT: F    1 MET cc_start: 0.6772 (ppp) cc_final: 0.6381 (pmm)
REVERT: F   11 LEU cc_start: 0.9185 (mt) cc_final: 0.8865 (mm)
REVERT: F   15 PHE cc_start: 0.7986 (m-80) cc_final: 0.7751 (m-80)
REVERT: F   73 ASP cc_start: 0.8635 (m-30) cc_final: 0.8181 (m-30)
REVERT: F  111 LEU cc_start: 0.9267 (tp) cc_final: 0.9013 (tt)
REVERT: F  168 LEU cc_start: 0.9481 (mp) cc_final: 0.9233 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 289
  average time/residue: 0.1691
  time to fit residues: 71.0318
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  : 1.083 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 19 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 75 optimal weight:    0.1980
   chunk 72 optimal weight:    9.9990
   chunk 93 optimal weight:    0.8980
   chunk 107 optimal weight:    0.5980
   chunk 7 optimal weight:    8.9990
   chunk 89 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3814 r_free = 0.3814 target = 0.101382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.082456 restraints weight = 31415.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.084846 restraints weight = 17690.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.086507 restraints weight = 11740.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9077  Z= 0.214
  Angle     :  0.754  11.214  12407  Z= 0.358
  Chirality :  0.045   0.237   1458
  Planarity :  0.005   0.051   1526
  Dihedral  :  6.061  65.522   1248
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.01 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  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:  0.24 (0.26), residues: 1118
  helix:  1.01 (0.20), residues: 688
  sheet: -1.57 (0.70), residues: 48
  loop : -1.11 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP F  55 
 HIS   0.004   0.001   HIS B 100 
 PHE   0.031   0.002   PHE C 103 
 TYR   0.013   0.001   TYR C  71 
 ARG   0.011   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
  288 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 288
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7914 (ppp) cc_final: 0.7581 (ppp)
REVERT: A   85 ILE cc_start: 0.5974 (pt) cc_final: 0.5653 (pt)
REVERT: A   99 HIS cc_start: 0.8214 (t-90) cc_final: 0.8000 (t-170)
REVERT: A  109 GLU cc_start: 0.9537 (tt0) cc_final: 0.9311 (tm-30)
REVERT: B    5 ARG cc_start: 0.8805 (mtm180) cc_final: 0.8183 (mtp180)
REVERT: B    6 ILE cc_start: 0.9105 (mp) cc_final: 0.8779 (mp)
REVERT: B   10 GLU cc_start: 0.8866 (mp0) cc_final: 0.8625 (mp0)
REVERT: B   29 LEU cc_start: 0.9493 (tp) cc_final: 0.9279 (tp)
REVERT: B   44 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8597 (tm-30)
REVERT: B  122 ASP cc_start: 0.8647 (p0) cc_final: 0.8429 (p0)
REVERT: B  175 PHE cc_start: 0.9165 (m-10) cc_final: 0.8841 (m-80)
REVERT: C   87 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8527 (tptm)
REVERT: C   90 ASN cc_start: 0.8872 (m-40) cc_final: 0.8456 (m-40)
REVERT: C   91 LEU cc_start: 0.9253 (tp) cc_final: 0.8985 (tp)
REVERT: C  118 MET cc_start: 0.8348 (ptp) cc_final: 0.7749 (ptp)
REVERT: C  146 TRP cc_start: 0.8781 (t60) cc_final: 0.8578 (t60)
REVERT: C  228 MET cc_start: 0.8868 (ttm) cc_final: 0.8330 (tmm)
REVERT: D   27 MET cc_start: 0.9166 (tpp) cc_final: 0.8682 (tpp)
REVERT: E    1 MET cc_start: 0.8279 (pmm) cc_final: 0.7878 (pmm)
REVERT: E    6 GLU cc_start: 0.8171 (pp20) cc_final: 0.7890 (pp20)
REVERT: E   93 GLU cc_start: 0.8883 (mp0) cc_final: 0.8384 (mp0)
REVERT: F    1 MET cc_start: 0.6706 (ppp) cc_final: 0.5442 (ptp)
REVERT: F   11 LEU cc_start: 0.9196 (mt) cc_final: 0.8792 (mm)
REVERT: F   15 PHE cc_start: 0.7915 (m-80) cc_final: 0.7624 (m-80)
REVERT: F   73 ASP cc_start: 0.8594 (m-30) cc_final: 0.8112 (m-30)
REVERT: F  111 LEU cc_start: 0.9270 (tp) cc_final: 0.9008 (tt)
REVERT: F  168 LEU cc_start: 0.9488 (mp) cc_final: 0.9220 (mt)
REVERT: F  209 PHE cc_start: 0.7233 (t80) cc_final: 0.6865 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 288
  average time/residue: 0.1841
  time to fit residues: 76.1135
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  : 0.969 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 70 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9980
   chunk 110 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 85 optimal weight:    0.0040
   chunk 57 optimal weight:    0.3980
   chunk 38 optimal weight:    0.8980
   chunk 73 optimal weight:    6.9990
   overall best weight:    0.5992

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.102272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.083246 restraints weight = 31183.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.085707 restraints weight = 17622.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.087342 restraints weight = 11709.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9077  Z= 0.200
  Angle     :  0.758  11.008  12407  Z= 0.358
  Chirality :  0.044   0.235   1458
  Planarity :  0.005   0.046   1526
  Dihedral  :  6.051  65.853   1248
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.65 %
    Favored  : 95.26 %
  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:  0.29 (0.25), residues: 1118
  helix:  1.06 (0.20), residues: 686
  sheet: -1.53 (0.70), residues: 48
  loop : -1.11 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  55 
 HIS   0.004   0.001   HIS A  96 
 PHE   0.020   0.001   PHE B  27 
 TYR   0.015   0.001   TYR C  71 
 ARG   0.010   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
  292 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 292
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7863 (ppp) cc_final: 0.7528 (ppp)
REVERT: A   85 ILE cc_start: 0.5940 (pt) cc_final: 0.5611 (pt)
REVERT: A   99 HIS cc_start: 0.8227 (t-90) cc_final: 0.7999 (t-170)
REVERT: A  109 GLU cc_start: 0.9552 (tt0) cc_final: 0.9308 (tm-30)
REVERT: B    5 ARG cc_start: 0.8829 (mtm180) cc_final: 0.8212 (mtp180)
REVERT: B    6 ILE cc_start: 0.9091 (mp) cc_final: 0.8741 (mp)
REVERT: B   10 GLU cc_start: 0.8870 (mp0) cc_final: 0.8583 (mp0)
REVERT: B   29 LEU cc_start: 0.9489 (tp) cc_final: 0.9276 (tp)
REVERT: B   44 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8591 (tm-30)
REVERT: B   68 ARG cc_start: 0.8400 (tmm160) cc_final: 0.7434 (mmm160)
REVERT: B  117 MET cc_start: 0.8684 (ppp) cc_final: 0.8339 (mmp)
REVERT: B  122 ASP cc_start: 0.8615 (p0) cc_final: 0.8403 (p0)
REVERT: B  175 PHE cc_start: 0.9158 (m-10) cc_final: 0.8850 (m-80)
REVERT: C   90 ASN cc_start: 0.8796 (m-40) cc_final: 0.8394 (m-40)
REVERT: C   91 LEU cc_start: 0.9222 (tp) cc_final: 0.8950 (tp)
REVERT: C  118 MET cc_start: 0.7958 (ptp) cc_final: 0.6580 (ptp)
REVERT: C  119 TRP cc_start: 0.7999 (m100) cc_final: 0.7476 (m100)
REVERT: C  146 TRP cc_start: 0.8786 (t60) cc_final: 0.8575 (t60)
REVERT: C  228 MET cc_start: 0.8861 (ttm) cc_final: 0.8315 (tmm)
REVERT: D   27 MET cc_start: 0.9153 (tpp) cc_final: 0.8674 (tpp)
REVERT: E    1 MET cc_start: 0.8307 (pmm) cc_final: 0.7925 (pmm)
REVERT: E    6 GLU cc_start: 0.8168 (pp20) cc_final: 0.7902 (pp20)
REVERT: E   93 GLU cc_start: 0.8860 (mp0) cc_final: 0.8336 (mp0)
REVERT: F    1 MET cc_start: 0.6445 (ppp) cc_final: 0.5213 (ptp)
REVERT: F   11 LEU cc_start: 0.9202 (mt) cc_final: 0.8874 (mm)
REVERT: F   73 ASP cc_start: 0.8653 (m-30) cc_final: 0.8202 (m-30)
REVERT: F  111 LEU cc_start: 0.9268 (tp) cc_final: 0.9005 (tt)
REVERT: F  168 LEU cc_start: 0.9503 (mp) cc_final: 0.9258 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 292
  average time/residue: 0.1742
  time to fit residues: 72.9960
Evaluate side-chains
  244 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 11 optimal weight:    9.9990
   chunk 39 optimal weight:   10.0000
   chunk 51 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 91 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   overall best weight:    1.3186

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.101267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.081919 restraints weight = 32106.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.084317 restraints weight = 18616.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.085938 restraints weight = 12662.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9077  Z= 0.229
  Angle     :  0.766  11.044  12407  Z= 0.361
  Chirality :  0.045   0.233   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  6.013  64.521   1248
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.46 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  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:  0.34 (0.26), residues: 1118
  helix:  1.14 (0.20), residues: 687
  sheet: -1.45 (0.71), residues: 48
  loop : -1.18 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP C  66 
 HIS   0.011   0.001   HIS F  17 
 PHE   0.028   0.002   PHE F  15 
 TYR   0.017   0.002   TYR C  58 
 ARG   0.014   0.001   ARG F  68 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2825.05 seconds
wall clock time: 51 minutes 33.89 seconds (3093.89 seconds total)