Starting phenix.real_space_refine
on Thu Jul  2 15:49:22 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7vfp_31957/07_2026/7vfp_31957.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vfp_31957/07_2026/7vfp_31957.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7vfp_31957/07_2026/7vfp_31957.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7vfp_31957/07_2026/7vfp_31957.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vfp_31957/07_2026/7vfp_31957.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vfp_31957/07_2026/7vfp_31957.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vfp_31957/07_2026/7vfp_31957.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vfp_31957/07_2026/7vfp_31957.map"
  }
  resolution = 4.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     P       3      5.49       5
     Mg      1      5.21       5
     S      46      5.16       5
     C    5789      2.51       5
     N    1513      2.21       5
     O    1504      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8857
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1586
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 6, 'TRANS': 195}
    Chain: "B"
      Number of atoms: 1663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1663
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 16, 'TRANS': 203}
    Chain: "C"
      Number of atoms: 1848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1848
          Classifications: {'peptide': 231}
          Link IDs: {'PTRANS': 11, 'TRANS': 219}
    Chain: "D"
      Number of atoms: 434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 434
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 2, 'TRANS': 52}
    Chain: "E"
      Number of atoms: 1586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1586
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 6, 'TRANS': 195}
    Chain: "F"
      Number of atoms: 1663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1663
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 16, 'TRANS': 203}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 34
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2, 'water': 2}
          Link IDs: {None: 3}
  Time building chain proxies: 1.59, per 1000 atoms: 0.18
  Number of scatterers: 8857
  At special positions: 0
  Unit cell: (104.832, 98.176, 113.152, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Fe      1     26.01
     S      46     16.00
     P       3     15.00
     Mg      1     11.99
     O    1504      8.00
     N    1513      7.00
     C    5789      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 303.7 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 6 sheets defined
      68.1% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 49
      removed outlier: 3.914A  pdb=" N   THR A  42 " --> pdb=" O   ALA A  38 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU A  44 " --> pdb=" O   LYS A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 69
    Processing helix  chain 'A' and resid 90 through 99
      removed outlier: 3.688A  pdb=" N   PHE A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   TYR A  98 " --> pdb=" O   ASN A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 114
    Processing helix  chain 'A' and resid 123 through 127
    Processing helix  chain 'A' and resid 130 through 138
    Processing helix  chain 'A' and resid 139 through 142
    Processing helix  chain 'A' and resid 158 through 176
      removed outlier: 3.503A  pdb=" N   GLN A 171 " --> pdb=" O   GLN A 167 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   HIS A 172 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLN A 175 " --> pdb=" O   GLN A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 194
    Processing helix  chain 'B' and resid 2 through 15
      removed outlier: 3.611A  pdb=" N   ALA B  14 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   PHE B  15 " --> pdb=" O   LEU B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 21
      No H-bonds generated for 'chain 'B' and resid 19 through 21'
    Processing helix  chain 'B' and resid 22 through 39
      removed outlier: 4.170A  pdb=" N   PHE B  35 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      Proline residue:  B  36  - end of helix
    Processing helix  chain 'B' and resid 42 through 49
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.629A  pdb=" N   GLU B  67 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ARG B  68 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE B  70 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   ASP B  72 " --> pdb=" O   ARG B  68 " (cutoff:3.500A)
      removed outlier: 5.410A  pdb=" N   ASP B  73 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLN B  75 " --> pdb=" O   ARG B  71 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASP B  76 " --> pdb=" O   ASP B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 119
      removed outlier: 3.534A  pdb=" N   VAL B  92 " --> pdb=" O   PRO B  88 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   LEU B 106 " --> pdb=" O   MET B 102 " (cutoff:3.500A)
      Proline residue:  B 107  - end of helix
      Proline residue:  B 113  - end of helix
      removed outlier: 3.580A  pdb=" N   MET B 117 " --> pdb=" O   PRO B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 154
      Proline residue:  B 138  - end of helix
      removed outlier: 3.868A  pdb=" N   GLY B 141 " --> pdb=" O   THR B 137 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   PHE B 142 " --> pdb=" O   PRO B 138 " (cutoff:3.500A)
      Proline residue:  B 146  - end of helix
      removed outlier: 3.517A  pdb=" N   LEU B 150 " --> pdb=" O   PRO B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 165
    Processing helix  chain 'B' and resid 166 through 168
      No H-bonds generated for 'chain 'B' and resid 166 through 168'
    Processing helix  chain 'B' and resid 169 through 185
    Processing helix  chain 'B' and resid 189 through 220
      removed outlier: 4.021A  pdb=" N   THR B 205 " --> pdb=" O   ALA B 201 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU B 206 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      Proline residue:  B 208  - end of helix
      removed outlier: 3.841A  pdb=" N   GLN B 220 " --> pdb=" O   ARG B 216 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 20
    Processing helix  chain 'C' and resid 21 through 40
    Processing helix  chain 'C' and resid 50 through 55
      removed outlier: 3.821A  pdb=" N   SER C  53 " --> pdb=" O   GLN C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 84
      Proline residue:  C  62  - end of helix
      removed outlier: 3.588A  pdb=" N   VAL C  83 " --> pdb=" O   PHE C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 115
      removed outlier: 3.504A  pdb=" N   ASN C  90 " --> pdb=" O   MET C  86 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   VAL C  93 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   ALA C  94 " --> pdb=" O   ASN C  90 " (cutoff:3.500A)
      Proline residue:  C  98  - end of helix
    Processing helix  chain 'C' and resid 115 through 120
    Processing helix  chain 'C' and resid 126 through 149
      removed outlier: 3.712A  pdb=" N   PHE C 149 " --> pdb=" O   LEU C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 157 through 185
      Proline residue:  C 171  - end of helix
      removed outlier: 3.591A  pdb=" N   HIS C 184 " --> pdb=" O   TRP C 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 198
    Processing helix  chain 'C' and resid 199 through 229
    Processing helix  chain 'C' and resid 230 through 231
      No H-bonds generated for 'chain 'C' and resid 230 through 231'
    Processing helix  chain 'C' and resid 232 through 236
    Processing helix  chain 'D' and resid 17 through 54
      Proline residue:  D  31  - end of helix
      removed outlier: 4.080A  pdb=" N   ALA D  51 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLN D  52 " --> pdb=" O   ARG D  48 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLN D  53 " --> pdb=" O   GLY D  49 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 39 through 48
    Processing helix  chain 'E' and resid 68 through 73
      removed outlier: 3.840A  pdb=" N   HIS E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 97
      removed outlier: 3.744A  pdb=" N   PHE E  97 " --> pdb=" O   GLU E  93 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 106 through 115
      removed outlier: 3.942A  pdb=" N   ALA E 110 " --> pdb=" O   GLN E 106 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 123 through 127
    Processing helix  chain 'E' and resid 128 through 138
      removed outlier: 3.919A  pdb=" N   ALA E 136 " --> pdb=" O   GLN E 132 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 139 through 142
    Processing helix  chain 'E' and resid 158 through 171
    Processing helix  chain 'E' and resid 172 through 176
      removed outlier: 3.564A  pdb=" N   GLN E 175 " --> pdb=" O   HIS E 172 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 194
      removed outlier: 3.582A  pdb=" N   ILE E 194 " --> pdb=" O   GLU E 191 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 17
    Processing helix  chain 'F' and resid 21 through 39
      removed outlier: 3.914A  pdb=" N   LEU F  25 " --> pdb=" O   ILE F  21 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   PHE F  35 " --> pdb=" O   VAL F  31 " (cutoff:3.500A)
      Proline residue:  F  36  - end of helix
    Processing helix  chain 'F' and resid 42 through 67
      removed outlier: 3.758A  pdb=" N   LEU F  46 " --> pdb=" O   GLU F  42 " (cutoff:3.500A)
      Proline residue:  F  51  - end of helix
    Processing helix  chain 'F' and resid 88 through 120
      removed outlier: 4.148A  pdb=" N   LEU F 106 " --> pdb=" O   MET F 102 " (cutoff:3.500A)
      Proline residue:  F 107  - end of helix
      Proline residue:  F 113  - end of helix
    Processing helix  chain 'F' and resid 122 through 152
      Proline residue:  F 138  - end of helix
      Proline residue:  F 146  - end of helix
    Processing helix  chain 'F' and resid 158 through 165
      removed outlier: 3.610A  pdb=" N   SER F 162 " --> pdb=" O   GLY F 158 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU F 164 " --> pdb=" O   LEU F 160 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL F 165 " --> pdb=" O   LEU F 161 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 166 through 168
      No H-bonds generated for 'chain 'F' and resid 166 through 168'
    Processing helix  chain 'F' and resid 169 through 185
      removed outlier: 3.665A  pdb=" N   MET F 185 " --> pdb=" O   ASP F 181 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 189 through 220
      removed outlier: 3.772A  pdb=" N   THR F 205 " --> pdb=" O   ALA F 201 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LEU F 206 " --> pdb=" O   GLY F 202 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER F 207 " --> pdb=" O   THR F 203 " (cutoff:3.500A)
      Proline residue:  F 208  - end of helix
      removed outlier: 3.774A  pdb=" N   GLN F 220 " --> pdb=" O   ARG F 216 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8
      removed outlier: 6.026A  pdb=" N   ALA A   4 " --> pdb=" O   LEU A  59 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   LEU A  59 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   GLU A   6 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 5.438A  pdb=" N   GLU A  57 " --> pdb=" O   GLU A   6 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11
    Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79
      removed outlier: 5.915A  pdb=" N   ILE A  79 " --> pdb=" O   ASP A 151 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU A 150 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 14 through 20
      removed outlier: 6.246A  pdb=" N   LEU E  16 " --> pdb=" O   ARG E  11 " (cutoff:3.500A)
      removed outlier: 8.842A  pdb=" N   ARG E  11 " --> pdb=" O   LEU E  16 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   SER E  18 " --> pdb=" O   CYS E   9 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   CYS E   9 " --> pdb=" O   SER E  18 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 14 through 20
      removed outlier: 6.246A  pdb=" N   LEU E  16 " --> pdb=" O   ARG E  11 " (cutoff:3.500A)
      removed outlier: 8.842A  pdb=" N   ARG E  11 " --> pdb=" O   LEU E  16 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   SER E  18 " --> pdb=" O   CYS E   9 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   CYS E   9 " --> pdb=" O   SER E  18 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   LEU E   7 " --> pdb=" O   ALA E  55 " (cutoff:3.500A)
      removed outlier: 7.319A  pdb=" N   ALA E  55 " --> pdb=" O   LEU E   7 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 77 through 79
      removed outlier: 6.121A  pdb=" N   LEU E  77 " --> pdb=" O   ILE E 149 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   ASP E 151 " --> pdb=" O   LEU E  77 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ILE E  79 " --> pdb=" O   ASP E 151 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   VAL E  30 " --> pdb=" O   LEU E 181 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   TRP E  29 " --> pdb=" O   ARG E 195 " (cutoff:3.500A)
      removed outlier: 8.328A  pdb=" N   ILE E 197 " --> pdb=" O   TRP E  29 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   GLN E  31 " --> pdb=" O   ILE E 197 " (cutoff:3.500A)

    502 hydrogen bonds defined for protein.
    1428 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.17

  Time building geometry restraints manager: 1.08 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: 4755
       17.41 -    34.81: 436
       34.81 -    52.22: 74
       52.22 -    69.63: 8
       69.63 -    87.03: 8
  Dihedral angle restraints: 5281
    sinusoidal: 2057
      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 5278 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:             2.760
  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:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.900
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   9077  Z= 0.220
  Angle     :  0.841  20.325  12407  Z= 0.481
  Chirality :  0.045   0.290   1458
  Planarity :  0.005   0.052   1526
  Dihedral  : 13.738  87.031   3197
  Min Nonbonded Distance : 1.933

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

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.25), residues: 1118
  helix:  0.89 (0.21), residues: 642
  sheet: -2.00 (0.64), residues: 49
  loop : -0.97 (0.30), residues: 427

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



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00392 /  0.22 ( 9077)
  covalent geometry    : angle       0.84070 /  0.48 (12407)
  hydrogen bonds       : bond        0.20737 / 13.85 (  500)
  hydrogen bonds       : angle       6.78865 /  4.77 ( 1428)

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

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 292
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8003 (ppp) cc_final: 0.7467 (ppp)
REVERT: A   99 HIS cc_start: 0.8130 (t-90) cc_final: 0.7803 (t-90)
REVERT: A  181 LEU cc_start: 0.8559 (mt) cc_final: 0.8264 (mt)
REVERT: B    5 ARG cc_start: 0.8925 (mtm180) cc_final: 0.8494 (mtp180)
REVERT: B   44 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8742 (tm-30)
REVERT: B   73 ASP cc_start: 0.8203 (m-30) cc_final: 0.7827 (m-30)
REVERT: B   83 MET cc_start: 0.7590 (tmm) cc_final: 0.6997 (tmm)
REVERT: B  133 LEU cc_start: 0.9593 (tp) cc_final: 0.9374 (tp)
REVERT: B  175 PHE cc_start: 0.8992 (m-80) cc_final: 0.8719 (m-80)
REVERT: C   88 MET cc_start: 0.8655 (mmp) cc_final: 0.8386 (mmt)
REVERT: C   90 ASN cc_start: 0.8851 (m-40) cc_final: 0.8540 (m-40)
REVERT: C  165 ILE cc_start: 0.9607 (mm) cc_final: 0.9353 (mm)
REVERT: C  169 ASN cc_start: 0.9103 (m110) cc_final: 0.8759 (m-40)
REVERT: C  215 THR cc_start: 0.9396 (p) cc_final: 0.8761 (p)
REVERT: C  219 MET cc_start: 0.8719 (mpp) cc_final: 0.8486 (mpp)
REVERT: C  228 MET cc_start: 0.8729 (ttm) cc_final: 0.8239 (tmm)
REVERT: E  113 GLN cc_start: 0.8485 (tp40) cc_final: 0.8197 (tp40)
REVERT: F   15 PHE cc_start: 0.7944 (m-80) cc_final: 0.7684 (m-80)
REVERT: F   68 ARG cc_start: 0.8488 (ppt170) cc_final: 0.8172 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 292
  average time/residue: 0.0633
  time to fit residues: 27.0868
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  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    0.3980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  94 ASN
E  96 HIS
E 160 ASN
E 171 GLN
E 188 ASN
F 100 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.099961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.080964 restraints weight = 30869.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.083313 restraints weight = 17832.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.084797 restraints weight = 11946.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.085978 restraints weight = 9096.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.086868 restraints weight = 7322.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9077  Z= 0.153
  Angle     :  0.717   7.437  12407  Z= 0.356
  Chirality :  0.044   0.199   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  5.682  72.231   1217
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.83 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  5.23 %
    Favored  : 94.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.25), residues: 1118
  helix:  0.79 (0.20), residues: 694
  sheet: -1.45 (0.69), residues: 49
  loop : -0.93 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  48 
 TYR   0.015   0.001   TYR D  17 
 PHE   0.023   0.002   PHE F  15 
 TRP   0.021   0.002   TRP C 119 
 HIS   0.006   0.001   HIS B 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.15 ( 9077)
  covalent geometry    : angle       0.71702 /  0.36 (12407)
  hydrogen bonds       : bond        0.05076 /  3.46 (  500)
  hydrogen bonds       : angle       5.09912 /  3.63 ( 1428)

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

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 286
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7922 (ppp) cc_final: 0.7622 (ppp)
REVERT: A   47 LEU cc_start: 0.8682 (mt) cc_final: 0.8481 (mt)
REVERT: A   99 HIS cc_start: 0.8154 (t-90) cc_final: 0.7901 (t-90)
REVERT: A  181 LEU cc_start: 0.8459 (mt) cc_final: 0.8204 (mt)
REVERT: B    5 ARG cc_start: 0.8915 (mtm180) cc_final: 0.8431 (mtp180)
REVERT: B   29 LEU cc_start: 0.9501 (tp) cc_final: 0.9299 (tp)
REVERT: B   44 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8794 (tm-30)
REVERT: B   73 ASP cc_start: 0.7939 (m-30) cc_final: 0.7634 (m-30)
REVERT: B  133 LEU cc_start: 0.9654 (tp) cc_final: 0.9422 (tp)
REVERT: C   86 MET cc_start: 0.8196 (mmm) cc_final: 0.7931 (mmm)
REVERT: C   90 ASN cc_start: 0.9012 (m-40) cc_final: 0.8638 (m-40)
REVERT: C  118 MET cc_start: 0.8248 (ptp) cc_final: 0.7900 (ptp)
REVERT: C  169 ASN cc_start: 0.9138 (m110) cc_final: 0.8904 (m-40)
REVERT: C  228 MET cc_start: 0.8795 (ttm) cc_final: 0.8215 (tmm)
REVERT: C  230 LYS cc_start: 0.8532 (pptt) cc_final: 0.8031 (pptt)
REVERT: D   20 PHE cc_start: 0.8937 (m-80) cc_final: 0.8671 (m-10)
REVERT: D   27 MET cc_start: 0.9053 (tpp) cc_final: 0.8706 (tpp)
REVERT: E    1 MET cc_start: 0.8003 (pmm) cc_final: 0.7738 (pmm)
REVERT: F   68 ARG cc_start: 0.8603 (ppt170) cc_final: 0.8257 (ttp80)
REVERT: F   71 ARG cc_start: 0.7666 (ttt180) cc_final: 0.7034 (ttm-80)
REVERT: F   73 ASP cc_start: 0.8812 (m-30) cc_final: 0.8418 (m-30)
REVERT: F  101 TRP cc_start: 0.8743 (t60) cc_final: 0.8458 (t60)
REVERT: F  164 LEU cc_start: 0.9356 (mt) cc_final: 0.9107 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 287
  average time/residue: 0.0738
  time to fit residues: 30.6484
Evaluate side-chains
  241 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 7 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   chunk 64 optimal weight:    3.9990
   chunk 89 optimal weight:    0.4980
   chunk 81 optimal weight:    8.9990
   chunk 83 optimal weight:    0.0980
   chunk 53 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0050
   chunk 43 optimal weight:    0.0370
   overall best weight:    0.2472

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  94 ASN
E 171 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.102548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.082960 restraints weight = 31042.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.085361 restraints weight = 18019.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.087077 restraints weight = 12279.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.088277 restraints weight = 9192.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.089079 restraints weight = 7456.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9077  Z= 0.134
  Angle     :  0.696   6.632  12407  Z= 0.339
  Chirality :  0.044   0.199   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  5.515  68.257   1217
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.56 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.91 %
    Favored  : 94.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.25), residues: 1118
  helix:  0.79 (0.20), residues: 694
  sheet: -1.34 (0.71), residues: 48
  loop : -1.03 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  48 
 TYR   0.012   0.001   TYR D  17 
 PHE   0.028   0.002   PHE F  15 
 TRP   0.019   0.002   TRP B  55 
 HIS   0.004   0.001   HIS B 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 9077)
  covalent geometry    : angle       0.69635 /  0.34 (12407)
  hydrogen bonds       : bond        0.04339 /  2.91 (  500)
  hydrogen bonds       : angle       4.84272 /  3.44 ( 1428)

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

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 299
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7813 (ppp) cc_final: 0.7510 (ppp)
REVERT: A   47 LEU cc_start: 0.8686 (mt) cc_final: 0.8477 (mt)
REVERT: A   76 LEU cc_start: 0.9097 (tt) cc_final: 0.8567 (tt)
REVERT: A   85 ILE cc_start: 0.5863 (pt) cc_final: 0.5556 (pt)
REVERT: A   99 HIS cc_start: 0.8182 (t-90) cc_final: 0.7940 (t-170)
REVERT: A  109 GLU cc_start: 0.9554 (tt0) cc_final: 0.9306 (tm-30)
REVERT: B    5 ARG cc_start: 0.8898 (mtm180) cc_final: 0.8452 (mtp180)
REVERT: B   44 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8780 (tm-30)
REVERT: B  122 ASP cc_start: 0.8624 (p0) cc_final: 0.8389 (p0)
REVERT: B  133 LEU cc_start: 0.9634 (tp) cc_final: 0.9369 (tp)
REVERT: C   90 ASN cc_start: 0.9025 (m-40) cc_final: 0.8628 (m-40)
REVERT: C  118 MET cc_start: 0.8503 (ptp) cc_final: 0.6188 (ptp)
REVERT: C  151 ASP cc_start: 0.8309 (t0) cc_final: 0.8026 (t0)
REVERT: C  153 ARG cc_start: 0.7703 (ttp-170) cc_final: 0.7319 (ptt-90)
REVERT: C  169 ASN cc_start: 0.9157 (m110) cc_final: 0.8761 (m-40)
REVERT: C  228 MET cc_start: 0.8787 (ttm) cc_final: 0.8172 (tmm)
REVERT: D   20 PHE cc_start: 0.8847 (m-80) cc_final: 0.8593 (m-10)
REVERT: D   27 MET cc_start: 0.9165 (tpp) cc_final: 0.8691 (tpp)
REVERT: E    6 GLU cc_start: 0.8067 (pp20) cc_final: 0.7779 (pp20)
REVERT: E   24 LEU cc_start: 0.8879 (mt) cc_final: 0.8544 (mp)
REVERT: E   93 GLU cc_start: 0.8717 (pt0) cc_final: 0.8505 (mp0)
REVERT: F   15 PHE cc_start: 0.8001 (m-80) cc_final: 0.7704 (m-80)
REVERT: F   68 ARG cc_start: 0.8662 (ppt170) cc_final: 0.8294 (ttp80)
REVERT: F   71 ARG cc_start: 0.7459 (ttt180) cc_final: 0.6750 (ttm-80)
REVERT: F   73 ASP cc_start: 0.8672 (m-30) cc_final: 0.8303 (m-30)
REVERT: F  104 THR cc_start: 0.8949 (p) cc_final: 0.8688 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 300
  average time/residue: 0.0637
  time to fit residues: 28.1754
Evaluate side-chains
  238 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 95 optimal weight:    0.8980
   chunk 91 optimal weight:    7.9990
   chunk 88 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0670
   chunk 21 optimal weight:    0.4980
   chunk 57 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.5518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  50 GLN
E 171 GLN
F  17 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.102174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.082342 restraints weight = 31685.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.084796 restraints weight = 18369.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.086471 restraints weight = 12438.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.087659 restraints weight = 9331.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.088425 restraints weight = 7593.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9077  Z= 0.130
  Angle     :  0.695   6.899  12407  Z= 0.336
  Chirality :  0.043   0.206   1458
  Planarity :  0.005   0.044   1526
  Dihedral  :  5.426  66.684   1217
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.20 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.47 %
    Favored  : 95.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.25), residues: 1118
  helix:  0.92 (0.20), residues: 694
  sheet: -1.53 (0.69), residues: 48
  loop : -1.01 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  48 
 TYR   0.013   0.001   TYR D  17 
 PHE   0.019   0.001   PHE F  15 
 TRP   0.018   0.001   TRP C  66 
 HIS   0.008   0.001   HIS F  17 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.13 ( 9077)
  covalent geometry    : angle       0.69453 /  0.34 (12407)
  hydrogen bonds       : bond        0.03855 /  2.60 (  500)
  hydrogen bonds       : angle       4.75097 /  3.36 ( 1428)

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

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 298
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7811 (ppp) cc_final: 0.7524 (ppp)
REVERT: A   35 SER cc_start: 0.7624 (m) cc_final: 0.7393 (t)
REVERT: A   47 LEU cc_start: 0.8655 (mt) cc_final: 0.8447 (mt)
REVERT: A   85 ILE cc_start: 0.5912 (pt) cc_final: 0.5581 (pt)
REVERT: A   99 HIS cc_start: 0.8212 (t-90) cc_final: 0.8000 (t-170)
REVERT: A  109 GLU cc_start: 0.9542 (tt0) cc_final: 0.9307 (tm-30)
REVERT: A  141 TRP cc_start: 0.7530 (m100) cc_final: 0.7266 (m100)
REVERT: B    5 ARG cc_start: 0.8922 (mtm180) cc_final: 0.8390 (mtp180)
REVERT: B   44 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8778 (tm-30)
REVERT: B  122 ASP cc_start: 0.8594 (p0) cc_final: 0.8394 (p0)
REVERT: B  133 LEU cc_start: 0.9629 (tp) cc_final: 0.9395 (tp)
REVERT: B  175 PHE cc_start: 0.9241 (m-10) cc_final: 0.8894 (m-80)
REVERT: C   90 ASN cc_start: 0.8932 (m-40) cc_final: 0.8412 (m-40)
REVERT: C   91 LEU cc_start: 0.9230 (tp) cc_final: 0.9026 (tp)
REVERT: C  118 MET cc_start: 0.8003 (ptp) cc_final: 0.6740 (ptp)
REVERT: C  119 TRP cc_start: 0.7739 (m100) cc_final: 0.7272 (m100)
REVERT: C  153 ARG cc_start: 0.7716 (ttp-170) cc_final: 0.7326 (ptt-90)
REVERT: C  169 ASN cc_start: 0.9140 (m110) cc_final: 0.8742 (m110)
REVERT: C  228 MET cc_start: 0.8745 (ttm) cc_final: 0.8233 (tmm)
REVERT: D   20 PHE cc_start: 0.8894 (m-80) cc_final: 0.8636 (m-10)
REVERT: D   27 MET cc_start: 0.9205 (tpp) cc_final: 0.8673 (tpp)
REVERT: E    6 GLU cc_start: 0.8075 (pp20) cc_final: 0.7823 (pp20)
REVERT: E   93 GLU cc_start: 0.8812 (pt0) cc_final: 0.8445 (mp0)
REVERT: F   15 PHE cc_start: 0.7961 (m-80) cc_final: 0.7667 (m-80)
REVERT: F   68 ARG cc_start: 0.8685 (ppt170) cc_final: 0.8330 (ttp80)
REVERT: F   73 ASP cc_start: 0.8598 (m-30) cc_final: 0.8239 (m-30)
REVERT: F  104 THR cc_start: 0.8955 (p) cc_final: 0.8708 (t)
REVERT: F  111 LEU cc_start: 0.9234 (tp) cc_final: 0.8966 (tt)
REVERT: F  143 LEU cc_start: 0.9405 (tp) cc_final: 0.9156 (tp)
REVERT: F  168 LEU cc_start: 0.9444 (mt) cc_final: 0.9122 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 299
  average time/residue: 0.0721
  time to fit residues: 31.6276
Evaluate side-chains
  247 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 27 optimal weight:    0.2980
   chunk 26 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0010
   chunk 32 optimal weight:    7.9990
   chunk 52 optimal weight:    0.6980
   chunk 110 optimal weight:    0.0970
   chunk 22 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 2 optimal weight:    7.9990
   overall best weight:    1.0186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3828 r_free = 0.3828 target = 0.101835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.082152 restraints weight = 31491.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.084543 restraints weight = 18437.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.086200 restraints weight = 12534.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.087362 restraints weight = 9385.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.087953 restraints weight = 7643.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9077  Z= 0.137
  Angle     :  0.697   8.145  12407  Z= 0.336
  Chirality :  0.044   0.230   1458
  Planarity :  0.005   0.044   1526
  Dihedral  :  5.366  65.898   1217
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.92 %
    Favored  : 94.99 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.25), residues: 1118
  helix:  0.99 (0.20), residues: 694
  sheet: -1.61 (0.69), residues: 48
  loop : -1.07 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  48 
 TYR   0.015   0.001   TYR C  58 
 PHE   0.017   0.001   PHE B  15 
 TRP   0.029   0.001   TRP C  66 
 HIS   0.006   0.001   HIS F  17 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.14 ( 9077)
  covalent geometry    : angle       0.69656 /  0.34 (12407)
  hydrogen bonds       : bond        0.03811 /  2.58 (  500)
  hydrogen bonds       : angle       4.70198 /  3.32 ( 1428)

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

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 291
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7819 (ppp) cc_final: 0.7499 (ppp)
REVERT: A   35 SER cc_start: 0.7585 (m) cc_final: 0.7382 (t)
REVERT: A   47 LEU cc_start: 0.8648 (mt) cc_final: 0.8434 (mt)
REVERT: A   85 ILE cc_start: 0.5916 (pt) cc_final: 0.5594 (pt)
REVERT: A   99 HIS cc_start: 0.8193 (t-90) cc_final: 0.7965 (t-170)
REVERT: A  109 GLU cc_start: 0.9552 (tt0) cc_final: 0.9298 (tm-30)
REVERT: B    5 ARG cc_start: 0.8884 (mtm180) cc_final: 0.8366 (mtp180)
REVERT: B   44 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8754 (tm-30)
REVERT: B   83 MET cc_start: 0.8144 (tmm) cc_final: 0.7894 (tmm)
REVERT: B  133 LEU cc_start: 0.9621 (tp) cc_final: 0.9375 (tp)
REVERT: B  175 PHE cc_start: 0.9261 (m-10) cc_final: 0.8934 (m-80)
REVERT: C   90 ASN cc_start: 0.8910 (m-40) cc_final: 0.8369 (m-40)
REVERT: C   91 LEU cc_start: 0.9287 (tp) cc_final: 0.8998 (tp)
REVERT: C  118 MET cc_start: 0.8056 (ptp) cc_final: 0.6647 (ptp)
REVERT: C  119 TRP cc_start: 0.7786 (m100) cc_final: 0.7268 (m100)
REVERT: C  153 ARG cc_start: 0.7588 (ttp-170) cc_final: 0.7311 (tmm-80)
REVERT: C  169 ASN cc_start: 0.9178 (m110) cc_final: 0.8766 (m110)
REVERT: C  228 MET cc_start: 0.8752 (ttm) cc_final: 0.8240 (tmm)
REVERT: D   20 PHE cc_start: 0.8885 (m-80) cc_final: 0.8623 (m-10)
REVERT: D   27 MET cc_start: 0.9229 (tpp) cc_final: 0.8813 (tpp)
REVERT: E    1 MET cc_start: 0.7983 (pmm) cc_final: 0.7708 (pmm)
REVERT: E    6 GLU cc_start: 0.8042 (pp20) cc_final: 0.7777 (pp20)
REVERT: E   93 GLU cc_start: 0.8861 (pt0) cc_final: 0.8463 (mp0)
REVERT: F   15 PHE cc_start: 0.7907 (m-80) cc_final: 0.7675 (m-80)
REVERT: F   68 ARG cc_start: 0.8699 (ppt170) cc_final: 0.8334 (ttp80)
REVERT: F   73 ASP cc_start: 0.8639 (m-30) cc_final: 0.8203 (m-30)
REVERT: F  104 THR cc_start: 0.8966 (p) cc_final: 0.8727 (t)
REVERT: F  111 LEU cc_start: 0.9285 (tp) cc_final: 0.8987 (tt)
REVERT: F  143 LEU cc_start: 0.9415 (tp) cc_final: 0.9182 (tp)
REVERT: F  168 LEU cc_start: 0.9472 (mt) cc_final: 0.9124 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 291
  average time/residue: 0.0687
  time to fit residues: 29.6595
Evaluate side-chains
  241 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 66 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0570
   chunk 88 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.9504

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  94 ASN
** E  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.101978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.082394 restraints weight = 31171.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.084823 restraints weight = 18195.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.086406 restraints weight = 12328.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.087585 restraints weight = 9295.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.088337 restraints weight = 7570.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2493

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= 0.135
  Angle     :  0.713   8.206  12407  Z= 0.341
  Chirality :  0.043   0.208   1458
  Planarity :  0.005   0.044   1526
  Dihedral  :  5.333  65.984   1217
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.10 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.26), residues: 1118
  helix:  1.05 (0.20), residues: 695
  sheet: -1.61 (0.69), residues: 48
  loop : -0.85 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG D  48 
 TYR   0.013   0.001   TYR C  58 
 PHE   0.016   0.001   PHE B  15 
 TRP   0.029   0.001   TRP C  66 
 HIS   0.004   0.001   HIS B 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.13 ( 9077)
  covalent geometry    : angle       0.71315 /  0.34 (12407)
  hydrogen bonds       : bond        0.03696 /  2.49 (  500)
  hydrogen bonds       : angle       4.63579 /  3.27 ( 1428)

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

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 288
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7780 (ppp) cc_final: 0.7359 (ppp)
REVERT: A   85 ILE cc_start: 0.5999 (pt) cc_final: 0.5642 (pt)
REVERT: A   99 HIS cc_start: 0.8194 (t-90) cc_final: 0.7991 (t-170)
REVERT: A  109 GLU cc_start: 0.9559 (tt0) cc_final: 0.9333 (tm-30)
REVERT: B    5 ARG cc_start: 0.8831 (mtm180) cc_final: 0.8308 (mtp180)
REVERT: B   44 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8693 (tm-30)
REVERT: B  122 ASP cc_start: 0.8577 (p0) cc_final: 0.8353 (p0)
REVERT: B  133 LEU cc_start: 0.9591 (tp) cc_final: 0.9361 (tp)
REVERT: B  175 PHE cc_start: 0.9248 (m-10) cc_final: 0.8899 (m-80)
REVERT: C   90 ASN cc_start: 0.8875 (m-40) cc_final: 0.8315 (m-40)
REVERT: C   91 LEU cc_start: 0.9282 (tp) cc_final: 0.8976 (tp)
REVERT: C  118 MET cc_start: 0.7986 (ptp) cc_final: 0.6519 (ptp)
REVERT: C  119 TRP cc_start: 0.7827 (m100) cc_final: 0.7275 (m100)
REVERT: C  153 ARG cc_start: 0.7578 (ttp-170) cc_final: 0.7378 (ptt-90)
REVERT: C  169 ASN cc_start: 0.9170 (m110) cc_final: 0.8761 (m110)
REVERT: C  228 MET cc_start: 0.8732 (ttm) cc_final: 0.8232 (tmm)
REVERT: D   20 PHE cc_start: 0.8862 (m-80) cc_final: 0.8640 (m-10)
REVERT: D   27 MET cc_start: 0.9235 (tpp) cc_final: 0.8702 (tpp)
REVERT: E    1 MET cc_start: 0.8024 (pmm) cc_final: 0.7772 (pmm)
REVERT: E    6 GLU cc_start: 0.8051 (pp20) cc_final: 0.7749 (pp20)
REVERT: E    7 LEU cc_start: 0.9189 (tp) cc_final: 0.8977 (tp)
REVERT: F   11 LEU cc_start: 0.9201 (mt) cc_final: 0.8782 (mm)
REVERT: F   73 ASP cc_start: 0.8576 (m-30) cc_final: 0.8135 (m-30)
REVERT: F  111 LEU cc_start: 0.9237 (tp) cc_final: 0.8993 (tt)
REVERT: F  143 LEU cc_start: 0.9393 (tp) cc_final: 0.9163 (tp)
REVERT: F  168 LEU cc_start: 0.9461 (mt) cc_final: 0.9101 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 288
  average time/residue: 0.0622
  time to fit residues: 26.7643
Evaluate side-chains
  246 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 108 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 109 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  94 ASN
** E  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.099607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.080544 restraints weight = 31142.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.082883 restraints weight = 17858.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.084439 restraints weight = 11958.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.085579 restraints weight = 8998.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.086274 restraints weight = 7291.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2582

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= 0.175
  Angle     :  0.753   8.313  12407  Z= 0.365
  Chirality :  0.045   0.236   1458
  Planarity :  0.005   0.047   1526
  Dihedral  :  5.389  64.213   1217
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.74 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.26), residues: 1118
  helix:  1.03 (0.20), residues: 701
  sheet: -1.64 (0.70), residues: 48
  loop : -1.01 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  48 
 TYR   0.014   0.002   TYR C  58 
 PHE   0.032   0.002   PHE F  15 
 TRP   0.033   0.002   TRP C  66 
 HIS   0.004   0.001   HIS B 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00408 /  0.18 ( 9077)
  covalent geometry    : angle       0.75288 /  0.37 (12407)
  hydrogen bonds       : bond        0.03806 /  2.58 (  500)
  hydrogen bonds       : angle       4.75103 /  3.35 ( 1428)

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

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7827 (ppp) cc_final: 0.7519 (ppp)
REVERT: A   85 ILE cc_start: 0.6065 (pt) cc_final: 0.5721 (pt)
REVERT: A  109 GLU cc_start: 0.9560 (tt0) cc_final: 0.9326 (tm-30)
REVERT: B    5 ARG cc_start: 0.8814 (mtm180) cc_final: 0.8126 (mtp180)
REVERT: B   10 GLU cc_start: 0.8965 (mp0) cc_final: 0.8688 (mp0)
REVERT: B   44 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8693 (tm-30)
REVERT: B   73 ASP cc_start: 0.8063 (m-30) cc_final: 0.7830 (m-30)
REVERT: B  175 PHE cc_start: 0.9247 (m-10) cc_final: 0.8916 (m-80)
REVERT: C   86 MET cc_start: 0.8165 (mmm) cc_final: 0.7962 (mmm)
REVERT: C   90 ASN cc_start: 0.8962 (m-40) cc_final: 0.8560 (m-40)
REVERT: C   91 LEU cc_start: 0.9306 (tp) cc_final: 0.9024 (tp)
REVERT: C  118 MET cc_start: 0.7991 (ptp) cc_final: 0.6425 (ptp)
REVERT: C  119 TRP cc_start: 0.7946 (m100) cc_final: 0.7313 (m100)
REVERT: C  153 ARG cc_start: 0.7706 (ttp-170) cc_final: 0.7441 (ptt-90)
REVERT: C  169 ASN cc_start: 0.9187 (m110) cc_final: 0.8720 (m110)
REVERT: C  228 MET cc_start: 0.8709 (ttm) cc_final: 0.8191 (tmm)
REVERT: D   27 MET cc_start: 0.9216 (tpp) cc_final: 0.8642 (tpp)
REVERT: E    1 MET cc_start: 0.8140 (pmm) cc_final: 0.7745 (pmm)
REVERT: E    6 GLU cc_start: 0.8026 (pp20) cc_final: 0.7682 (pp20)
REVERT: E    8 LEU cc_start: 0.9257 (pt) cc_final: 0.9042 (pt)
REVERT: F   11 LEU cc_start: 0.9220 (mt) cc_final: 0.8908 (mm)
REVERT: F   15 PHE cc_start: 0.7994 (m-80) cc_final: 0.7505 (m-80)
REVERT: F   73 ASP cc_start: 0.8517 (m-30) cc_final: 0.8052 (m-30)
REVERT: F  111 LEU cc_start: 0.9298 (tp) cc_final: 0.8989 (tt)
REVERT: F  143 LEU cc_start: 0.9422 (tp) cc_final: 0.9167 (tp)
REVERT: F  168 LEU cc_start: 0.9525 (mt) cc_final: 0.9138 (mt)
REVERT: F  209 PHE cc_start: 0.7306 (t80) cc_final: 0.7103 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 280
  average time/residue: 0.0724
  time to fit residues: 30.0733
Evaluate side-chains
  238 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 53 optimal weight:    0.1980
   chunk 28 optimal weight:    0.0000
   chunk 59 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 3 optimal weight:    8.9990
   chunk 54 optimal weight:    0.9990
   chunk 76 optimal weight:    7.9990
   chunk 1 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.0390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  94 ASN
** E  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.101117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.081555 restraints weight = 31348.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.083931 restraints weight = 18296.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.085528 restraints weight = 12443.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.086665 restraints weight = 9411.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.087241 restraints weight = 7705.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9077  Z= 0.140
  Angle     :  0.747   8.782  12407  Z= 0.356
  Chirality :  0.044   0.238   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  5.364  65.916   1217
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 14.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.74 %
    Favored  : 95.17 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.26), residues: 1118
  helix:  1.11 (0.20), residues: 692
  sheet: -1.67 (0.69), residues: 48
  loop : -1.11 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.000   ARG D  48 
 TYR   0.011   0.001   TYR C  58 
 PHE   0.025   0.002   PHE F  15 
 TRP   0.026   0.002   TRP C  66 
 HIS   0.009   0.001   HIS A  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.14 ( 9077)
  covalent geometry    : angle       0.74673 /  0.36 (12407)
  hydrogen bonds       : bond        0.03680 /  2.50 (  500)
  hydrogen bonds       : angle       4.67678 /  3.30 ( 1428)

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

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 291
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7841 (ppp) cc_final: 0.7538 (ppp)
REVERT: A   85 ILE cc_start: 0.5924 (pt) cc_final: 0.5568 (pt)
REVERT: A  109 GLU cc_start: 0.9566 (tt0) cc_final: 0.9331 (tm-30)
REVERT: B    5 ARG cc_start: 0.8822 (mtm180) cc_final: 0.8194 (mtp180)
REVERT: B   10 GLU cc_start: 0.8913 (mp0) cc_final: 0.8670 (mp0)
REVERT: B   44 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8650 (tm-30)
REVERT: B  122 ASP cc_start: 0.8582 (p0) cc_final: 0.8368 (p0)
REVERT: B  175 PHE cc_start: 0.9291 (m-10) cc_final: 0.8956 (m-80)
REVERT: C   90 ASN cc_start: 0.8948 (m-40) cc_final: 0.8365 (m-40)
REVERT: C   91 LEU cc_start: 0.9269 (tp) cc_final: 0.9025 (tp)
REVERT: C  118 MET cc_start: 0.8012 (ptp) cc_final: 0.6387 (ptp)
REVERT: C  119 TRP cc_start: 0.7956 (m100) cc_final: 0.7367 (m100)
REVERT: C  153 ARG cc_start: 0.7722 (ttp-170) cc_final: 0.7494 (ptt-90)
REVERT: C  169 ASN cc_start: 0.9182 (m110) cc_final: 0.8786 (m-40)
REVERT: C  228 MET cc_start: 0.8740 (ttm) cc_final: 0.8255 (tmm)
REVERT: D   27 MET cc_start: 0.9177 (tpp) cc_final: 0.8673 (tpp)
REVERT: E    1 MET cc_start: 0.8162 (pmm) cc_final: 0.7842 (pmm)
REVERT: E    6 GLU cc_start: 0.8042 (pp20) cc_final: 0.7802 (pp20)
REVERT: F   11 LEU cc_start: 0.9238 (mt) cc_final: 0.8929 (mm)
REVERT: F   15 PHE cc_start: 0.7955 (m-80) cc_final: 0.7587 (m-80)
REVERT: F   73 ASP cc_start: 0.8577 (m-30) cc_final: 0.8125 (m-30)
REVERT: F  111 LEU cc_start: 0.9243 (tp) cc_final: 0.8986 (tt)
REVERT: F  143 LEU cc_start: 0.9388 (tp) cc_final: 0.9151 (tp)
REVERT: F  168 LEU cc_start: 0.9489 (mt) cc_final: 0.9116 (mt)
REVERT: F  209 PHE cc_start: 0.7254 (t80) cc_final: 0.7034 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 291
  average time/residue: 0.0812
  time to fit residues: 34.4376
Evaluate side-chains
  237 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 37 optimal weight:    0.2980
   chunk 67 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 100 optimal weight:    2.9990
   chunk 86 optimal weight:    9.9990
   chunk 76 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  94 ASN
** E  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.101297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.082375 restraints weight = 30533.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.084675 restraints weight = 17353.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.086317 restraints weight = 11740.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.087485 restraints weight = 8784.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.088243 restraints weight = 7087.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9077  Z= 0.134
  Angle     :  0.751  11.945  12407  Z= 0.355
  Chirality :  0.045   0.233   1458
  Planarity :  0.005   0.050   1526
  Dihedral  :  5.323  65.692   1217
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.74 %
    Favored  : 95.17 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.26), residues: 1118
  helix:  1.05 (0.20), residues: 689
  sheet: -1.67 (0.68), residues: 48
  loop : -1.12 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG F  68 
 TYR   0.012   0.001   TYR C  58 
 PHE   0.029   0.001   PHE C 103 
 TRP   0.029   0.002   TRP C  66 
 HIS   0.008   0.001   HIS A  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.13 ( 9077)
  covalent geometry    : angle       0.75055 /  0.36 (12407)
  hydrogen bonds       : bond        0.03621 /  2.45 (  500)
  hydrogen bonds       : angle       4.66538 /  3.29 ( 1428)

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

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7814 (ppp) cc_final: 0.7517 (ppp)
REVERT: A   85 ILE cc_start: 0.5868 (pt) cc_final: 0.5526 (pt)
REVERT: A  109 GLU cc_start: 0.9541 (tt0) cc_final: 0.9327 (tm-30)
REVERT: B    5 ARG cc_start: 0.8792 (mtm180) cc_final: 0.8143 (mtp180)
REVERT: B   10 GLU cc_start: 0.8902 (mp0) cc_final: 0.8653 (mp0)
REVERT: B   29 LEU cc_start: 0.9525 (tp) cc_final: 0.9323 (tp)
REVERT: B   44 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8637 (tm-30)
REVERT: B   68 ARG cc_start: 0.8422 (ttp80) cc_final: 0.7534 (mmm160)
REVERT: B  122 ASP cc_start: 0.8547 (p0) cc_final: 0.8343 (p0)
REVERT: B  133 LEU cc_start: 0.9587 (tp) cc_final: 0.9384 (tp)
REVERT: B  175 PHE cc_start: 0.9219 (m-10) cc_final: 0.8877 (m-80)
REVERT: C   90 ASN cc_start: 0.8973 (m-40) cc_final: 0.8525 (m-40)
REVERT: C   91 LEU cc_start: 0.9285 (tp) cc_final: 0.8993 (tp)
REVERT: C  118 MET cc_start: 0.7962 (ptp) cc_final: 0.6399 (ptp)
REVERT: C  119 TRP cc_start: 0.8023 (m100) cc_final: 0.7462 (m100)
REVERT: C  146 TRP cc_start: 0.8725 (t60) cc_final: 0.8496 (t60)
REVERT: C  153 ARG cc_start: 0.7669 (ttp-170) cc_final: 0.7429 (ptt-90)
REVERT: C  169 ASN cc_start: 0.9205 (m110) cc_final: 0.8803 (m-40)
REVERT: C  228 MET cc_start: 0.8706 (ttm) cc_final: 0.8244 (tmm)
REVERT: D   27 MET cc_start: 0.9163 (tpp) cc_final: 0.8659 (tpp)
REVERT: E    1 MET cc_start: 0.8122 (pmm) cc_final: 0.7761 (pmm)
REVERT: E    6 GLU cc_start: 0.8023 (pp20) cc_final: 0.7762 (pp20)
REVERT: E   93 GLU cc_start: 0.8703 (mp0) cc_final: 0.8471 (mm-30)
REVERT: F   11 LEU cc_start: 0.9236 (mt) cc_final: 0.8916 (mm)
REVERT: F   15 PHE cc_start: 0.7829 (m-80) cc_final: 0.7588 (m-80)
REVERT: F   73 ASP cc_start: 0.8574 (m-30) cc_final: 0.8133 (m-30)
REVERT: F  111 LEU cc_start: 0.9233 (tp) cc_final: 0.8980 (tt)
REVERT: F  143 LEU cc_start: 0.9388 (tp) cc_final: 0.9143 (tp)
REVERT: F  168 LEU cc_start: 0.9514 (mt) cc_final: 0.9156 (mt)
REVERT: F  209 PHE cc_start: 0.7157 (t80) cc_final: 0.6884 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 289
  average time/residue: 0.0761
  time to fit residues: 32.2715
Evaluate side-chains
  245 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 94 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 107 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 111 optimal weight:    0.8980
   chunk 39 optimal weight:    9.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  94 ASN
A  99 HIS
** E  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.101139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.081547 restraints weight = 31649.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.083938 restraints weight = 18302.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.085530 restraints weight = 12426.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.086712 restraints weight = 9419.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.087460 restraints weight = 7668.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9077  Z= 0.135
  Angle     :  0.755  11.363  12407  Z= 0.356
  Chirality :  0.045   0.236   1458
  Planarity :  0.005   0.047   1526
  Dihedral  :  5.273  65.378   1217
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.92 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.26), residues: 1118
  helix:  1.10 (0.20), residues: 695
  sheet: -1.55 (0.69), residues: 48
  loop : -1.05 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  48 
 TYR   0.011   0.001   TYR C  58 
 PHE   0.030   0.002   PHE B  27 
 TRP   0.029   0.002   TRP C  66 
 HIS   0.003   0.001   HIS A  73 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.14 ( 9077)
  covalent geometry    : angle       0.75463 /  0.36 (12407)
  hydrogen bonds       : bond        0.03575 /  2.42 (  500)
  hydrogen bonds       : angle       4.61903 /  3.25 ( 1428)

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

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 287
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7722 (ppp) cc_final: 0.7408 (ppp)
REVERT: A   85 ILE cc_start: 0.5940 (pt) cc_final: 0.5601 (pt)
REVERT: A   99 HIS cc_start: 0.7948 (t-90) cc_final: 0.7725 (t-90)
REVERT: A  109 GLU cc_start: 0.9536 (tt0) cc_final: 0.9325 (tm-30)
REVERT: B    5 ARG cc_start: 0.8798 (mtm180) cc_final: 0.8167 (mtp180)
REVERT: B    6 ILE cc_start: 0.9100 (mp) cc_final: 0.8661 (mp)
REVERT: B   10 GLU cc_start: 0.8922 (mp0) cc_final: 0.8613 (mp0)
REVERT: B   44 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8642 (tm-30)
REVERT: B   68 ARG cc_start: 0.8420 (ttp80) cc_final: 0.7549 (mmm160)
REVERT: B  122 ASP cc_start: 0.8583 (p0) cc_final: 0.8357 (p0)
REVERT: B  175 PHE cc_start: 0.9224 (m-10) cc_final: 0.8915 (m-80)
REVERT: C   90 ASN cc_start: 0.8964 (m-40) cc_final: 0.8517 (m-40)
REVERT: C   91 LEU cc_start: 0.9265 (tp) cc_final: 0.8993 (tp)
REVERT: C  118 MET cc_start: 0.7938 (ptp) cc_final: 0.6343 (ptp)
REVERT: C  119 TRP cc_start: 0.8044 (m100) cc_final: 0.7482 (m100)
REVERT: C  146 TRP cc_start: 0.8767 (t60) cc_final: 0.8533 (t60)
REVERT: C  153 ARG cc_start: 0.7676 (ttp-170) cc_final: 0.7427 (ptt-90)
REVERT: C  169 ASN cc_start: 0.9195 (m110) cc_final: 0.8783 (m-40)
REVERT: C  228 MET cc_start: 0.8698 (ttm) cc_final: 0.8197 (tmm)
REVERT: D   27 MET cc_start: 0.9156 (tpp) cc_final: 0.8657 (tpp)
REVERT: E    6 GLU cc_start: 0.8095 (pp20) cc_final: 0.7821 (pp20)
REVERT: F   11 LEU cc_start: 0.9210 (mt) cc_final: 0.8893 (mm)
REVERT: F   15 PHE cc_start: 0.7838 (m-80) cc_final: 0.7635 (m-80)
REVERT: F   73 ASP cc_start: 0.8655 (m-30) cc_final: 0.8139 (m-30)
REVERT: F  111 LEU cc_start: 0.9263 (tp) cc_final: 0.8997 (tt)
REVERT: F  143 LEU cc_start: 0.9390 (tp) cc_final: 0.9135 (tp)
REVERT: F  168 LEU cc_start: 0.9494 (mt) cc_final: 0.9125 (mt)
REVERT: F  209 PHE cc_start: 0.7173 (t80) cc_final: 0.6909 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 287
  average time/residue: 0.0766
  time to fit residues: 32.2508
Evaluate side-chains
  245 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 80 optimal weight:    4.9990
   chunk 105 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 3 optimal weight:    8.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  94 ASN
** E  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.100890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.081412 restraints weight = 31402.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.083802 restraints weight = 18162.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.085394 restraints weight = 12303.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.086560 restraints weight = 9324.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.087303 restraints weight = 7621.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9077  Z= 0.141
  Angle     :  0.755  10.849  12407  Z= 0.358
  Chirality :  0.045   0.238   1458
  Planarity :  0.005   0.045   1526
  Dihedral  :  5.273  64.729   1217
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.83 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.26), residues: 1118
  helix:  1.16 (0.20), residues: 693
  sheet: -1.47 (0.70), residues: 48
  loop : -1.03 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  48 
 TYR   0.011   0.001   TYR C  58 
 PHE   0.020   0.001   PHE F  15 
 TRP   0.029   0.002   TRP C  66 
 HIS   0.003   0.001   HIS B 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.14 ( 9077)
  covalent geometry    : angle       0.75505 /  0.36 (12407)
  hydrogen bonds       : bond        0.03568 /  2.42 (  500)
  hydrogen bonds       : angle       4.59599 /  3.24 ( 1428)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1493.65 seconds
wall clock time: 26 minutes 31.63 seconds (1591.63 seconds total)