Starting phenix.real_space_refine
on Wed Mar  4 03:52:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rpo_24618/03_2026/7rpo_24618.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rpo_24618/03_2026/7rpo_24618.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rpo_24618/03_2026/7rpo_24618.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rpo_24618/03_2026/7rpo_24618.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rpo_24618/03_2026/7rpo_24618.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rpo_24618/03_2026/7rpo_24618.map"
  }
  resolution = 4.16
  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=   0.026
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: 6
    Type Number    sf(0)   Gaussians
     Mn      4      7.51       5
     P      63      5.49       5
     S      25      5.16       5
     C    6571      2.51       5
     N    1753      2.21       5
     O    2186      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10602
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 252, 1953
          Classifications: {'peptide': 252}
          Link IDs: {'PTRANS': 8, 'TRANS': 243}
    Chain: "B"
      Number of atoms: 1922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1922
          Classifications: {'peptide': 243}
          Link IDs: {'PTRANS': 9, 'TRANS': 233}
    Chain: "C"
      Number of atoms: 1941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1941
          Classifications: {'peptide': 245}
          Link IDs: {'PTRANS': 5, 'TRANS': 239}
    Chain: "X"
      Number of atoms: 408
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 408
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "Y"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 229
          Classifications: {'DNA': 11}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 10}
    Chain: "Z"
      Number of atoms: 634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 634
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "E"
      Number of atoms: 3489
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 3489
          Classifications: {'peptide': 439}
          Link IDs: {'PTRANS': 13, 'TRANS': 425}
    Chain: "X"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 24
          Unusual residues: {' MN': 2, 'AMP%rna2p': 1}
          Classifications: {'RNA_mixed': 1, 'undetermined': 2}
          Modifications used: {'rna2p': 1}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 2.60, per 1000 atoms: 0.25
  Number of scatterers: 10602
  At special positions: 0
  Unit cell: (118.5, 109.5, 124.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      4     24.99
     S      25     16.00
     P      63     15.00
     O    2186      8.00
     N    1753      7.00
     C    6571      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 542.1 milliseconds
  

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2218

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      27.8% alpha, 21.5% beta
      30 base pairs and 47 stacking pairs defined.
    Time for finding SS restraints: 1.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 21
      removed outlier: 3.600A  pdb=" N   PHE A  12 " --> pdb=" O   ASN A   8 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   SER A  14 " --> pdb=" O   LYS A  10 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 79
      removed outlier: 3.929A  pdb=" N   ILE A  78 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 150
      removed outlier: 3.599A  pdb=" N   VAL A 150 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 165
      removed outlier: 3.960A  pdb=" N   ASP A 164 " --> pdb=" O   THR A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 211
      removed outlier: 3.538A  pdb=" N   GLY A 211 " --> pdb=" O   ASP A 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 20
    Processing helix  chain 'B' and resid 73 through 81
      removed outlier: 3.572A  pdb=" N   ASN B  77 " --> pdb=" O   LEU B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 145
    Processing helix  chain 'B' and resid 147 through 151
      removed outlier: 3.896A  pdb=" N   LEU B 150 " --> pdb=" O   LEU B 147 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   GLY B 151 " --> pdb=" O   SER B 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 147 through 151'
    Processing helix  chain 'B' and resid 199 through 204
    Processing helix  chain 'B' and resid 205 through 207
      No H-bonds generated for 'chain 'B' and resid 205 through 207'
    Processing helix  chain 'C' and resid 9 through 19
      removed outlier: 3.935A  pdb=" N   ASP C  13 " --> pdb=" O   ARG C   9 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ILE C  14 " --> pdb=" O   VAL C  10 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   ILE C  15 " --> pdb=" O   LEU C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 77
    Processing helix  chain 'C' and resid 136 through 147
      removed outlier: 3.843A  pdb=" N   LYS C 140 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   SER C 141 " --> pdb=" O   ASP C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 205
      removed outlier: 3.838A  pdb=" N   VAL C 204 " --> pdb=" O   LEU C 201 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 12
      removed outlier: 3.889A  pdb=" N   LYS E  12 " --> pdb=" O   GLU E   8 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 33
      removed outlier: 3.778A  pdb=" N   THR E  23 " --> pdb=" O   ARG E  19 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   ALA E  24 " --> pdb=" O   LEU E  20 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ALA E  27 " --> pdb=" O   THR E  23 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ASP E  28 " --> pdb=" O   ALA E  24 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   LEU E  29 " --> pdb=" O   LEU E  25 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   LEU E  30 " --> pdb=" O   LEU E  26 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 37 through 47
      removed outlier: 3.893A  pdb=" N   GLN E  46 " --> pdb=" O   VAL E  42 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLY E  47 " --> pdb=" O   TYR E  43 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 75
      removed outlier: 3.649A  pdb=" N   LEU E  66 " --> pdb=" O   GLY E  62 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ILE E  67 " --> pdb=" O   GLU E  63 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LYS E  68 " --> pdb=" O   LYS E  64 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 77 through 88
      removed outlier: 3.727A  pdb=" N   THR E  87 " --> pdb=" O   ASN E  83 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE E  88 " --> pdb=" O   LEU E  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 97
      removed outlier: 4.004A  pdb=" N   ARG E  97 " --> pdb=" O   GLU E  93 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 98 through 100
      No H-bonds generated for 'chain 'E' and resid 98 through 100'
    Processing helix  chain 'E' and resid 120 through 134
      removed outlier: 3.583A  pdb=" N   LEU E 133 " --> pdb=" O   SER E 129 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR E 134 " --> pdb=" O   LYS E 130 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 138 through 153
      removed outlier: 3.931A  pdb=" N   LEU E 142 " --> pdb=" O   GLY E 138 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ARG E 145 " --> pdb=" O   ASP E 141 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LEU E 146 " --> pdb=" O   LEU E 142 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY E 149 " --> pdb=" O   ARG E 145 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   LEU E 150 " --> pdb=" O   LEU E 146 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU E 151 " --> pdb=" O   LEU E 147 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 168
      removed outlier: 3.924A  pdb=" N   ARG E 164 " --> pdb=" O   LYS E 160 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 176 through 187
    Processing helix  chain 'E' and resid 190 through 192
      No H-bonds generated for 'chain 'E' and resid 190 through 192'
    Processing helix  chain 'E' and resid 193 through 204
      removed outlier: 4.138A  pdb=" N   ILE E 197 " --> pdb=" O   ALA E 193 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 207 through 218
    Processing helix  chain 'E' and resid 246 through 252
    Processing helix  chain 'E' and resid 290 through 293
      removed outlier: 3.589A  pdb=" N   VAL E 293 " --> pdb=" O   PRO E 290 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 290 through 293'
    Processing helix  chain 'E' and resid 294 through 299
    Processing helix  chain 'E' and resid 323 through 328
    Processing helix  chain 'E' and resid 339 through 343
    Processing helix  chain 'E' and resid 366 through 373
    Processing helix  chain 'E' and resid 392 through 406
      removed outlier: 3.582A  pdb=" N   LYS E 397 " --> pdb=" O   VAL E 393 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   SER E 398 " --> pdb=" O   GLU E 394 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG E 402 " --> pdb=" O   SER E 398 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6
      removed outlier: 3.520A  pdb=" N   ILE A 101 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ILE A 100 " --> pdb=" O   ILE A 113 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LYS A 110 " --> pdb=" O   GLU C 175 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLU C 175 " --> pdb=" O   LYS A 110 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 71
      removed outlier: 3.816A  pdb=" N   THR A  66 " --> pdb=" O   PHE A  30 " (cutoff:3.500A)
      removed outlier: 10.054A  pdb=" N   SER A  25 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 8.324A  pdb=" N   LEU A  40 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
      removed outlier: 5.526A  pdb=" N   ILE A  27 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   ARG A  38 " --> pdb=" O   ILE A  27 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ASN A  29 " --> pdb=" O   PHE A  36 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   PHE A  36 " --> pdb=" O   ASN A  29 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR A  31 " --> pdb=" O   GLY A  34 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ILE A  35 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   MET A  50 " --> pdb=" O   SER A  37 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   HIS A  39 " --> pdb=" O   ALA A  48 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ALA A  48 " --> pdb=" O   HIS A  39 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ARG A  51 " --> pdb=" O   HIS A 240 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   MET A 241 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL A 233 " --> pdb=" O   MET A 241 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE A 231 " --> pdb=" O   PHE A 243 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASN A 135 " --> pdb=" O   SER A 191 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   SER A 191 " --> pdb=" O   ASN A 135 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR A 137 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   GLU A 189 " --> pdb=" O   THR A 137 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 181
      removed outlier: 3.747A  pdb=" N   TYR A 177 " --> pdb=" O   ALA A 170 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ALA A 170 " --> pdb=" O   TYR A 177 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ILE A 168 " --> pdb=" O   ALA A 179 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ILE A 166 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLU A 169 " --> pdb=" O   ARG A 158 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ARG A 158 " --> pdb=" O   GLU A 169 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   GLY A 171 " --> pdb=" O   GLU A 156 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   GLU A 156 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 61
      removed outlier: 5.231A  pdb=" N   GLY B  59 " --> pdb=" O   LYS B   5 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   LYS B   5 " --> pdb=" O   GLY B  59 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   SER B  92 " --> pdb=" O   THR B  99 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   THR B  99 " --> pdb=" O   SER B  92 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 68 through 72
      removed outlier: 3.948A  pdb=" N   PHE B  71 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   ALA B  26 " --> pdb=" O   PHE B  71 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   GLU B  25 " --> pdb=" O   ILE B  40 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ILE B  40 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 5.326A  pdb=" N   ASN B  27 " --> pdb=" O   SER B  38 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   SER B  38 " --> pdb=" O   ASN B  27 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG B  36 " --> pdb=" O   ILE B  29 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE B  35 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU B  48 " --> pdb=" O   GLY B  39 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASP B  49 " --> pdb=" O   ASP B 238 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   TYR B 236 " --> pdb=" O   PHE B  51 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG B 228 " --> pdb=" O   GLU B 216 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   SER B 214 " --> pdb=" O   LYS B 230 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 194 through 197
      removed outlier: 3.839A  pdb=" N   LEU B 163 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU B 178 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   THR B 173 " --> pdb=" O   ASN C 110 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LYS B 175 " --> pdb=" O   GLU C 108 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLU C 108 " --> pdb=" O   LYS B 175 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 66 through 70
      removed outlier: 3.714A  pdb=" N   PHE C  67 " --> pdb=" O   LEU C  27 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   PHE C  69 " --> pdb=" O   ALA C  25 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   ALA C  25 " --> pdb=" O   PHE C  69 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   GLU C  24 " --> pdb=" O   LEU C  39 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   LEU C  39 " --> pdb=" O   GLU C  24 " (cutoff:3.500A)
      removed outlier: 5.556A  pdb=" N   VAL C  26 " --> pdb=" O   VAL C  37 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   VAL C  37 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA C  38 " --> pdb=" O   ILE C  47 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ILE C  47 " --> pdb=" O   ALA C  38 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU C  46 " --> pdb=" O   LEU C 239 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   SER C  48 " --> pdb=" O   THR C 237 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LYS C 235 " --> pdb=" O   ASN C  50 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   VAL C 236 " --> pdb=" O   PHE C 228 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   PHE C 228 " --> pdb=" O   VAL C 236 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   TYR C 238 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LEU C 226 " --> pdb=" O   TYR C 238 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 388 through 389
      removed outlier: 3.956A  pdb=" N   GLY E 410 " --> pdb=" O   LYS E 260 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL E 411 " --> pdb=" O   LEU E 434 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU E 434 " --> pdb=" O   VAL E 411 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ILE E 432 " --> pdb=" O   VAL E 413 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 275 through 278
      removed outlier: 3.626A  pdb=" N   GLY E 309 " --> pdb=" O   ALA E 266 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LYS E 270 " --> pdb=" O   PHE E 305 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   ILE E 306 " --> pdb=" O   LEU E 352 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   LEU E 352 " --> pdb=" O   ILE E 306 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   GLU E 308 " --> pdb=" O   PHE E 350 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL E 312 " --> pdb=" O   ASN E 346 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASN E 346 " --> pdb=" O   VAL E 312 " (cutoff:3.500A)

    309 hydrogen bonds defined for protein.
    849 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      77 hydrogen bonds
      154 hydrogen bond angles
      0 basepair planarities
      30 basepair parallelities
      47 stacking parallelities
  Total time for adding SS restraints: 1.83

  Time building geometry restraints manager: 1.06 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2890
        1.33 -     1.45: 1884
        1.45 -     1.57: 5953
        1.57 -     1.69: 122
        1.69 -     1.80: 50
  Bond restraints: 10899
  Sorted by residual:
  bond pdb=" CA  LYS C 178 "
       pdb=" C   LYS C 178 "
    ideal  model  delta    sigma   weight residual
    1.522  1.545 -0.023 1.72e-02 3.38e+03 1.77e+00
  bond pdb=" N   GLY E 309 "
       pdb=" CA  GLY E 309 "
    ideal  model  delta    sigma   weight residual
    1.453  1.442  0.011 8.60e-03 1.35e+04 1.65e+00
  bond pdb=" C3'  DA Z  22 "
       pdb=" O3'  DA Z  22 "
    ideal  model  delta    sigma   weight residual
    1.422  1.459 -0.037 3.00e-02 1.11e+03 1.53e+00
  bond pdb=" C3'  DT Z  30 "
       pdb=" O3'  DT Z  30 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.45e+00
  bond pdb=" C4  AMP E 701 "
       pdb=" C5  AMP E 701 "
    ideal  model  delta    sigma   weight residual
    1.490  1.467  0.023 2.00e-02 2.50e+03 1.35e+00
  ... (remaining 10894 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 14618
        1.45 -     2.91: 308
        2.91 -     4.36: 28
        4.36 -     5.81: 7
        5.81 -     7.27: 2
  Bond angle restraints: 14963
  Sorted by residual:
  angle pdb=" C   LEU A 249 "
        pdb=" CA  LEU A 249 "
        pdb=" CB  LEU A 249 "
      ideal   model   delta    sigma   weight residual
     117.23  109.96    7.27 1.36e+00 5.41e-01 2.86e+01
  angle pdb=" CA  LEU A 249 "
        pdb=" C   LEU A 249 "
        pdb=" N   LEU A 250 "
      ideal   model   delta    sigma   weight residual
     119.98  116.82    3.16 8.50e-01 1.38e+00 1.38e+01
  angle pdb=" N   GLY E 136 "
        pdb=" CA  GLY E 136 "
        pdb=" C   GLY E 136 "
      ideal   model   delta    sigma   weight residual
     111.78  116.72   -4.94 1.69e+00 3.50e-01 8.53e+00
  angle pdb=" N   ASP B 213 "
        pdb=" CA  ASP B 213 "
        pdb=" C   ASP B 213 "
      ideal   model   delta    sigma   weight residual
     113.18  110.35    2.83 1.33e+00 5.65e-01 4.53e+00
  angle pdb=" N   GLY B 183 "
        pdb=" CA  GLY B 183 "
        pdb=" C   GLY B 183 "
      ideal   model   delta    sigma   weight residual
     113.18  118.10   -4.92 2.37e+00 1.78e-01 4.30e+00
  ... (remaining 14958 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.40: 6079
       30.40 -    60.80: 379
       60.80 -    91.19: 4
       91.19 -   121.59: 0
      121.59 -   151.99: 5
  Dihedral angle restraints: 6467
    sinusoidal: 3035
      harmonic: 3432
  Sorted by residual:
  dihedral pdb=" C4'  DT Z  30 "
           pdb=" C3'  DT Z  30 "
           pdb=" O3'  DT Z  30 "
           pdb=" P    DC Z  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   68.01  151.99     1      3.50e+01 8.16e-04 1.48e+01
  dihedral pdb=" C4'  DA Z  22 "
           pdb=" C3'  DA Z  22 "
           pdb=" O3'  DA Z  22 "
           pdb=" P    DC Z  23 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   70.14  149.86     1      3.50e+01 8.16e-04 1.46e+01
  dihedral pdb=" C4'  DC Z  26 "
           pdb=" C3'  DC Z  26 "
           pdb=" O3'  DC Z  26 "
           pdb=" P    DG Z  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   71.90  148.10     1      3.50e+01 8.16e-04 1.45e+01
  ... (remaining 6464 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1089
       0.029 -    0.058: 416
       0.058 -    0.086: 104
       0.086 -    0.115: 96
       0.115 -    0.144: 18
  Chirality restraints: 1723
  Sorted by residual:
  chirality pdb=" CA  ILE E 306 "
            pdb=" N   ILE E 306 "
            pdb=" C   ILE E 306 "
            pdb=" CB  ILE E 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.18e-01
  chirality pdb=" CA  ILE B  68 "
            pdb=" N   ILE B  68 "
            pdb=" C   ILE B  68 "
            pdb=" CB  ILE B  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.18e-01
  chirality pdb=" CA  ILE B  35 "
            pdb=" N   ILE B  35 "
            pdb=" C   ILE B  35 "
            pdb=" CB  ILE B  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.96e-01
  ... (remaining 1720 not shown)

  Planarity restraints: 1683
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  93 "    0.022 5.00e-02 4.00e+02   3.40e-02 1.85e+00
        pdb=" N   PRO C  94 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO C  94 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C  94 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 121 "    0.022 5.00e-02 4.00e+02   3.34e-02 1.78e+00
        pdb=" N   PRO C 122 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO C 122 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 122 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 227 "   -0.021 5.00e-02 4.00e+02   3.21e-02 1.65e+00
        pdb=" N   PRO A 228 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 228 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 228 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1680 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.39: 27
        2.39 -     3.02: 5691
        3.02 -     3.64: 14979
        3.64 -     4.27: 21306
        4.27 -     4.90: 35049
  Nonbonded interactions: 77052
  Sorted by model distance:
  nonbonded pdb=" O1P AMP E 701 "
            pdb="MN    MN E 703 "
     model   vdw
     1.759 2.320
  nonbonded pdb=" O   GLY E  60 "
            pdb="MN    MN X 101 "
     model   vdw
     1.776 2.320
  nonbonded pdb=" OE2 GLU E 409 "
            pdb="MN    MN E 703 "
     model   vdw
     1.815 2.320
  nonbonded pdb=" O3'  DG X  20 "
            pdb="MN    MN X 101 "
     model   vdw
     2.187 2.320
  nonbonded pdb=" OG  SER C 211 "
            pdb=" O   ASN C 229 "
     model   vdw
     2.192 3.040
  ... (remaining 77047 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.410
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6937
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      :  0.003   0.051  10900  Z= 0.128
  Angle     :  0.502   7.267  14963  Z= 0.281
  Chirality :  0.040   0.144   1723
  Planarity :  0.003   0.034   1683
  Dihedral  : 16.970 151.990   4249
  Min Nonbonded Distance : 1.759

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  9.76 %
    Favored  : 88.60 %
  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: -2.01 (0.25), residues: 1171
  helix: -0.03 (0.33), residues: 294
  sheet: -0.27 (0.32), residues: 303
  loop : -2.74 (0.23), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 330 
 TYR   0.008   0.001   TYR A 177 
 PHE   0.010   0.001   PHE C 228 
 TRP   0.004   0.001   TRP E  50 
 HIS   0.002   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (10899)
  covalent geometry    : angle       0.50240 (14963)
  hydrogen bonds       : bond        0.24462 (  386)
  hydrogen bonds       : angle       8.23261 ( 1003)
  Misc. bond           : bond        0.05146 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  414 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 397
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 VAL cc_start: 0.7540 (t) cc_final: 0.7181 (m)
REVERT: A   24 ASP cc_start: 0.5986 (t70) cc_final: 0.5304 (t0)
REVERT: A   28 LEU cc_start: 0.7221 (mt) cc_final: 0.6808 (mp)
REVERT: A   39 HIS cc_start: 0.7684 (t-90) cc_final: 0.7404 (t-90)
REVERT: A   47 MET cc_start: 0.7688 (ttt) cc_final: 0.7285 (ttt)
REVERT: A   57 LEU cc_start: 0.8144 (mt) cc_final: 0.7881 (mt)
REVERT: A   59 GLU cc_start: 0.8294 (tp30) cc_final: 0.7918 (tp30)
REVERT: A   77 LYS cc_start: 0.8708 (pttt) cc_final: 0.8505 (ptpt)
REVERT: A   79 LEU cc_start: 0.7529 (mt) cc_final: 0.6939 (mt)
REVERT: A   99 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8157 (mtpp)
REVERT: A  101 ILE cc_start: 0.7816 (mt) cc_final: 0.7476 (mp)
REVERT: A  110 LYS cc_start: 0.7390 (ttmt) cc_final: 0.7137 (ttmm)
REVERT: A  136 PHE cc_start: 0.7173 (p90) cc_final: 0.6649 (p90)
REVERT: A  156 GLU cc_start: 0.8103 (mp0) cc_final: 0.7807 (mp0)
REVERT: A  159 ILE cc_start: 0.8047 (mt) cc_final: 0.7839 (mm)
REVERT: A  190 LEU cc_start: 0.7604 (tp) cc_final: 0.7360 (mt)
REVERT: A  212 LEU cc_start: 0.7787 (mt) cc_final: 0.7577 (tp)
REVERT: A  213 ARG cc_start: 0.7061 (mtt90) cc_final: 0.6718 (mtt90)
REVERT: A  221 VAL cc_start: 0.8086 (t) cc_final: 0.7727 (p)
REVERT: A  231 ILE cc_start: 0.8109 (mt) cc_final: 0.7564 (tt)
REVERT: A  233 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.7489 (p)
REVERT: B   30 VAL cc_start: 0.8305 (t) cc_final: 0.8098 (t)
REVERT: B   78 ASP cc_start: 0.6720 (m-30) cc_final: 0.6407 (m-30)
REVERT: B   81 LYS cc_start: 0.7912 (ttmm) cc_final: 0.7663 (ttpp)
REVERT: B  156 ILE cc_start: 0.8086 (mm) cc_final: 0.7777 (mt)
REVERT: B  162 LYS cc_start: 0.8349 (mttp) cc_final: 0.7958 (mmmt)
REVERT: B  168 ILE cc_start: 0.8419 (tt) cc_final: 0.8152 (tt)
REVERT: B  184 THR cc_start: 0.6611 (OUTLIER) cc_final: 0.6388 (p)
REVERT: B  200 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6910 (tm-30)
REVERT: C    2 LYS cc_start: 0.7911 (mttt) cc_final: 0.7638 (tppt)
REVERT: C    3 VAL cc_start: 0.8648 (t) cc_final: 0.8389 (p)
REVERT: C    6 ASP cc_start: 0.7991 (t0) cc_final: 0.7649 (t0)
REVERT: C    7 ASP cc_start: 0.7609 (t70) cc_final: 0.7132 (t0)
REVERT: C   23 ASP cc_start: 0.8016 (m-30) cc_final: 0.7815 (m-30)
REVERT: C   30 LYS cc_start: 0.8021 (mptt) cc_final: 0.7562 (mmmm)
REVERT: C   31 GLN cc_start: 0.8039 (mp10) cc_final: 0.7804 (mt0)
REVERT: C   75 MET cc_start: 0.6836 (tmm) cc_final: 0.6633 (tpp)
REVERT: C  139 PHE cc_start: 0.8027 (t80) cc_final: 0.7575 (t80)
REVERT: C  140 LYS cc_start: 0.8082 (ttpt) cc_final: 0.7502 (tttm)
REVERT: C  167 GLU cc_start: 0.7801 (pp20) cc_final: 0.7390 (pp20)
REVERT: C  191 GLU cc_start: 0.7005 (mp0) cc_final: 0.6749 (mp0)
REVERT: C  205 LEU cc_start: 0.8461 (mt) cc_final: 0.7856 (tp)
REVERT: C  229 ASN cc_start: 0.7470 (t0) cc_final: 0.7201 (t0)
REVERT: E    1 MET cc_start: 0.7067 (mmm) cc_final: 0.6704 (mmm)
REVERT: E    2 GLU cc_start: 0.7234 (pm20) cc_final: 0.7029 (pm20)
REVERT: E   11 ASP cc_start: 0.6648 (t70) cc_final: 0.6334 (t0)
REVERT: E   13 LEU cc_start: 0.7464 (tp) cc_final: 0.7235 (tp)
REVERT: E   36 THR cc_start: 0.7292 (p) cc_final: 0.6691 (p)
REVERT: E   46 GLN cc_start: 0.7562 (tm-30) cc_final: 0.7351 (tm-30)
REVERT: E   48 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7854 (mmmm)
REVERT: E   49 LEU cc_start: 0.7264 (mp) cc_final: 0.7025 (mt)
REVERT: E   67 ILE cc_start: 0.8020 (mt) cc_final: 0.7668 (pt)
REVERT: E   86 LYS cc_start: 0.7898 (tptp) cc_final: 0.7462 (mmmm)
REVERT: E  101 LYS cc_start: 0.8699 (pttm) cc_final: 0.8184 (pttm)
REVERT: E  111 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6244 (pp)
REVERT: E  126 SER cc_start: 0.8510 (t) cc_final: 0.7909 (p)
REVERT: E  169 ARG cc_start: 0.7185 (ptt180) cc_final: 0.6933 (ptt90)
REVERT: E  174 ILE cc_start: 0.7888 (mm) cc_final: 0.7595 (tt)
REVERT: E  197 ILE cc_start: 0.7992 (mm) cc_final: 0.7692 (tp)
REVERT: E  203 LEU cc_start: 0.7947 (mt) cc_final: 0.7669 (mt)
REVERT: E  206 ASP cc_start: 0.7730 (p0) cc_final: 0.7526 (p0)
REVERT: E  212 LYS cc_start: 0.7262 (pttm) cc_final: 0.6989 (pttp)
REVERT: E  236 MET cc_start: 0.7580 (ptp) cc_final: 0.7362 (ptp)
REVERT: E  239 GLU cc_start: 0.7244 (tp30) cc_final: 0.6136 (mp0)
REVERT: E  291 ASP cc_start: 0.7755 (p0) cc_final: 0.7513 (p0)
REVERT: E  321 MET cc_start: 0.6543 (mmm) cc_final: 0.5649 (mmm)
REVERT: E  325 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6995 (tp-100)
REVERT: E  326 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7435 (tp30)
REVERT: E  328 MET cc_start: 0.7739 (mtm) cc_final: 0.7095 (mtm)
REVERT: E  336 ILE cc_start: 0.7362 (mt) cc_final: 0.6787 (mm)
REVERT: E  360 TYR cc_start: 0.7426 (m-80) cc_final: 0.6726 (m-80)
REVERT: E  373 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7817 (mm-30)
REVERT: E  397 LYS cc_start: 0.7841 (mmmt) cc_final: 0.7605 (mmtp)
REVERT: E  434 LEU cc_start: 0.8334 (tp) cc_final: 0.7901 (pt)
  outliers start: 17
  outliers final: 4
  residues processed: 410
  average time/residue: 0.1254
  time to fit residues: 68.0114
Evaluate side-chains
  350 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 343
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0670
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.4980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 117 optimal weight:    4.9990
   overall best weight:    0.6120

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

Flipped N/Q/H residues before XYZ refinement:
A 135 ASN
B 116 GLN
E 102 GLN
E 228 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.138567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.116189 restraints weight = 18660.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.119056 restraints weight = 11433.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.121049 restraints weight = 7990.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.122451 restraints weight = 6115.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.123415 restraints weight = 5012.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3583
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3578 r_free = 0.3578    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3578
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10900  Z= 0.139
  Angle     :  0.593   7.286  14963  Z= 0.322
  Chirality :  0.044   0.163   1723
  Planarity :  0.004   0.050   1683
  Dihedral  : 20.753 151.162   1931
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.42 %
    Favored  : 97.39 %
  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: -2.09 (0.24), residues: 1171
  helix: -0.31 (0.31), residues: 307
  sheet:  0.09 (0.32), residues: 316
  loop : -3.06 (0.22), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 427 
 TYR   0.010   0.001   TYR E 259 
 PHE   0.022   0.002   PHE C 139 
 TRP   0.018   0.002   TRP E  50 
 HIS   0.003   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10899)
  covalent geometry    : angle       0.59349 (14963)
  hydrogen bonds       : bond        0.04946 (  386)
  hydrogen bonds       : angle       5.97442 ( 1003)
  Misc. bond           : bond        0.00075 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  358 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 356
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.5577 (t70) cc_final: 0.5243 (t0)
REVERT: A   47 MET cc_start: 0.7183 (ttt) cc_final: 0.6929 (ttt)
REVERT: A   57 LEU cc_start: 0.8178 (mt) cc_final: 0.7877 (mt)
REVERT: A  110 LYS cc_start: 0.7177 (ttmt) cc_final: 0.6918 (ttmm)
REVERT: A  116 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7656 (tptt)
REVERT: A  159 ILE cc_start: 0.8064 (mt) cc_final: 0.7721 (mm)
REVERT: A  212 LEU cc_start: 0.7458 (mt) cc_final: 0.7169 (tp)
REVERT: A  213 ARG cc_start: 0.6897 (mtt90) cc_final: 0.6546 (mtt90)
REVERT: A  229 MET cc_start: 0.6477 (ttt) cc_final: 0.6044 (ttt)
REVERT: B   21 ASP cc_start: 0.7596 (t0) cc_final: 0.6745 (t0)
REVERT: B  132 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8086 (ttmm)
REVERT: B  155 ASN cc_start: 0.7463 (t0) cc_final: 0.7255 (t0)
REVERT: B  159 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7564 (ttmm)
REVERT: C    3 VAL cc_start: 0.8295 (t) cc_final: 0.7815 (p)
REVERT: C    6 ASP cc_start: 0.7282 (t0) cc_final: 0.7071 (t0)
REVERT: C    7 ASP cc_start: 0.7838 (t70) cc_final: 0.7426 (t0)
REVERT: C   75 MET cc_start: 0.6911 (tmm) cc_final: 0.6691 (tpp)
REVERT: C   76 LYS cc_start: 0.8107 (ttpt) cc_final: 0.7883 (ttpt)
REVERT: C   77 ILE cc_start: 0.8325 (pt) cc_final: 0.8032 (tt)
REVERT: C   85 GLU cc_start: 0.7442 (mp0) cc_final: 0.7048 (mp0)
REVERT: C   95 ASP cc_start: 0.8199 (t70) cc_final: 0.7830 (t70)
REVERT: C  100 ASN cc_start: 0.7591 (m-40) cc_final: 0.7375 (m-40)
REVERT: C  108 GLU cc_start: 0.7057 (pp20) cc_final: 0.6713 (tm-30)
REVERT: C  112 ARG cc_start: 0.8248 (tpp80) cc_final: 0.7967 (tpp80)
REVERT: C  140 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7581 (tttm)
REVERT: C  154 VAL cc_start: 0.8030 (t) cc_final: 0.7823 (t)
REVERT: C  165 LYS cc_start: 0.7809 (pttp) cc_final: 0.7244 (ptpt)
REVERT: C  205 LEU cc_start: 0.8181 (mt) cc_final: 0.7924 (tp)
REVERT: C  209 LYS cc_start: 0.8095 (ptmm) cc_final: 0.7585 (ptmm)
REVERT: C  215 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7771 (ttmm)
REVERT: C  230 MET cc_start: 0.5438 (mtm) cc_final: 0.5171 (mtm)
REVERT: E    6 ILE cc_start: 0.6561 (tp) cc_final: 0.6287 (tp)
REVERT: E   46 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7500 (tm-30)
REVERT: E   86 LYS cc_start: 0.7669 (tppt) cc_final: 0.7459 (mmmm)
REVERT: E  101 LYS cc_start: 0.8628 (pttm) cc_final: 0.8192 (pttm)
REVERT: E  126 SER cc_start: 0.8327 (t) cc_final: 0.7899 (p)
REVERT: E  127 THR cc_start: 0.8173 (m) cc_final: 0.7780 (p)
REVERT: E  135 THR cc_start: 0.7991 (m) cc_final: 0.7736 (p)
REVERT: E  174 ILE cc_start: 0.7974 (mm) cc_final: 0.7577 (tt)
REVERT: E  197 ILE cc_start: 0.8048 (mm) cc_final: 0.7728 (tp)
REVERT: E  228 GLN cc_start: 0.6184 (OUTLIER) cc_final: 0.5714 (pp30)
REVERT: E  239 GLU cc_start: 0.7571 (tp30) cc_final: 0.6353 (mp0)
REVERT: E  265 ARG cc_start: 0.7725 (mtp180) cc_final: 0.7325 (mtp-110)
REVERT: E  274 LYS cc_start: 0.6929 (mppt) cc_final: 0.6402 (mppt)
REVERT: E  277 ILE cc_start: 0.8535 (mp) cc_final: 0.8305 (mt)
REVERT: E  290 PRO cc_start: 0.8003 (Cg_endo) cc_final: 0.7672 (Cg_exo)
REVERT: E  325 GLN cc_start: 0.7179 (mm-40) cc_final: 0.6839 (tp40)
REVERT: E  326 GLU cc_start: 0.7579 (tp30) cc_final: 0.6837 (tp30)
REVERT: E  328 MET cc_start: 0.7485 (mtm) cc_final: 0.7195 (mtm)
REVERT: E  329 HIS cc_start: 0.7212 (m90) cc_final: 0.5912 (m90)
REVERT: E  360 TYR cc_start: 0.7355 (m-80) cc_final: 0.6594 (m-80)
REVERT: E  363 LYS cc_start: 0.8323 (mmtt) cc_final: 0.8028 (mmtp)
REVERT: E  397 LYS cc_start: 0.7761 (mmmt) cc_final: 0.7484 (mmtp)
REVERT: E  434 LEU cc_start: 0.8462 (tp) cc_final: 0.7947 (pt)
  outliers start: 2
  outliers final: 0
  residues processed: 357
  average time/residue: 0.1253
  time to fit residues: 58.8820
Evaluate side-chains
  315 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 314
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 70 optimal weight:    0.7980
   chunk 91 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 106 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
B 204 ASN
E 228 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.134893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.112995 restraints weight = 19164.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.115673 restraints weight = 12020.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.117533 restraints weight = 8519.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.118835 restraints weight = 6613.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.119714 restraints weight = 5474.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3550
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3550 r_free = 0.3550    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3550 r_free = 0.3550    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3550
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6932
moved from start:          0.3054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10900  Z= 0.159
  Angle     :  0.611  10.594  14963  Z= 0.327
  Chirality :  0.044   0.157   1723
  Planarity :  0.004   0.049   1683
  Dihedral  : 20.861 150.127   1931
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.39 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.19 %
    Favored  : 96.71 %
  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: -2.10 (0.24), residues: 1171
  helix: -0.33 (0.31), residues: 304
  sheet:  0.08 (0.32), residues: 315
  loop : -3.04 (0.22), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 234 
 TYR   0.023   0.002   TYR C  59 
 PHE   0.016   0.002   PHE C 228 
 TRP   0.016   0.002   TRP E  50 
 HIS   0.003   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (10899)
  covalent geometry    : angle       0.61056 (14963)
  hydrogen bonds       : bond        0.04896 (  386)
  hydrogen bonds       : angle       5.42997 ( 1003)
  Misc. bond           : bond        0.00048 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  353 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 352
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 PHE cc_start: 0.6389 (t80) cc_final: 0.6044 (t80)
REVERT: A   24 ASP cc_start: 0.5712 (t70) cc_final: 0.5360 (t0)
REVERT: A   54 LYS cc_start: 0.7265 (ptmt) cc_final: 0.7058 (ptmm)
REVERT: A   55 ASP cc_start: 0.7771 (t0) cc_final: 0.7559 (t0)
REVERT: A   57 LEU cc_start: 0.8143 (mt) cc_final: 0.7835 (mt)
REVERT: A   69 LYS cc_start: 0.7716 (mppt) cc_final: 0.7236 (mmtm)
REVERT: A   91 LEU cc_start: 0.8136 (tp) cc_final: 0.7491 (tt)
REVERT: A  116 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7735 (tptt)
REVERT: A  156 GLU cc_start: 0.8006 (mp0) cc_final: 0.7798 (mm-30)
REVERT: A  213 ARG cc_start: 0.6820 (mtt90) cc_final: 0.6608 (mtt90)
REVERT: A  229 MET cc_start: 0.6367 (ttt) cc_final: 0.6110 (ttt)
REVERT: B   21 ASP cc_start: 0.7550 (t0) cc_final: 0.6698 (t0)
REVERT: B   35 ILE cc_start: 0.8471 (mm) cc_final: 0.8214 (tp)
REVERT: B   66 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7861 (mmmt)
REVERT: B  107 THR cc_start: 0.8038 (p) cc_final: 0.7755 (t)
REVERT: B  132 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7899 (ttmm)
REVERT: B  153 VAL cc_start: 0.7887 (t) cc_final: 0.7623 (p)
REVERT: B  159 LYS cc_start: 0.7900 (ttpp) cc_final: 0.7638 (ttmm)
REVERT: B  162 LYS cc_start: 0.8327 (mttp) cc_final: 0.7711 (mttp)
REVERT: C    3 VAL cc_start: 0.8599 (t) cc_final: 0.8103 (p)
REVERT: C    6 ASP cc_start: 0.7372 (t0) cc_final: 0.7111 (t0)
REVERT: C    7 ASP cc_start: 0.7807 (t70) cc_final: 0.7459 (t0)
REVERT: C   28 LYS cc_start: 0.8192 (mttp) cc_final: 0.7992 (mttm)
REVERT: C   75 MET cc_start: 0.7077 (tmm) cc_final: 0.6794 (tpp)
REVERT: C   84 LYS cc_start: 0.7733 (mttp) cc_final: 0.7499 (mttp)
REVERT: C  109 PHE cc_start: 0.8054 (m-80) cc_final: 0.7798 (m-80)
REVERT: C  130 ILE cc_start: 0.8659 (mp) cc_final: 0.8381 (mm)
REVERT: C  165 LYS cc_start: 0.8038 (pttp) cc_final: 0.7403 (ptpt)
REVERT: C  167 GLU cc_start: 0.7471 (pp20) cc_final: 0.7216 (pp20)
REVERT: C  171 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6941 (mm-30)
REVERT: C  193 LYS cc_start: 0.7547 (mppt) cc_final: 0.7099 (mppt)
REVERT: C  205 LEU cc_start: 0.8288 (mt) cc_final: 0.7950 (tp)
REVERT: C  209 LYS cc_start: 0.8134 (ptmm) cc_final: 0.7644 (ptmm)
REVERT: C  215 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7790 (ttmm)
REVERT: E    6 ILE cc_start: 0.6641 (tp) cc_final: 0.6302 (tp)
REVERT: E   46 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7602 (tm-30)
REVERT: E   86 LYS cc_start: 0.7758 (tppt) cc_final: 0.7492 (mmmm)
REVERT: E   93 GLU cc_start: 0.8023 (tp30) cc_final: 0.7739 (tp30)
REVERT: E  101 LYS cc_start: 0.8553 (pttm) cc_final: 0.8103 (pttm)
REVERT: E  110 PHE cc_start: 0.6351 (m-80) cc_final: 0.6126 (m-10)
REVERT: E  126 SER cc_start: 0.8319 (t) cc_final: 0.7789 (p)
REVERT: E  135 THR cc_start: 0.7816 (m) cc_final: 0.7515 (p)
REVERT: E  142 LEU cc_start: 0.8223 (mt) cc_final: 0.7987 (mt)
REVERT: E  174 ILE cc_start: 0.7979 (mm) cc_final: 0.7663 (tt)
REVERT: E  194 SER cc_start: 0.7907 (p) cc_final: 0.7623 (p)
REVERT: E  197 ILE cc_start: 0.8019 (mm) cc_final: 0.7757 (tp)
REVERT: E  209 ASN cc_start: 0.6549 (m-40) cc_final: 0.6015 (m-40)
REVERT: E  228 GLN cc_start: 0.6167 (OUTLIER) cc_final: 0.5633 (pp30)
REVERT: E  236 MET cc_start: 0.7613 (ptp) cc_final: 0.7384 (ptp)
REVERT: E  239 GLU cc_start: 0.7551 (tp30) cc_final: 0.6358 (mp0)
REVERT: E  265 ARG cc_start: 0.7789 (mtp180) cc_final: 0.7078 (mtp-110)
REVERT: E  274 LYS cc_start: 0.7071 (mppt) cc_final: 0.6633 (mppt)
REVERT: E  280 ARG cc_start: 0.7867 (tpt170) cc_final: 0.7639 (tpt90)
REVERT: E  281 ARG cc_start: 0.7013 (mtm180) cc_final: 0.6571 (mtm180)
REVERT: E  290 PRO cc_start: 0.7969 (Cg_endo) cc_final: 0.7616 (Cg_exo)
REVERT: E  304 GLU cc_start: 0.7609 (mp0) cc_final: 0.6994 (pm20)
REVERT: E  325 GLN cc_start: 0.7150 (mm-40) cc_final: 0.6891 (tp40)
REVERT: E  328 MET cc_start: 0.7452 (mtm) cc_final: 0.7187 (mtm)
REVERT: E  363 LYS cc_start: 0.8323 (mmtt) cc_final: 0.8081 (mmtp)
REVERT: E  397 LYS cc_start: 0.7772 (mmmt) cc_final: 0.7425 (mmtp)
REVERT: E  434 LEU cc_start: 0.8353 (tp) cc_final: 0.7925 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 353
  average time/residue: 0.1263
  time to fit residues: 58.5383
Evaluate side-chains
  314 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 313
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 103 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 106 optimal weight:    0.3980
   chunk 60 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.135880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.114274 restraints weight = 19115.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.116905 restraints weight = 12095.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.118747 restraints weight = 8596.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.120018 restraints weight = 6666.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.120950 restraints weight = 5526.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3561
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3561 r_free = 0.3561    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3561 r_free = 0.3561    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3561
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6915
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10900  Z= 0.138
  Angle     :  0.587   9.245  14963  Z= 0.315
  Chirality :  0.044   0.195   1723
  Planarity :  0.004   0.049   1683
  Dihedral  : 20.851 148.931   1931
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.24), residues: 1171
  helix: -0.39 (0.31), residues: 309
  sheet:  0.27 (0.32), residues: 311
  loop : -3.00 (0.22), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 103 
 TYR   0.016   0.001   TYR C  59 
 PHE   0.017   0.002   PHE E  10 
 TRP   0.015   0.001   TRP E  50 
 HIS   0.003   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10899)
  covalent geometry    : angle       0.58686 (14963)
  hydrogen bonds       : bond        0.04336 (  386)
  hydrogen bonds       : angle       5.25452 ( 1003)
  Misc. bond           : bond        0.00077 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 344
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7494 (mttt) cc_final: 0.7175 (mttt)
REVERT: A   24 ASP cc_start: 0.5545 (t70) cc_final: 0.5181 (t0)
REVERT: A   26 ILE cc_start: 0.7392 (tt) cc_final: 0.7184 (tt)
REVERT: A   55 ASP cc_start: 0.7793 (t0) cc_final: 0.7545 (t0)
REVERT: A   57 LEU cc_start: 0.8131 (mt) cc_final: 0.7876 (mt)
REVERT: A   69 LYS cc_start: 0.7749 (mppt) cc_final: 0.7201 (mmtm)
REVERT: A   79 LEU cc_start: 0.7512 (mt) cc_final: 0.7270 (mt)
REVERT: A   91 LEU cc_start: 0.8084 (tp) cc_final: 0.7740 (tt)
REVERT: A  116 LYS cc_start: 0.7979 (mtmm) cc_final: 0.7626 (tppt)
REVERT: A  136 PHE cc_start: 0.6851 (p90) cc_final: 0.6541 (p90)
REVERT: A  156 GLU cc_start: 0.7976 (mp0) cc_final: 0.7772 (mm-30)
REVERT: A  227 LEU cc_start: 0.7433 (tp) cc_final: 0.7059 (tt)
REVERT: A  229 MET cc_start: 0.6333 (ttt) cc_final: 0.6078 (ttt)
REVERT: B   21 ASP cc_start: 0.7588 (t0) cc_final: 0.6548 (t0)
REVERT: B   66 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7908 (mmmt)
REVERT: B  107 THR cc_start: 0.8048 (p) cc_final: 0.7766 (t)
REVERT: B  132 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7741 (ttmm)
REVERT: B  145 ASP cc_start: 0.6458 (m-30) cc_final: 0.6133 (t0)
REVERT: B  153 VAL cc_start: 0.8234 (t) cc_final: 0.7983 (p)
REVERT: B  159 LYS cc_start: 0.7766 (ttpp) cc_final: 0.7528 (ttmm)
REVERT: B  162 LYS cc_start: 0.7909 (mttp) cc_final: 0.7441 (mttp)
REVERT: C    2 LYS cc_start: 0.7552 (tppt) cc_final: 0.7328 (tppt)
REVERT: C    3 VAL cc_start: 0.8501 (t) cc_final: 0.7937 (p)
REVERT: C    7 ASP cc_start: 0.7856 (t70) cc_final: 0.7484 (t0)
REVERT: C   23 ASP cc_start: 0.7928 (m-30) cc_final: 0.7503 (m-30)
REVERT: C   75 MET cc_start: 0.6955 (tmm) cc_final: 0.6672 (tpp)
REVERT: C   76 LYS cc_start: 0.8102 (ttpt) cc_final: 0.7756 (ttmt)
REVERT: C   84 LYS cc_start: 0.7756 (mttp) cc_final: 0.7507 (mttp)
REVERT: C   85 GLU cc_start: 0.7365 (mp0) cc_final: 0.6899 (mp0)
REVERT: C  130 ILE cc_start: 0.8678 (mp) cc_final: 0.8425 (mm)
REVERT: C  165 LYS cc_start: 0.8027 (pttp) cc_final: 0.7453 (ptpt)
REVERT: C  167 GLU cc_start: 0.7419 (pp20) cc_final: 0.7215 (pp20)
REVERT: C  171 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6968 (mm-30)
REVERT: C  205 LEU cc_start: 0.8179 (mt) cc_final: 0.7854 (tp)
REVERT: C  209 LYS cc_start: 0.8146 (ptmm) cc_final: 0.7615 (ptmm)
REVERT: C  215 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7800 (ttmm)
REVERT: E    6 ILE cc_start: 0.6726 (tp) cc_final: 0.6338 (tp)
REVERT: E   36 THR cc_start: 0.7744 (p) cc_final: 0.7321 (p)
REVERT: E   49 LEU cc_start: 0.7271 (mt) cc_final: 0.6973 (mt)
REVERT: E   93 GLU cc_start: 0.8034 (tp30) cc_final: 0.7679 (tp30)
REVERT: E  101 LYS cc_start: 0.8528 (pttm) cc_final: 0.8104 (pttm)
REVERT: E  110 PHE cc_start: 0.6447 (m-80) cc_final: 0.5764 (m-80)
REVERT: E  126 SER cc_start: 0.8308 (t) cc_final: 0.7802 (p)
REVERT: E  127 THR cc_start: 0.8135 (m) cc_final: 0.7847 (m)
REVERT: E  135 THR cc_start: 0.8001 (m) cc_final: 0.7785 (p)
REVERT: E  142 LEU cc_start: 0.8124 (mt) cc_final: 0.7860 (mt)
REVERT: E  174 ILE cc_start: 0.7968 (mm) cc_final: 0.7641 (tt)
REVERT: E  194 SER cc_start: 0.7881 (p) cc_final: 0.7353 (p)
REVERT: E  197 ILE cc_start: 0.7978 (mm) cc_final: 0.7548 (tp)
REVERT: E  198 GLU cc_start: 0.6986 (tt0) cc_final: 0.6689 (pt0)
REVERT: E  203 LEU cc_start: 0.7741 (mt) cc_final: 0.7525 (mt)
REVERT: E  223 LYS cc_start: 0.7519 (mmtp) cc_final: 0.7247 (mmtm)
REVERT: E  239 GLU cc_start: 0.7575 (tp30) cc_final: 0.6441 (mp0)
REVERT: E  265 ARG cc_start: 0.7775 (mtp180) cc_final: 0.7039 (mtp180)
REVERT: E  274 LYS cc_start: 0.7048 (mppt) cc_final: 0.6605 (mppt)
REVERT: E  281 ARG cc_start: 0.7052 (mtm180) cc_final: 0.6567 (mtm180)
REVERT: E  290 PRO cc_start: 0.8005 (Cg_endo) cc_final: 0.7612 (Cg_exo)
REVERT: E  325 GLN cc_start: 0.7141 (mm-40) cc_final: 0.6799 (tp40)
REVERT: E  326 GLU cc_start: 0.7695 (tp30) cc_final: 0.6844 (tp30)
REVERT: E  328 MET cc_start: 0.7434 (mtm) cc_final: 0.7129 (mtm)
REVERT: E  329 HIS cc_start: 0.7201 (m90) cc_final: 0.5832 (m90)
REVERT: E  363 LYS cc_start: 0.8322 (mmtt) cc_final: 0.8090 (mmtp)
REVERT: E  397 LYS cc_start: 0.7754 (mmmt) cc_final: 0.7346 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 344
  average time/residue: 0.1277
  time to fit residues: 57.6373
Evaluate side-chains
  311 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 311
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0570
   chunk 6 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0470
   chunk 110 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.4796

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.137051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.115574 restraints weight = 18999.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.118116 restraints weight = 12042.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.119920 restraints weight = 8600.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.121178 restraints weight = 6704.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.121987 restraints weight = 5570.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3576
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6892
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10900  Z= 0.121
  Angle     :  0.585   8.638  14963  Z= 0.310
  Chirality :  0.043   0.162   1723
  Planarity :  0.004   0.051   1683
  Dihedral  : 20.843 149.170   1931
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  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: -1.95 (0.25), residues: 1171
  helix: -0.30 (0.31), residues: 307
  sheet:  0.21 (0.32), residues: 322
  loop : -2.95 (0.23), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 103 
 TYR   0.015   0.001   TYR E 354 
 PHE   0.027   0.002   PHE A  30 
 TRP   0.018   0.002   TRP E  50 
 HIS   0.003   0.000   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10899)
  covalent geometry    : angle       0.58478 (14963)
  hydrogen bonds       : bond        0.03897 (  386)
  hydrogen bonds       : angle       5.10407 ( 1003)
  Misc. bond           : bond        0.00109 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 338
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 PHE cc_start: 0.6260 (t80) cc_final: 0.6001 (t80)
REVERT: A   24 ASP cc_start: 0.5711 (t70) cc_final: 0.5279 (t0)
REVERT: A   55 ASP cc_start: 0.7707 (t0) cc_final: 0.7477 (t0)
REVERT: A   57 LEU cc_start: 0.8056 (mt) cc_final: 0.7820 (mt)
REVERT: A   69 LYS cc_start: 0.7823 (mppt) cc_final: 0.7502 (mmtp)
REVERT: A   91 LEU cc_start: 0.7884 (tp) cc_final: 0.7339 (tt)
REVERT: A  116 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7612 (tppt)
REVERT: A  119 LYS cc_start: 0.7100 (mppt) cc_final: 0.6843 (mppt)
REVERT: A  206 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7772 (ttmm)
REVERT: A  229 MET cc_start: 0.6327 (ttt) cc_final: 0.6054 (ttt)
REVERT: B   21 ASP cc_start: 0.7612 (t0) cc_final: 0.6545 (t0)
REVERT: B   32 LYS cc_start: 0.8123 (tmtt) cc_final: 0.7904 (tptp)
REVERT: B  107 THR cc_start: 0.8032 (p) cc_final: 0.7720 (t)
REVERT: B  132 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7696 (ttmm)
REVERT: B  153 VAL cc_start: 0.8212 (t) cc_final: 0.7939 (p)
REVERT: B  159 LYS cc_start: 0.7738 (ttpp) cc_final: 0.7507 (ttmm)
REVERT: B  162 LYS cc_start: 0.7749 (mttp) cc_final: 0.7297 (mttp)
REVERT: C    3 VAL cc_start: 0.8424 (t) cc_final: 0.7991 (p)
REVERT: C    7 ASP cc_start: 0.7834 (t70) cc_final: 0.7450 (t0)
REVERT: C   16 GLN cc_start: 0.7892 (tp40) cc_final: 0.7549 (tp40)
REVERT: C   75 MET cc_start: 0.6931 (tmm) cc_final: 0.6690 (tpp)
REVERT: C   84 LYS cc_start: 0.7678 (mttp) cc_final: 0.7409 (mttp)
REVERT: C  130 ILE cc_start: 0.8675 (mp) cc_final: 0.8404 (mm)
REVERT: C  165 LYS cc_start: 0.7976 (pttp) cc_final: 0.7308 (ptpt)
REVERT: C  171 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6882 (mm-30)
REVERT: C  190 LYS cc_start: 0.8434 (mtpt) cc_final: 0.8151 (mtpt)
REVERT: C  193 LYS cc_start: 0.7886 (mppt) cc_final: 0.7646 (mppt)
REVERT: C  195 SER cc_start: 0.8403 (m) cc_final: 0.8162 (p)
REVERT: C  205 LEU cc_start: 0.8152 (mt) cc_final: 0.7886 (tp)
REVERT: C  209 LYS cc_start: 0.8140 (ptmm) cc_final: 0.7795 (ttpp)
REVERT: E    6 ILE cc_start: 0.6665 (tp) cc_final: 0.6300 (tp)
REVERT: E   15 LYS cc_start: 0.8425 (mtmm) cc_final: 0.7982 (mmtm)
REVERT: E   93 GLU cc_start: 0.7984 (tp30) cc_final: 0.7654 (tp30)
REVERT: E  101 LYS cc_start: 0.8530 (pttm) cc_final: 0.8108 (pttm)
REVERT: E  110 PHE cc_start: 0.6297 (m-80) cc_final: 0.5700 (m-80)
REVERT: E  126 SER cc_start: 0.8305 (t) cc_final: 0.7844 (p)
REVERT: E  127 THR cc_start: 0.8166 (m) cc_final: 0.7809 (p)
REVERT: E  135 THR cc_start: 0.7915 (m) cc_final: 0.7582 (p)
REVERT: E  174 ILE cc_start: 0.7989 (mm) cc_final: 0.7677 (tp)
REVERT: E  194 SER cc_start: 0.7890 (p) cc_final: 0.6736 (p)
REVERT: E  197 ILE cc_start: 0.7932 (mm) cc_final: 0.7497 (tp)
REVERT: E  223 LYS cc_start: 0.7438 (mmtp) cc_final: 0.7147 (mmtm)
REVERT: E  239 GLU cc_start: 0.7346 (tp30) cc_final: 0.6318 (mp0)
REVERT: E  265 ARG cc_start: 0.7747 (mtp180) cc_final: 0.7038 (mtp180)
REVERT: E  274 LYS cc_start: 0.7064 (mppt) cc_final: 0.6569 (mppt)
REVERT: E  290 PRO cc_start: 0.7970 (Cg_endo) cc_final: 0.7639 (Cg_exo)
REVERT: E  325 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6678 (tp40)
REVERT: E  326 GLU cc_start: 0.7670 (tp30) cc_final: 0.6720 (tp30)
REVERT: E  328 MET cc_start: 0.7383 (mtm) cc_final: 0.7090 (mtm)
REVERT: E  329 HIS cc_start: 0.7149 (m90) cc_final: 0.5953 (m90)
REVERT: E  363 LYS cc_start: 0.8295 (mmtt) cc_final: 0.8040 (mmtp)
REVERT: E  394 GLU cc_start: 0.7297 (pm20) cc_final: 0.6958 (tp30)
REVERT: E  397 LYS cc_start: 0.7683 (mmmt) cc_final: 0.7342 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 338
  average time/residue: 0.1286
  time to fit residues: 57.2032
Evaluate side-chains
  307 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 307
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 90 optimal weight:    5.9990
   chunk 1 optimal weight:    0.4980
   chunk 30 optimal weight:    0.1980
   chunk 97 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 114 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 115 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B 157 HIS
E 102 GLN
** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.136007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.114722 restraints weight = 19421.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.117266 restraints weight = 12333.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.119067 restraints weight = 8781.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.120306 restraints weight = 6818.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.121208 restraints weight = 5661.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3551
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3551 r_free = 0.3551    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3551 r_free = 0.3551    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3551
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6915
moved from start:          0.3700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10900  Z= 0.146
  Angle     :  0.611   9.786  14963  Z= 0.326
  Chirality :  0.044   0.160   1723
  Planarity :  0.004   0.051   1683
  Dihedral  : 20.930 148.688   1931
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.94 (0.25), residues: 1171
  helix: -0.30 (0.31), residues: 306
  sheet:  0.20 (0.32), residues: 322
  loop : -2.93 (0.23), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 103 
 TYR   0.019   0.002   TYR E 354 
 PHE   0.022   0.002   PHE E  10 
 TRP   0.018   0.002   TRP E  50 
 HIS   0.007   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (10899)
  covalent geometry    : angle       0.61146 (14963)
  hydrogen bonds       : bond        0.04307 (  386)
  hydrogen bonds       : angle       5.06138 ( 1003)
  Misc. bond           : bond        0.00124 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  340 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 340
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.5690 (t70) cc_final: 0.5321 (t0)
REVERT: A   55 ASP cc_start: 0.7646 (t0) cc_final: 0.7297 (t0)
REVERT: A   57 LEU cc_start: 0.8062 (mt) cc_final: 0.7779 (mt)
REVERT: A   59 GLU cc_start: 0.7904 (tp30) cc_final: 0.7626 (tp30)
REVERT: A   69 LYS cc_start: 0.7821 (mppt) cc_final: 0.7482 (mmtp)
REVERT: A   91 LEU cc_start: 0.7928 (tp) cc_final: 0.7276 (tt)
REVERT: A   99 LYS cc_start: 0.8007 (tptt) cc_final: 0.7760 (tppp)
REVERT: A  116 LYS cc_start: 0.7962 (mtmm) cc_final: 0.7630 (tptt)
REVERT: A  119 LYS cc_start: 0.7039 (mppt) cc_final: 0.6825 (mppt)
REVERT: A  143 LEU cc_start: 0.7607 (mm) cc_final: 0.7280 (mt)
REVERT: A  206 LYS cc_start: 0.7898 (ttmm) cc_final: 0.7679 (ttmm)
REVERT: A  227 LEU cc_start: 0.7499 (tp) cc_final: 0.7154 (tt)
REVERT: A  229 MET cc_start: 0.6295 (ttt) cc_final: 0.6054 (ttt)
REVERT: B   21 ASP cc_start: 0.7345 (t0) cc_final: 0.6260 (t0)
REVERT: B   22 PHE cc_start: 0.7406 (m-10) cc_final: 0.7135 (m-10)
REVERT: B  107 THR cc_start: 0.8043 (p) cc_final: 0.7768 (t)
REVERT: B  132 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7708 (ttmm)
REVERT: B  153 VAL cc_start: 0.8311 (t) cc_final: 0.8039 (p)
REVERT: B  162 LYS cc_start: 0.7729 (mttp) cc_final: 0.7288 (mttp)
REVERT: C    3 VAL cc_start: 0.8577 (t) cc_final: 0.8101 (p)
REVERT: C    7 ASP cc_start: 0.7662 (t70) cc_final: 0.7116 (t0)
REVERT: C   16 GLN cc_start: 0.8026 (tp40) cc_final: 0.7561 (tp40)
REVERT: C   28 LYS cc_start: 0.8051 (mttp) cc_final: 0.6970 (mttm)
REVERT: C   30 LYS cc_start: 0.7751 (mmtp) cc_final: 0.7533 (tppp)
REVERT: C   35 GLU cc_start: 0.6915 (mp0) cc_final: 0.6412 (mp0)
REVERT: C   76 LYS cc_start: 0.8063 (ttpt) cc_final: 0.7829 (ttpt)
REVERT: C   84 LYS cc_start: 0.7728 (mttp) cc_final: 0.7466 (mttp)
REVERT: C   85 GLU cc_start: 0.7505 (mp0) cc_final: 0.6841 (mp0)
REVERT: C  130 ILE cc_start: 0.8707 (mp) cc_final: 0.8450 (mm)
REVERT: C  165 LYS cc_start: 0.7799 (pttp) cc_final: 0.7518 (ptpt)
REVERT: C  171 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6884 (mm-30)
REVERT: C  205 LEU cc_start: 0.8256 (mt) cc_final: 0.7950 (tp)
REVERT: C  209 LYS cc_start: 0.8156 (ptmm) cc_final: 0.7821 (ttpp)
REVERT: C  220 ASN cc_start: 0.6597 (t0) cc_final: 0.6361 (t0)
REVERT: E    1 MET cc_start: 0.7087 (mtm) cc_final: 0.6883 (mtm)
REVERT: E    6 ILE cc_start: 0.6852 (tp) cc_final: 0.6188 (tt)
REVERT: E   36 THR cc_start: 0.7534 (p) cc_final: 0.7081 (p)
REVERT: E   86 LYS cc_start: 0.7740 (tptm) cc_final: 0.7513 (mmmm)
REVERT: E   93 GLU cc_start: 0.7895 (tp30) cc_final: 0.7578 (tp30)
REVERT: E  126 SER cc_start: 0.8268 (t) cc_final: 0.7863 (p)
REVERT: E  127 THR cc_start: 0.8154 (m) cc_final: 0.7785 (p)
REVERT: E  135 THR cc_start: 0.8293 (m) cc_final: 0.7995 (p)
REVERT: E  174 ILE cc_start: 0.7956 (mm) cc_final: 0.7623 (tp)
REVERT: E  194 SER cc_start: 0.7478 (p) cc_final: 0.6508 (p)
REVERT: E  198 GLU cc_start: 0.6356 (pm20) cc_final: 0.6009 (pm20)
REVERT: E  223 LYS cc_start: 0.7485 (mmtp) cc_final: 0.7277 (mmtm)
REVERT: E  226 LYS cc_start: 0.6715 (tptt) cc_final: 0.6494 (tppt)
REVERT: E  236 MET cc_start: 0.7660 (ptp) cc_final: 0.7452 (ptp)
REVERT: E  239 GLU cc_start: 0.7319 (tp30) cc_final: 0.6334 (mp0)
REVERT: E  248 LEU cc_start: 0.6721 (mp) cc_final: 0.6495 (mp)
REVERT: E  265 ARG cc_start: 0.7784 (mtp180) cc_final: 0.7076 (mtp-110)
REVERT: E  274 LYS cc_start: 0.7051 (mppt) cc_final: 0.6544 (mppt)
REVERT: E  281 ARG cc_start: 0.6680 (mtm180) cc_final: 0.6304 (mtm110)
REVERT: E  290 PRO cc_start: 0.7959 (Cg_endo) cc_final: 0.7621 (Cg_exo)
REVERT: E  325 GLN cc_start: 0.7092 (mm-40) cc_final: 0.6741 (tp40)
REVERT: E  326 GLU cc_start: 0.7675 (tp30) cc_final: 0.6680 (tp30)
REVERT: E  328 MET cc_start: 0.7354 (mtm) cc_final: 0.6987 (mtm)
REVERT: E  329 HIS cc_start: 0.7196 (m90) cc_final: 0.6029 (m90)
REVERT: E  360 TYR cc_start: 0.7266 (m-80) cc_final: 0.7050 (m-10)
REVERT: E  363 LYS cc_start: 0.8319 (mmtt) cc_final: 0.8116 (mmtp)
REVERT: E  394 GLU cc_start: 0.7299 (pm20) cc_final: 0.6970 (tp30)
REVERT: E  397 LYS cc_start: 0.7681 (mmmt) cc_final: 0.7390 (mmtp)
REVERT: E  409 GLU cc_start: 0.6532 (mt-10) cc_final: 0.6296 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 340
  average time/residue: 0.1270
  time to fit residues: 56.4140
Evaluate side-chains
  318 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 318
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 106 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   chunk 114 optimal weight:    2.9990
   chunk 79 optimal weight:    0.2980
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.135514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.114236 restraints weight = 19121.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.116815 restraints weight = 12113.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.118612 restraints weight = 8627.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.119726 restraints weight = 6717.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.120722 restraints weight = 5623.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3559
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3559 r_free = 0.3559    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3559 r_free = 0.3559    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3559
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.3831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10900  Z= 0.153
  Angle     :  0.628  10.056  14963  Z= 0.332
  Chirality :  0.044   0.171   1723
  Planarity :  0.004   0.053   1683
  Dihedral  : 20.975 149.600   1931
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  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: -1.91 (0.25), residues: 1171
  helix: -0.31 (0.31), residues: 306
  sheet:  0.26 (0.32), residues: 317
  loop : -2.88 (0.23), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 103 
 TYR   0.018   0.002   TYR E 354 
 PHE   0.023   0.002   PHE A  30 
 TRP   0.024   0.002   TRP E  50 
 HIS   0.003   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (10899)
  covalent geometry    : angle       0.62829 (14963)
  hydrogen bonds       : bond        0.04359 (  386)
  hydrogen bonds       : angle       5.01502 ( 1003)
  Misc. bond           : bond        0.00116 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 341
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.5802 (t70) cc_final: 0.5382 (t0)
REVERT: A   59 GLU cc_start: 0.7856 (tp30) cc_final: 0.7486 (tp30)
REVERT: A   69 LYS cc_start: 0.7819 (mppt) cc_final: 0.7432 (mmtp)
REVERT: A   99 LYS cc_start: 0.8088 (tptt) cc_final: 0.7830 (tppp)
REVERT: A  110 LYS cc_start: 0.7118 (ttmt) cc_final: 0.6847 (ttmm)
REVERT: A  116 LYS cc_start: 0.8006 (mtmm) cc_final: 0.7770 (tptt)
REVERT: A  119 LYS cc_start: 0.7042 (mppt) cc_final: 0.6837 (mppt)
REVERT: A  143 LEU cc_start: 0.7647 (mm) cc_final: 0.7328 (mt)
REVERT: A  206 LYS cc_start: 0.7925 (ttmm) cc_final: 0.7642 (ttmm)
REVERT: A  227 LEU cc_start: 0.7528 (tp) cc_final: 0.7145 (tt)
REVERT: A  229 MET cc_start: 0.6258 (ttt) cc_final: 0.6057 (ttt)
REVERT: B   21 ASP cc_start: 0.7375 (t0) cc_final: 0.6201 (t0)
REVERT: B   22 PHE cc_start: 0.7525 (m-10) cc_final: 0.7176 (m-10)
REVERT: B   30 VAL cc_start: 0.8118 (t) cc_final: 0.7898 (t)
REVERT: B   35 ILE cc_start: 0.8452 (mm) cc_final: 0.8175 (tp)
REVERT: B  132 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7697 (ttmm)
REVERT: B  153 VAL cc_start: 0.8318 (t) cc_final: 0.8080 (p)
REVERT: B  162 LYS cc_start: 0.7694 (mttp) cc_final: 0.7336 (mttp)
REVERT: C    3 VAL cc_start: 0.8512 (t) cc_final: 0.8105 (p)
REVERT: C    7 ASP cc_start: 0.7656 (t70) cc_final: 0.7227 (t0)
REVERT: C   16 GLN cc_start: 0.7933 (tp40) cc_final: 0.7216 (tp40)
REVERT: C   75 MET cc_start: 0.7521 (tpp) cc_final: 0.7104 (tpp)
REVERT: C  165 LYS cc_start: 0.7858 (pttp) cc_final: 0.7548 (ptpt)
REVERT: C  171 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6890 (mm-30)
REVERT: C  195 SER cc_start: 0.8537 (m) cc_final: 0.8166 (p)
REVERT: C  205 LEU cc_start: 0.8223 (mt) cc_final: 0.7948 (tp)
REVERT: C  209 LYS cc_start: 0.8151 (ptmm) cc_final: 0.7848 (ttpp)
REVERT: C  220 ASN cc_start: 0.6628 (t0) cc_final: 0.6309 (t0)
REVERT: E    1 MET cc_start: 0.7203 (mtm) cc_final: 0.6958 (mtm)
REVERT: E    6 ILE cc_start: 0.6800 (tp) cc_final: 0.6429 (tp)
REVERT: E   15 LYS cc_start: 0.8584 (mtmm) cc_final: 0.8074 (mmtt)
REVERT: E   36 THR cc_start: 0.7519 (p) cc_final: 0.7115 (p)
REVERT: E   93 GLU cc_start: 0.7954 (tp30) cc_final: 0.7619 (tp30)
REVERT: E  101 LYS cc_start: 0.8488 (pttm) cc_final: 0.8234 (pttm)
REVERT: E  110 PHE cc_start: 0.6534 (m-80) cc_final: 0.6097 (m-80)
REVERT: E  126 SER cc_start: 0.8297 (t) cc_final: 0.7823 (p)
REVERT: E  171 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7874 (mtm-85)
REVERT: E  174 ILE cc_start: 0.8016 (mm) cc_final: 0.7589 (tp)
REVERT: E  194 SER cc_start: 0.7407 (p) cc_final: 0.6501 (p)
REVERT: E  198 GLU cc_start: 0.6359 (pm20) cc_final: 0.5963 (pm20)
REVERT: E  224 THR cc_start: 0.7116 (p) cc_final: 0.6864 (p)
REVERT: E  226 LYS cc_start: 0.6743 (tptt) cc_final: 0.6503 (tppt)
REVERT: E  239 GLU cc_start: 0.7310 (tp30) cc_final: 0.6296 (mp0)
REVERT: E  274 LYS cc_start: 0.7126 (mppt) cc_final: 0.6538 (mppt)
REVERT: E  281 ARG cc_start: 0.6768 (mtm180) cc_final: 0.6496 (mtm180)
REVERT: E  283 GLU cc_start: 0.6938 (pm20) cc_final: 0.6643 (pm20)
REVERT: E  290 PRO cc_start: 0.7957 (Cg_endo) cc_final: 0.7526 (Cg_exo)
REVERT: E  291 ASP cc_start: 0.7546 (p0) cc_final: 0.7095 (p0)
REVERT: E  325 GLN cc_start: 0.7049 (mm-40) cc_final: 0.6701 (tp40)
REVERT: E  326 GLU cc_start: 0.7680 (tp30) cc_final: 0.6632 (tp30)
REVERT: E  328 MET cc_start: 0.7405 (mtm) cc_final: 0.7023 (mtm)
REVERT: E  329 HIS cc_start: 0.7227 (m90) cc_final: 0.6019 (m90)
REVERT: E  363 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8108 (mmtp)
REVERT: E  394 GLU cc_start: 0.7286 (pm20) cc_final: 0.6933 (tp30)
REVERT: E  397 LYS cc_start: 0.7694 (mmmt) cc_final: 0.7383 (mmtp)
REVERT: E  409 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6361 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 341
  average time/residue: 0.1280
  time to fit residues: 57.0907
Evaluate side-chains
  312 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 312
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 78 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9980
   chunk 111 optimal weight:    6.9990
   chunk 63 optimal weight:    0.3980
   chunk 41 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 157 HIS
** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.135515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.114093 restraints weight = 19095.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.116651 restraints weight = 12162.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.118427 restraints weight = 8698.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.119646 restraints weight = 6775.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.120539 restraints weight = 5649.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3554
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3554 r_free = 0.3554    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3554 r_free = 0.3554    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3554
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.3962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10900  Z= 0.148
  Angle     :  0.647   9.027  14963  Z= 0.343
  Chirality :  0.045   0.183   1723
  Planarity :  0.004   0.053   1683
  Dihedral  : 20.991 149.582   1931
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  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: -1.94 (0.25), residues: 1171
  helix: -0.32 (0.31), residues: 306
  sheet:  0.27 (0.32), residues: 314
  loop : -2.91 (0.23), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 103 
 TYR   0.017   0.001   TYR E 354 
 PHE   0.025   0.002   PHE C  65 
 TRP   0.027   0.002   TRP E  50 
 HIS   0.007   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (10899)
  covalent geometry    : angle       0.64689 (14963)
  hydrogen bonds       : bond        0.04328 (  386)
  hydrogen bonds       : angle       5.05106 ( 1003)
  Misc. bond           : bond        0.00105 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 337
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.5867 (t70) cc_final: 0.5459 (t0)
REVERT: A   55 ASP cc_start: 0.7594 (t0) cc_final: 0.7287 (t0)
REVERT: A   59 GLU cc_start: 0.7861 (tp30) cc_final: 0.7392 (tp30)
REVERT: A   69 LYS cc_start: 0.7837 (mppt) cc_final: 0.7486 (mmtp)
REVERT: A   93 GLU cc_start: 0.8822 (pp20) cc_final: 0.8230 (pp20)
REVERT: A  110 LYS cc_start: 0.7100 (ttmt) cc_final: 0.6885 (ttmm)
REVERT: A  116 LYS cc_start: 0.8024 (mtmm) cc_final: 0.7745 (tptt)
REVERT: A  143 LEU cc_start: 0.7666 (mm) cc_final: 0.7351 (mt)
REVERT: A  206 LYS cc_start: 0.7911 (ttmm) cc_final: 0.7660 (ttmm)
REVERT: A  227 LEU cc_start: 0.7540 (tp) cc_final: 0.7107 (tt)
REVERT: B   21 ASP cc_start: 0.7335 (t0) cc_final: 0.6181 (t0)
REVERT: B   22 PHE cc_start: 0.7569 (m-10) cc_final: 0.7179 (m-10)
REVERT: B   33 GLU cc_start: 0.7444 (mp0) cc_final: 0.7002 (mp0)
REVERT: B   35 ILE cc_start: 0.8443 (mm) cc_final: 0.8189 (tp)
REVERT: B  132 LYS cc_start: 0.7941 (ttmt) cc_final: 0.7669 (ttmm)
REVERT: B  153 VAL cc_start: 0.8325 (t) cc_final: 0.8094 (p)
REVERT: B  159 LYS cc_start: 0.7727 (ttmm) cc_final: 0.7472 (ttmm)
REVERT: B  162 LYS cc_start: 0.7709 (mttp) cc_final: 0.7327 (mttp)
REVERT: C    3 VAL cc_start: 0.8538 (t) cc_final: 0.8019 (p)
REVERT: C    7 ASP cc_start: 0.7635 (t70) cc_final: 0.7197 (t0)
REVERT: C   24 GLU cc_start: 0.7315 (mp0) cc_final: 0.7114 (mp0)
REVERT: C   28 LYS cc_start: 0.8179 (mttm) cc_final: 0.7753 (mttp)
REVERT: C   70 ASN cc_start: 0.8533 (t0) cc_final: 0.8298 (t0)
REVERT: C   77 ILE cc_start: 0.8334 (pt) cc_final: 0.8112 (tt)
REVERT: C   84 LYS cc_start: 0.7751 (mttp) cc_final: 0.7436 (mttp)
REVERT: C   88 GLU cc_start: 0.7180 (pp20) cc_final: 0.6590 (pp20)
REVERT: C  109 PHE cc_start: 0.8174 (m-80) cc_final: 0.7883 (m-80)
REVERT: C  140 LYS cc_start: 0.7936 (ttpt) cc_final: 0.7684 (tttm)
REVERT: C  165 LYS cc_start: 0.7817 (pttp) cc_final: 0.7483 (ptpt)
REVERT: C  171 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6885 (mm-30)
REVERT: C  175 GLU cc_start: 0.6915 (pt0) cc_final: 0.6631 (pt0)
REVERT: C  195 SER cc_start: 0.8529 (m) cc_final: 0.8140 (p)
REVERT: C  205 LEU cc_start: 0.8215 (mt) cc_final: 0.7984 (tp)
REVERT: C  209 LYS cc_start: 0.8156 (ptmm) cc_final: 0.7850 (ttpp)
REVERT: E    1 MET cc_start: 0.7246 (mtm) cc_final: 0.6975 (mtm)
REVERT: E   36 THR cc_start: 0.7775 (p) cc_final: 0.7358 (p)
REVERT: E   86 LYS cc_start: 0.7841 (tptm) cc_final: 0.7616 (mmmm)
REVERT: E   93 GLU cc_start: 0.7925 (tp30) cc_final: 0.7608 (tp30)
REVERT: E  101 LYS cc_start: 0.8489 (pttm) cc_final: 0.8235 (pttm)
REVERT: E  110 PHE cc_start: 0.6780 (m-80) cc_final: 0.6435 (m-80)
REVERT: E  126 SER cc_start: 0.8293 (t) cc_final: 0.7794 (p)
REVERT: E  127 THR cc_start: 0.8025 (m) cc_final: 0.7713 (m)
REVERT: E  174 ILE cc_start: 0.8049 (mm) cc_final: 0.7608 (tp)
REVERT: E  198 GLU cc_start: 0.6316 (pm20) cc_final: 0.6105 (pm20)
REVERT: E  209 ASN cc_start: 0.7893 (p0) cc_final: 0.7299 (p0)
REVERT: E  224 THR cc_start: 0.7138 (p) cc_final: 0.6884 (p)
REVERT: E  239 GLU cc_start: 0.7324 (tp30) cc_final: 0.6292 (mp0)
REVERT: E  265 ARG cc_start: 0.7523 (mtp180) cc_final: 0.6704 (mtp180)
REVERT: E  274 LYS cc_start: 0.7179 (mppt) cc_final: 0.6574 (mppt)
REVERT: E  281 ARG cc_start: 0.6855 (mtm180) cc_final: 0.6525 (mtm180)
REVERT: E  290 PRO cc_start: 0.7875 (Cg_endo) cc_final: 0.7450 (Cg_exo)
REVERT: E  321 MET cc_start: 0.5966 (mmp) cc_final: 0.5763 (mmp)
REVERT: E  326 GLU cc_start: 0.7677 (tp30) cc_final: 0.6660 (tp30)
REVERT: E  329 HIS cc_start: 0.7194 (m90) cc_final: 0.5829 (m90)
REVERT: E  394 GLU cc_start: 0.7304 (pm20) cc_final: 0.6933 (tp30)
REVERT: E  397 LYS cc_start: 0.7685 (mmmt) cc_final: 0.7375 (mmtp)
REVERT: E  409 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6357 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 337
  average time/residue: 0.1249
  time to fit residues: 55.1665
Evaluate side-chains
  317 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 317
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 104 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0020
   chunk 73 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 119 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.9190

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

Flipped N/Q/H residues before XYZ refinement:
B 116 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.135012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.113577 restraints weight = 19140.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.116093 restraints weight = 12110.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.117856 restraints weight = 8660.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.119117 restraints weight = 6764.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.119897 restraints weight = 5637.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3542
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3542 r_free = 0.3542    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3542 r_free = 0.3542    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3542
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.4075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10900  Z= 0.159
  Angle     :  0.669   9.058  14963  Z= 0.354
  Chirality :  0.045   0.171   1723
  Planarity :  0.004   0.051   1683
  Dihedral  : 21.050 150.840   1931
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.48 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  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: -2.02 (0.24), residues: 1171
  helix: -0.37 (0.31), residues: 306
  sheet:  0.13 (0.31), residues: 321
  loop : -2.96 (0.23), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 103 
 TYR   0.018   0.002   TYR C  59 
 PHE   0.022   0.002   PHE E  10 
 TRP   0.030   0.003   TRP E  50 
 HIS   0.003   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (10899)
  covalent geometry    : angle       0.66918 (14963)
  hydrogen bonds       : bond        0.04526 (  386)
  hydrogen bonds       : angle       5.05886 ( 1003)
  Misc. bond           : bond        0.00108 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 337
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.8110 (ttpt) cc_final: 0.7318 (tmmt)
REVERT: A   24 ASP cc_start: 0.5942 (t70) cc_final: 0.5542 (t0)
REVERT: A   55 ASP cc_start: 0.7580 (t0) cc_final: 0.7261 (t0)
REVERT: A   57 LEU cc_start: 0.8000 (mt) cc_final: 0.7794 (mt)
REVERT: A   69 LYS cc_start: 0.7857 (mppt) cc_final: 0.7503 (mmtt)
REVERT: A   93 GLU cc_start: 0.8699 (pp20) cc_final: 0.8498 (pp20)
REVERT: A  116 LYS cc_start: 0.8012 (mtmm) cc_final: 0.7753 (tptt)
REVERT: A  206 LYS cc_start: 0.7892 (ttmm) cc_final: 0.7644 (ttmm)
REVERT: A  229 MET cc_start: 0.5908 (ttp) cc_final: 0.5553 (ttp)
REVERT: B   21 ASP cc_start: 0.7325 (t0) cc_final: 0.6168 (t0)
REVERT: B   22 PHE cc_start: 0.7598 (m-10) cc_final: 0.7188 (m-10)
REVERT: B   30 VAL cc_start: 0.8134 (t) cc_final: 0.7618 (t)
REVERT: B   33 GLU cc_start: 0.7201 (mp0) cc_final: 0.6962 (mp0)
REVERT: B   35 ILE cc_start: 0.8459 (mm) cc_final: 0.8251 (tp)
REVERT: B   66 LYS cc_start: 0.7946 (mmmt) cc_final: 0.7690 (mmmt)
REVERT: B   67 GLU cc_start: 0.5852 (mp0) cc_final: 0.5358 (mp0)
REVERT: B  107 THR cc_start: 0.8040 (p) cc_final: 0.7592 (t)
REVERT: B  132 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7642 (ttmm)
REVERT: B  153 VAL cc_start: 0.8019 (t) cc_final: 0.7799 (p)
REVERT: B  159 LYS cc_start: 0.7790 (ttmm) cc_final: 0.7534 (ttmm)
REVERT: B  162 LYS cc_start: 0.7704 (mttp) cc_final: 0.7333 (mttp)
REVERT: C    3 VAL cc_start: 0.8566 (t) cc_final: 0.8131 (p)
REVERT: C    7 ASP cc_start: 0.7665 (t70) cc_final: 0.7247 (t0)
REVERT: C   24 GLU cc_start: 0.7306 (mp0) cc_final: 0.7097 (mp0)
REVERT: C   75 MET cc_start: 0.7520 (tpp) cc_final: 0.7307 (tpp)
REVERT: C   77 ILE cc_start: 0.8363 (pt) cc_final: 0.8112 (tt)
REVERT: C   84 LYS cc_start: 0.7729 (mttp) cc_final: 0.7448 (mttp)
REVERT: C  109 PHE cc_start: 0.8197 (m-80) cc_final: 0.7812 (m-80)
REVERT: C  140 LYS cc_start: 0.7990 (ttpt) cc_final: 0.7654 (tttm)
REVERT: C  165 LYS cc_start: 0.7858 (pttp) cc_final: 0.7581 (ptpt)
REVERT: C  171 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6903 (mm-30)
REVERT: C  175 GLU cc_start: 0.6862 (pt0) cc_final: 0.6590 (pt0)
REVERT: C  195 SER cc_start: 0.8554 (m) cc_final: 0.8182 (p)
REVERT: C  209 LYS cc_start: 0.8151 (ptmm) cc_final: 0.7836 (ttpp)
REVERT: E    1 MET cc_start: 0.7268 (mtm) cc_final: 0.7039 (mtm)
REVERT: E    6 ILE cc_start: 0.6722 (tp) cc_final: 0.6475 (tp)
REVERT: E   11 ASP cc_start: 0.7116 (t0) cc_final: 0.6903 (t0)
REVERT: E   36 THR cc_start: 0.7807 (p) cc_final: 0.7389 (p)
REVERT: E   49 LEU cc_start: 0.7219 (mt) cc_final: 0.6954 (mt)
REVERT: E   86 LYS cc_start: 0.7849 (tptm) cc_final: 0.7601 (mmmm)
REVERT: E   93 GLU cc_start: 0.7880 (tp30) cc_final: 0.7583 (tp30)
REVERT: E  101 LYS cc_start: 0.8488 (pttm) cc_final: 0.8216 (pttm)
REVERT: E  110 PHE cc_start: 0.6878 (m-80) cc_final: 0.6520 (m-80)
REVERT: E  111 LEU cc_start: 0.6465 (pt) cc_final: 0.6052 (pt)
REVERT: E  126 SER cc_start: 0.8279 (t) cc_final: 0.7794 (p)
REVERT: E  127 THR cc_start: 0.8016 (m) cc_final: 0.7742 (m)
REVERT: E  174 ILE cc_start: 0.8047 (mm) cc_final: 0.7614 (tp)
REVERT: E  198 GLU cc_start: 0.6334 (pm20) cc_final: 0.6017 (pm20)
REVERT: E  203 LEU cc_start: 0.7747 (mt) cc_final: 0.7512 (mt)
REVERT: E  224 THR cc_start: 0.7067 (p) cc_final: 0.6790 (p)
REVERT: E  239 GLU cc_start: 0.7361 (tp30) cc_final: 0.6296 (mp0)
REVERT: E  265 ARG cc_start: 0.7527 (mtp180) cc_final: 0.6913 (mtp180)
REVERT: E  270 LYS cc_start: 0.7262 (tttt) cc_final: 0.7055 (ttmt)
REVERT: E  274 LYS cc_start: 0.7202 (mppt) cc_final: 0.6660 (mppt)
REVERT: E  281 ARG cc_start: 0.6824 (mtm180) cc_final: 0.6576 (mtm180)
REVERT: E  290 PRO cc_start: 0.7963 (Cg_endo) cc_final: 0.7441 (Cg_exo)
REVERT: E  291 ASP cc_start: 0.7516 (p0) cc_final: 0.7182 (p0)
REVERT: E  325 GLN cc_start: 0.7071 (tp40) cc_final: 0.6754 (tp40)
REVERT: E  326 GLU cc_start: 0.7779 (tp30) cc_final: 0.6653 (tp30)
REVERT: E  329 HIS cc_start: 0.7212 (m90) cc_final: 0.5840 (m90)
REVERT: E  394 GLU cc_start: 0.7350 (pm20) cc_final: 0.7027 (tp30)
REVERT: E  397 LYS cc_start: 0.7772 (mmmt) cc_final: 0.7446 (mmtp)
REVERT: E  409 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6414 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 337
  average time/residue: 0.1287
  time to fit residues: 56.8162
Evaluate side-chains
  310 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 310
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 115 optimal weight:    0.0020
   chunk 114 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.9590

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

Flipped N/Q/H residues before XYZ refinement:
B 116 GLN
B 157 HIS
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.134772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.113262 restraints weight = 18890.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.115853 restraints weight = 12038.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.117609 restraints weight = 8587.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.118835 restraints weight = 6722.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.119709 restraints weight = 5603.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3541
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3541 r_free = 0.3541    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3541 r_free = 0.3541    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3541
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.4182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10900  Z= 0.165
  Angle     :  0.680  11.281  14963  Z= 0.361
  Chirality :  0.046   0.175   1723
  Planarity :  0.004   0.048   1683
  Dihedral  : 21.095 151.614   1931
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.82 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  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: -2.07 (0.24), residues: 1171
  helix: -0.48 (0.30), residues: 305
  sheet:  0.13 (0.31), residues: 324
  loop : -2.97 (0.23), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 103 
 TYR   0.027   0.002   TYR B 197 
 PHE   0.032   0.002   PHE B  71 
 TRP   0.026   0.002   TRP E  50 
 HIS   0.007   0.001   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (10899)
  covalent geometry    : angle       0.68035 (14963)
  hydrogen bonds       : bond        0.04640 (  386)
  hydrogen bonds       : angle       5.04332 ( 1003)
  Misc. bond           : bond        0.00105 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 327
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.7738 (ttpt) cc_final: 0.7345 (tmmt)
REVERT: A   24 ASP cc_start: 0.5912 (t70) cc_final: 0.5534 (t0)
REVERT: A   55 ASP cc_start: 0.7745 (t0) cc_final: 0.7537 (t0)
REVERT: A   57 LEU cc_start: 0.7978 (mt) cc_final: 0.7755 (mt)
REVERT: A   69 LYS cc_start: 0.7828 (mppt) cc_final: 0.7458 (mmtp)
REVERT: A  107 SER cc_start: 0.7788 (m) cc_final: 0.7110 (p)
REVERT: A  116 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7771 (tptt)
REVERT: A  180 PHE cc_start: 0.6995 (m-80) cc_final: 0.6735 (m-80)
REVERT: A  206 LYS cc_start: 0.7913 (ttmm) cc_final: 0.7643 (ttmm)
REVERT: A  229 MET cc_start: 0.5821 (ttp) cc_final: 0.5510 (ttp)
REVERT: B   21 ASP cc_start: 0.7275 (t0) cc_final: 0.6144 (t0)
REVERT: B   22 PHE cc_start: 0.7567 (m-10) cc_final: 0.7120 (m-10)
REVERT: B   30 VAL cc_start: 0.8466 (t) cc_final: 0.7984 (t)
REVERT: B   33 GLU cc_start: 0.7129 (mp0) cc_final: 0.6894 (mp0)
REVERT: B   35 ILE cc_start: 0.8502 (mm) cc_final: 0.8277 (tp)
REVERT: B   67 GLU cc_start: 0.5871 (mp0) cc_final: 0.5396 (mp0)
REVERT: B  132 LYS cc_start: 0.7958 (ttmt) cc_final: 0.7659 (ttmm)
REVERT: B  159 LYS cc_start: 0.7830 (ttmm) cc_final: 0.7618 (ttmm)
REVERT: B  162 LYS cc_start: 0.7711 (mttp) cc_final: 0.7381 (mttp)
REVERT: C    3 VAL cc_start: 0.8459 (t) cc_final: 0.8127 (p)
REVERT: C    7 ASP cc_start: 0.7657 (t70) cc_final: 0.7211 (t0)
REVERT: C   10 VAL cc_start: 0.8102 (t) cc_final: 0.7900 (t)
REVERT: C   35 GLU cc_start: 0.7315 (pm20) cc_final: 0.7085 (pm20)
REVERT: C   55 MET cc_start: 0.6891 (ttm) cc_final: 0.6683 (ttm)
REVERT: C   77 ILE cc_start: 0.8310 (pt) cc_final: 0.8092 (tt)
REVERT: C   84 LYS cc_start: 0.7841 (mttp) cc_final: 0.7447 (mttp)
REVERT: C  140 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7710 (tttm)
REVERT: C  165 LYS cc_start: 0.7830 (pttp) cc_final: 0.7576 (ptpt)
REVERT: C  171 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6909 (mm-30)
REVERT: C  175 GLU cc_start: 0.6943 (pt0) cc_final: 0.6631 (pt0)
REVERT: C  195 SER cc_start: 0.8564 (m) cc_final: 0.8172 (p)
REVERT: C  209 LYS cc_start: 0.8159 (ptmm) cc_final: 0.7838 (ttpp)
REVERT: E    1 MET cc_start: 0.7240 (mtm) cc_final: 0.7017 (mtm)
REVERT: E   11 ASP cc_start: 0.7143 (t0) cc_final: 0.6918 (t0)
REVERT: E   36 THR cc_start: 0.7866 (p) cc_final: 0.7472 (p)
REVERT: E   49 LEU cc_start: 0.7322 (mt) cc_final: 0.7052 (mt)
REVERT: E   86 LYS cc_start: 0.7840 (tptm) cc_final: 0.7605 (mmmm)
REVERT: E   93 GLU cc_start: 0.7922 (tp30) cc_final: 0.7610 (tp30)
REVERT: E  101 LYS cc_start: 0.8502 (pttm) cc_final: 0.8225 (pttm)
REVERT: E  111 LEU cc_start: 0.6480 (pt) cc_final: 0.6079 (pt)
REVERT: E  126 SER cc_start: 0.8303 (t) cc_final: 0.7829 (p)
REVERT: E  127 THR cc_start: 0.8058 (m) cc_final: 0.7767 (m)
REVERT: E  174 ILE cc_start: 0.8022 (mm) cc_final: 0.7633 (tp)
REVERT: E  198 GLU cc_start: 0.6342 (pm20) cc_final: 0.6020 (pm20)
REVERT: E  203 LEU cc_start: 0.7767 (mt) cc_final: 0.7508 (mt)
REVERT: E  224 THR cc_start: 0.7151 (p) cc_final: 0.6947 (p)
REVERT: E  239 GLU cc_start: 0.7340 (tp30) cc_final: 0.6289 (mp0)
REVERT: E  265 ARG cc_start: 0.7501 (mtp180) cc_final: 0.6753 (mtp180)
REVERT: E  274 LYS cc_start: 0.7170 (mppt) cc_final: 0.6761 (mppt)
REVERT: E  281 ARG cc_start: 0.6842 (mtm180) cc_final: 0.6642 (mtm180)
REVERT: E  290 PRO cc_start: 0.8009 (Cg_endo) cc_final: 0.7553 (Cg_exo)
REVERT: E  291 ASP cc_start: 0.7604 (p0) cc_final: 0.7145 (p0)
REVERT: E  324 PHE cc_start: 0.7573 (t80) cc_final: 0.7114 (t80)
REVERT: E  325 GLN cc_start: 0.7273 (tp40) cc_final: 0.6878 (tp40)
REVERT: E  326 GLU cc_start: 0.7738 (tp30) cc_final: 0.6501 (tp30)
REVERT: E  329 HIS cc_start: 0.7094 (m90) cc_final: 0.5717 (m-70)
REVERT: E  394 GLU cc_start: 0.7428 (pm20) cc_final: 0.7140 (tp30)
REVERT: E  397 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7443 (mmtp)
REVERT: E  409 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6372 (mt-10)
REVERT: E  414 LYS cc_start: 0.7935 (mmpt) cc_final: 0.7727 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 327
  average time/residue: 0.1309
  time to fit residues: 55.8246
Evaluate side-chains
  304 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 304
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 81 optimal weight:    0.1980
   chunk 82 optimal weight:    0.2980
   chunk 74 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 110 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
B 116 GLN
E  75 ASN
** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.135832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.114240 restraints weight = 19136.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.116834 restraints weight = 12154.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.118619 restraints weight = 8664.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.119749 restraints weight = 6750.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.120721 restraints weight = 5656.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3553
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3553
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6915
moved from start:          0.4266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10900  Z= 0.143
  Angle     :  0.671  11.144  14963  Z= 0.354
  Chirality :  0.045   0.166   1723
  Planarity :  0.004   0.047   1683
  Dihedral  : 21.051 150.135   1931
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.24), residues: 1171
  helix: -0.50 (0.30), residues: 311
  sheet:  0.04 (0.30), residues: 331
  loop : -2.88 (0.24), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 103 
 TYR   0.021   0.002   TYR B 197 
 PHE   0.028   0.002   PHE B  71 
 TRP   0.035   0.003   TRP E  50 
 HIS   0.004   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (10899)
  covalent geometry    : angle       0.67124 (14963)
  hydrogen bonds       : bond        0.04298 (  386)
  hydrogen bonds       : angle       4.97113 ( 1003)
  Misc. bond           : bond        0.00095 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1990.39 seconds
wall clock time: 34 minutes 53.61 seconds (2093.61 seconds total)