Starting phenix.real_space_refine
on Mon Jul 28 19:55:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rpo_24618/07_2025/7rpo_24618.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rpo_24618/07_2025/7rpo_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rpo_24618/07_2025/7rpo_24618.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rpo_24618/07_2025/7rpo_24618.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rpo_24618/07_2025/7rpo_24618.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rpo_24618/07_2025/7rpo_24618.cif"
  }
  resolution = 4.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.026
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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.59, per 1000 atoms: 0.62
  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: 2.51
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 4.03
  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: 3.83

  Time building geometry restraints manager: 2.91 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:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     29.640
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.010
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.004   0.001   TRP E  50 
 HIS   0.002   0.001   HIS A  39 
 PHE   0.010   0.001   PHE C 228 
 TYR   0.008   0.001   TYR A 177 
 ARG   0.002   0.000   ARG E 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24462 (  386)
  hydrogen bonds       : angle       8.23261 ( 1003)
  covalent geometry    : bond        0.00251 (10899)
  covalent geometry    : angle       0.50240 (14963)
  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  : 1.134 
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: 0.7855 (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: 0.6243 (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: 0.7434 (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: 0.2824
  time to fit residues: 152.0839
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  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0370
   chunk 62 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 95 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0770
   chunk 110 optimal weight:    6.9990
   overall best weight:    0.7418

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.137977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.115643 restraints weight = 18451.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.118487 restraints weight = 11401.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.120469 restraints weight = 7970.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
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 = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3537 r_free = 0.3537    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3537
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6937
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10900  Z= 0.151
  Angle     :  0.600   7.351  14963  Z= 0.327
  Chirality :  0.044   0.159   1723
  Planarity :  0.004   0.051   1683
  Dihedral  : 20.775 151.983   1931
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.61 %
    Favored  : 97.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.24), residues: 1171
  helix: -0.34 (0.31), residues: 306
  sheet:  0.01 (0.31), residues: 323
  loop : -3.04 (0.23), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E  50 
 HIS   0.003   0.001   HIS A 240 
 PHE   0.021   0.002   PHE C 228 
 TYR   0.010   0.001   TYR B 201 
 ARG   0.005   0.001   ARG E 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05024 (  386)
  hydrogen bonds       : angle       5.94795 ( 1003)
  covalent geometry    : bond        0.00321 (10899)
  covalent geometry    : angle       0.59966 (14963)
  Misc. bond           : bond        0.00082 (    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: 1
    poor density    : 357
  time to evaluate  : 0.996 
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: symmetry clash
REVERT: A   24 ASP cc_start: 0.5587 (t70) cc_final: 0.5237 (t0)
REVERT: A   47 MET cc_start: 0.7229 (ttt) cc_final: 0.6965 (ttt)
REVERT: A   57 LEU cc_start: 0.8195 (mt) cc_final: 0.7889 (mt)
REVERT: A   59 GLU cc_start: 0.8339 (tp30) cc_final: 0.8125 (tp30)
REVERT: A  110 LYS cc_start: 0.7215 (ttmt) cc_final: 0.6950 (ttmm)
REVERT: A  116 LYS cc_start: 0.8070 (mtmm) cc_final: 0.7759 (tptt)
REVERT: A  212 LEU cc_start: 0.7387 (mt) cc_final: 0.7102 (tp)
REVERT: A  213 ARG cc_start: 0.6937 (mtt90) cc_final: 0.6656 (mtt90)
REVERT: A  229 MET cc_start: 0.6533 (ttt) cc_final: 0.6096 (ttt)
REVERT: B   21 ASP cc_start: 0.7536 (t0) cc_final: 0.6691 (t0)
REVERT: B  132 LYS cc_start: 0.8506 (ttmt) cc_final: 0.8065 (ttmm)
REVERT: B  159 LYS cc_start: 0.7876 (ttpp) cc_final: 0.7609 (ttmm)
REVERT: C    3 VAL cc_start: 0.8307 (t) cc_final: 0.7831 (p)
REVERT: C    6 ASP cc_start: 0.7319 (t0) cc_final: 0.7104 (t0)
REVERT: C    7 ASP cc_start: 0.7743 (t70) cc_final: 0.7349 (t0)
REVERT: C   75 MET cc_start: 0.7016 (tmm) cc_final: 0.6798 (tpp)
REVERT: C   76 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7887 (ttpt)
REVERT: C   77 ILE cc_start: 0.8309 (pt) cc_final: 0.8012 (tt)
REVERT: C   85 GLU cc_start: 0.7429 (mp0) cc_final: 0.7034 (mp0)
REVERT: C   95 ASP cc_start: 0.8215 (t70) cc_final: 0.7521 (t70)
REVERT: C  100 ASN cc_start: 0.7611 (m-40) cc_final: 0.7351 (m-40)
REVERT: C  108 GLU cc_start: 0.7127 (pp20) cc_final: 0.6922 (tm-30)
REVERT: C  112 ARG cc_start: 0.8254 (tpp80) cc_final: 0.7926 (tpp80)
REVERT: C  140 LYS cc_start: 0.8110 (ttpt) cc_final: 0.7610 (tttm)
REVERT: C  165 LYS cc_start: 0.7828 (pttp) cc_final: 0.7262 (ptpt)
REVERT: C  171 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7159 (mm-30)
REVERT: C  205 LEU cc_start: 0.8189 (mt) cc_final: 0.7923 (tp)
REVERT: C  209 LYS cc_start: 0.8115 (ptmm) cc_final: 0.7601 (ptmm)
REVERT: C  215 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7820 (ttmm)
REVERT: C  230 MET cc_start: 0.5441 (mtm) cc_final: 0.5170 (mtm)
REVERT: E    6 ILE cc_start: 0.6485 (tp) cc_final: 0.6215 (tp)
REVERT: E   46 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7529 (tm-30)
REVERT: E   86 LYS cc_start: 0.7707 (tppt) cc_final: 0.7465 (mmmm)
REVERT: E  101 LYS cc_start: 0.8665 (pttm) cc_final: 0.8211 (pttm)
REVERT: E  117 GLU cc_start: 0.5085 (mp0) cc_final: 0.4620 (mp0)
REVERT: E  126 SER cc_start: 0.8352 (t) cc_final: 0.7918 (p)
REVERT: E  127 THR cc_start: 0.8176 (m) cc_final: 0.7779 (p)
REVERT: E  135 THR cc_start: 0.8010 (m) cc_final: 0.7744 (p)
REVERT: E  174 ILE cc_start: 0.7958 (mm) cc_final: 0.7554 (tt)
REVERT: E  194 SER cc_start: 0.7856 (p) cc_final: 0.7593 (p)
REVERT: E  197 ILE cc_start: 0.8040 (mm) cc_final: 0.7709 (tp)
REVERT: E  239 GLU cc_start: 0.7564 (tp30) cc_final: 0.6356 (mp0)
REVERT: E  265 ARG cc_start: 0.7758 (mtp180) cc_final: 0.7319 (mtp-110)
REVERT: E  274 LYS cc_start: 0.6938 (mppt) cc_final: 0.6437 (mppt)
REVERT: E  277 ILE cc_start: 0.8556 (mp) cc_final: 0.8336 (mt)
REVERT: E  290 PRO cc_start: 0.8010 (Cg_endo) cc_final: 0.7714 (Cg_exo)
REVERT: E  306 ILE cc_start: 0.8050 (mt) cc_final: 0.7841 (mp)
REVERT: E  325 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6855 (tp40)
REVERT: E  326 GLU cc_start: 0.7545 (tp30) cc_final: 0.6706 (tp30)
REVERT: E  328 MET cc_start: 0.7535 (mtm) cc_final: 0.7217 (mtm)
REVERT: E  329 HIS cc_start: 0.7236 (m90) cc_final: 0.5911 (m90)
REVERT: E  360 TYR cc_start: 0.7393 (m-80) cc_final: 0.6583 (m-80)
REVERT: E  363 LYS cc_start: 0.8336 (mmtt) cc_final: 0.8057 (mmtp)
REVERT: E  397 LYS cc_start: 0.7777 (mmmt) cc_final: 0.7485 (mmtp)
REVERT: E  434 LEU cc_start: 0.8478 (tp) cc_final: 0.7957 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 357
  average time/residue: 0.2949
  time to fit residues: 138.5171
Evaluate side-chains
  316 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 316
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 117 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 43 optimal weight:    0.4980
   chunk 95 optimal weight:    0.0570
   chunk 112 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.6298

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.135927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.114446 restraints weight = 19222.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.117083 restraints weight = 11909.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.118935 restraints weight = 8444.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    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 = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.3032

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= 0.135
  Angle     :  0.585   9.477  14963  Z= 0.314
  Chirality :  0.043   0.158   1723
  Planarity :  0.004   0.050   1683
  Dihedral  : 20.798 148.944   1931
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.24), residues: 1171
  helix: -0.31 (0.31), residues: 307
  sheet:  0.20 (0.32), residues: 312
  loop : -3.03 (0.22), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  50 
 HIS   0.002   0.001   HIS A  39 
 PHE   0.017   0.002   PHE E  10 
 TYR   0.019   0.001   TYR C  59 
 ARG   0.007   0.000   ARG E 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04472 (  386)
  hydrogen bonds       : angle       5.39287 ( 1003)
  covalent geometry    : bond        0.00297 (10899)
  covalent geometry    : angle       0.58498 (14963)
  Misc. bond           : bond        0.00043 (    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
  349 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 349
  time to evaluate  : 1.017 
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: 0.5629 (t70) cc_final: 0.5283 (t0)
REVERT: A   57 LEU cc_start: 0.8128 (mt) cc_final: 0.7848 (mt)
REVERT: A   59 GLU cc_start: 0.8300 (tp30) cc_final: 0.8078 (tp30)
REVERT: A   91 LEU cc_start: 0.8108 (tp) cc_final: 0.7859 (tt)
REVERT: A  110 LYS cc_start: 0.7226 (ttmt) cc_final: 0.6880 (ttmm)
REVERT: A  116 LYS cc_start: 0.8048 (mtmm) cc_final: 0.7733 (tptt)
REVERT: A  119 LYS cc_start: 0.7113 (mppt) cc_final: 0.6728 (mppt)
REVERT: A  156 GLU cc_start: 0.8036 (mp0) cc_final: 0.7806 (mm-30)
REVERT: A  229 MET cc_start: 0.6525 (ttt) cc_final: 0.6174 (ttt)
REVERT: B   21 ASP cc_start: 0.7564 (t0) cc_final: 0.6707 (t0)
REVERT: B   66 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7879 (mmmt)
REVERT: B  107 THR cc_start: 0.8026 (p) cc_final: 0.7738 (t)
REVERT: B  132 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7805 (ttmm)
REVERT: B  153 VAL cc_start: 0.8274 (t) cc_final: 0.7901 (p)
REVERT: B  155 ASN cc_start: 0.7579 (t0) cc_final: 0.7251 (t0)
REVERT: B  159 LYS cc_start: 0.7893 (ttpp) cc_final: 0.7579 (ttmm)
REVERT: B  162 LYS cc_start: 0.8007 (mttp) cc_final: 0.7790 (mttp)
REVERT: B  177 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6923 (tm-30)
REVERT: B  200 GLU cc_start: 0.6844 (tm-30) cc_final: 0.6615 (tm-30)
REVERT: C    3 VAL cc_start: 0.8422 (t) cc_final: 0.7947 (p)
REVERT: C    6 ASP cc_start: 0.7373 (t0) cc_final: 0.7128 (t0)
REVERT: C    7 ASP cc_start: 0.7769 (t70) cc_final: 0.7401 (t0)
REVERT: C   30 LYS cc_start: 0.7669 (mmtm) cc_final: 0.7405 (tppp)
REVERT: C   75 MET cc_start: 0.6992 (tmm) cc_final: 0.6692 (tpp)
REVERT: C   84 LYS cc_start: 0.7750 (mttp) cc_final: 0.7522 (mttp)
REVERT: C   85 GLU cc_start: 0.7307 (mp0) cc_final: 0.7073 (mp0)
REVERT: C  109 PHE cc_start: 0.8047 (m-80) cc_final: 0.7806 (m-80)
REVERT: C  130 ILE cc_start: 0.8630 (mp) cc_final: 0.8382 (mm)
REVERT: C  165 LYS cc_start: 0.7982 (pttp) cc_final: 0.7363 (ptpt)
REVERT: C  171 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7085 (mm-30)
REVERT: C  205 LEU cc_start: 0.8231 (mt) cc_final: 0.7923 (tp)
REVERT: C  209 LYS cc_start: 0.8133 (ptmm) cc_final: 0.7603 (ptmm)
REVERT: C  215 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7836 (ttmm)
REVERT: E    6 ILE cc_start: 0.6733 (tp) cc_final: 0.6409 (tp)
REVERT: E   13 LEU cc_start: 0.7507 (tp) cc_final: 0.7285 (tp)
REVERT: E   15 LYS cc_start: 0.8459 (mtmt) cc_final: 0.8081 (mmtm)
REVERT: E   36 THR cc_start: 0.7850 (p) cc_final: 0.7441 (p)
REVERT: E   46 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7562 (tm-30)
REVERT: E   93 GLU cc_start: 0.8037 (tp30) cc_final: 0.7776 (tp30)
REVERT: E  101 LYS cc_start: 0.8657 (pttm) cc_final: 0.8209 (pttm)
REVERT: E  117 GLU cc_start: 0.5038 (mp0) cc_final: 0.4654 (mp0)
REVERT: E  126 SER cc_start: 0.8305 (t) cc_final: 0.7843 (p)
REVERT: E  127 THR cc_start: 0.8115 (m) cc_final: 0.7793 (p)
REVERT: E  135 THR cc_start: 0.7839 (m) cc_final: 0.7560 (p)
REVERT: E  171 ARG cc_start: 0.8206 (mtm-85) cc_final: 0.7849 (mtm-85)
REVERT: E  174 ILE cc_start: 0.7964 (mm) cc_final: 0.7713 (tp)
REVERT: E  197 ILE cc_start: 0.8000 (mm) cc_final: 0.7747 (tp)
REVERT: E  209 ASN cc_start: 0.6599 (m-40) cc_final: 0.6078 (m-40)
REVERT: E  239 GLU cc_start: 0.7563 (tp30) cc_final: 0.6363 (mp0)
REVERT: E  265 ARG cc_start: 0.7768 (mtp180) cc_final: 0.7056 (mtp180)
REVERT: E  274 LYS cc_start: 0.6943 (mppt) cc_final: 0.6516 (mppt)
REVERT: E  281 ARG cc_start: 0.6965 (mtm180) cc_final: 0.6277 (mtm180)
REVERT: E  290 PRO cc_start: 0.7960 (Cg_endo) cc_final: 0.7656 (Cg_exo)
REVERT: E  326 GLU cc_start: 0.7671 (tp30) cc_final: 0.6724 (tp30)
REVERT: E  328 MET cc_start: 0.7458 (mtm) cc_final: 0.7131 (mmp)
REVERT: E  329 HIS cc_start: 0.7276 (m90) cc_final: 0.5874 (m90)
REVERT: E  363 LYS cc_start: 0.8333 (mmtt) cc_final: 0.8071 (mmtp)
REVERT: E  397 LYS cc_start: 0.7772 (mmmt) cc_final: 0.7414 (mmtp)
REVERT: E  434 LEU cc_start: 0.8471 (tp) cc_final: 0.7951 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 349
  average time/residue: 0.3079
  time to fit residues: 142.0259
Evaluate side-chains
  322 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 322
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 67 optimal weight:    0.0060
   chunk 37 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 33 optimal weight:    0.3980
   chunk 46 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 117 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.5596

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.136821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.115149 restraints weight = 18927.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.117805 restraints weight = 11890.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.119649 restraints weight = 8430.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    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 = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10900  Z= 0.125
  Angle     :  0.574   9.246  14963  Z= 0.307
  Chirality :  0.043   0.157   1723
  Planarity :  0.004   0.047   1683
  Dihedral  : 20.804 149.190   1931
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.24), residues: 1171
  helix: -0.33 (0.31), residues: 307
  sheet:  0.38 (0.32), residues: 311
  loop : -2.98 (0.22), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  50 
 HIS   0.003   0.001   HIS A  39 
 PHE   0.018   0.001   PHE E  10 
 TYR   0.015   0.001   TYR C  59 
 ARG   0.006   0.000   ARG A 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04078 (  386)
  hydrogen bonds       : angle       5.20483 ( 1003)
  covalent geometry    : bond        0.00275 (10899)
  covalent geometry    : angle       0.57421 (14963)
  Misc. bond           : bond        0.00158 (    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
  337 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 337
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7441 (mttt) cc_final: 0.7193 (mttt)
REVERT: A   24 ASP cc_start: 0.5635 (t70) cc_final: 0.5214 (t0)
REVERT: A   57 LEU cc_start: 0.8144 (mt) cc_final: 0.7885 (mt)
REVERT: A   59 GLU cc_start: 0.8321 (tp30) cc_final: 0.8045 (tp30)
REVERT: A   65 PRO cc_start: 0.6547 (Cg_exo) cc_final: 0.6275 (Cg_endo)
REVERT: A   69 LYS cc_start: 0.7719 (mppt) cc_final: 0.7261 (mmtm)
REVERT: A   91 LEU cc_start: 0.7995 (tp) cc_final: 0.7762 (tt)
REVERT: A  116 LYS cc_start: 0.7996 (mtmm) cc_final: 0.7653 (tptt)
REVERT: A  119 LYS cc_start: 0.7028 (mppt) cc_final: 0.6718 (mppt)
REVERT: A  156 GLU cc_start: 0.8001 (mp0) cc_final: 0.7755 (mm-30)
REVERT: A  227 LEU cc_start: 0.7384 (tp) cc_final: 0.7005 (tt)
REVERT: A  229 MET cc_start: 0.6446 (ttt) cc_final: 0.6155 (ttt)
REVERT: B   21 ASP cc_start: 0.7652 (t0) cc_final: 0.6793 (t0)
REVERT: B  103 ASP cc_start: 0.6910 (m-30) cc_final: 0.6693 (m-30)
REVERT: B  107 THR cc_start: 0.8015 (p) cc_final: 0.7746 (t)
REVERT: B  132 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7774 (ttmm)
REVERT: B  153 VAL cc_start: 0.8355 (t) cc_final: 0.8056 (p)
REVERT: B  162 LYS cc_start: 0.7899 (mttp) cc_final: 0.7339 (mttp)
REVERT: C    3 VAL cc_start: 0.8392 (t) cc_final: 0.7885 (p)
REVERT: C    7 ASP cc_start: 0.7831 (t70) cc_final: 0.7464 (t0)
REVERT: C   30 LYS cc_start: 0.7789 (mmtm) cc_final: 0.7239 (tppp)
REVERT: C   35 GLU cc_start: 0.6886 (mp0) cc_final: 0.6591 (pm20)
REVERT: C   75 MET cc_start: 0.6917 (tmm) cc_final: 0.6706 (tpp)
REVERT: C   76 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7815 (ttpt)
REVERT: C   77 ILE cc_start: 0.8321 (pt) cc_final: 0.8015 (tt)
REVERT: C   85 GLU cc_start: 0.7459 (mp0) cc_final: 0.7188 (mp0)
REVERT: C  108 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6769 (tm-30)
REVERT: C  130 ILE cc_start: 0.8642 (mp) cc_final: 0.8377 (mm)
REVERT: C  154 VAL cc_start: 0.7800 (t) cc_final: 0.7418 (p)
REVERT: C  165 LYS cc_start: 0.7974 (pttp) cc_final: 0.7287 (ptpt)
REVERT: C  171 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7120 (mm-30)
REVERT: C  205 LEU cc_start: 0.8220 (mt) cc_final: 0.7919 (tp)
REVERT: C  209 LYS cc_start: 0.8115 (ptmm) cc_final: 0.7759 (ttpp)
REVERT: C  215 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7797 (ttmm)
REVERT: E    6 ILE cc_start: 0.6726 (tp) cc_final: 0.6357 (tp)
REVERT: E   15 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8017 (mmtm)
REVERT: E   49 LEU cc_start: 0.7265 (mt) cc_final: 0.6833 (mt)
REVERT: E   86 LYS cc_start: 0.7815 (tptm) cc_final: 0.7546 (mmmm)
REVERT: E   93 GLU cc_start: 0.8005 (tp30) cc_final: 0.7726 (tp30)
REVERT: E  126 SER cc_start: 0.8306 (t) cc_final: 0.7848 (p)
REVERT: E  127 THR cc_start: 0.8114 (m) cc_final: 0.7776 (p)
REVERT: E  135 THR cc_start: 0.8257 (m) cc_final: 0.8002 (p)
REVERT: E  174 ILE cc_start: 0.7932 (mm) cc_final: 0.7617 (tt)
REVERT: E  197 ILE cc_start: 0.7967 (mm) cc_final: 0.7536 (tp)
REVERT: E  198 GLU cc_start: 0.6963 (tt0) cc_final: 0.6699 (pt0)
REVERT: E  203 LEU cc_start: 0.7729 (mt) cc_final: 0.7521 (mt)
REVERT: E  223 LYS cc_start: 0.7523 (mmtp) cc_final: 0.7239 (mmtm)
REVERT: E  239 GLU cc_start: 0.7584 (tp30) cc_final: 0.6469 (mp0)
REVERT: E  265 ARG cc_start: 0.7724 (mtp180) cc_final: 0.7098 (mtp-110)
REVERT: E  274 LYS cc_start: 0.7070 (mppt) cc_final: 0.6600 (mppt)
REVERT: E  281 ARG cc_start: 0.6890 (mtm180) cc_final: 0.6636 (mtm180)
REVERT: E  290 PRO cc_start: 0.7993 (Cg_endo) cc_final: 0.7622 (Cg_exo)
REVERT: E  325 GLN cc_start: 0.7268 (tp40) cc_final: 0.6774 (tp-100)
REVERT: E  326 GLU cc_start: 0.7667 (tp30) cc_final: 0.6449 (tp30)
REVERT: E  329 HIS cc_start: 0.7225 (m90) cc_final: 0.6014 (m90)
REVERT: E  363 LYS cc_start: 0.8323 (mmtt) cc_final: 0.8068 (mmtp)
REVERT: E  397 LYS cc_start: 0.7741 (mmmt) cc_final: 0.7352 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 337
  average time/residue: 0.2951
  time to fit residues: 129.4108
Evaluate side-chains
  308 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 308
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 83 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9980
   chunk 79 optimal weight:    0.5980
   chunk 77 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3761 r_free = 0.3761 target = 0.135667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.114428 restraints weight = 18899.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.117007 restraints weight = 11938.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.118803 restraints weight = 8524.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3529
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3529 r_free = 0.3529    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3529 r_free = 0.3529    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3529
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10900  Z= 0.154
  Angle     :  0.616   8.953  14963  Z= 0.329
  Chirality :  0.044   0.159   1723
  Planarity :  0.004   0.047   1683
  Dihedral  : 20.907 148.969   1931
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.24), residues: 1171
  helix: -0.33 (0.31), residues: 305
  sheet:  0.34 (0.32), residues: 314
  loop : -2.98 (0.23), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP E  50 
 HIS   0.007   0.001   HIS B 157 
 PHE   0.021   0.002   PHE E  10 
 TYR   0.022   0.002   TYR B 197 
 ARG   0.005   0.000   ARG E  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04493 (  386)
  hydrogen bonds       : angle       5.15293 ( 1003)
  covalent geometry    : bond        0.00340 (10899)
  covalent geometry    : angle       0.61624 (14963)
  Misc. bond           : bond        0.00158 (    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
  335 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 335
  time to evaluate  : 1.163 
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: 0.5672 (t70) cc_final: 0.5304 (t0)
REVERT: A   57 LEU cc_start: 0.8033 (mt) cc_final: 0.7813 (mt)
REVERT: A   59 GLU cc_start: 0.8332 (tp30) cc_final: 0.8047 (tp30)
REVERT: A   65 PRO cc_start: 0.6637 (Cg_exo) cc_final: 0.6372 (Cg_endo)
REVERT: A   69 LYS cc_start: 0.7703 (mppt) cc_final: 0.7223 (mmtm)
REVERT: A  116 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7686 (tppt)
REVERT: A  119 LYS cc_start: 0.7127 (mppt) cc_final: 0.6872 (mppt)
REVERT: A  229 MET cc_start: 0.6381 (ttt) cc_final: 0.6096 (ttt)
REVERT: B   21 ASP cc_start: 0.7660 (t0) cc_final: 0.6689 (t0)
REVERT: B  103 ASP cc_start: 0.6967 (m-30) cc_final: 0.6655 (m-30)
REVERT: B  132 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7695 (ttmm)
REVERT: B  153 VAL cc_start: 0.8326 (t) cc_final: 0.8061 (p)
REVERT: B  162 LYS cc_start: 0.7818 (mttp) cc_final: 0.7445 (mttp)
REVERT: B  218 TYR cc_start: 0.7938 (m-80) cc_final: 0.7736 (m-80)
REVERT: C    3 VAL cc_start: 0.8563 (t) cc_final: 0.8126 (p)
REVERT: C    7 ASP cc_start: 0.7828 (t70) cc_final: 0.7408 (t0)
REVERT: C   30 LYS cc_start: 0.7829 (mmtm) cc_final: 0.7583 (tppp)
REVERT: C   35 GLU cc_start: 0.6904 (mp0) cc_final: 0.6357 (mp0)
REVERT: C   75 MET cc_start: 0.7053 (tmm) cc_final: 0.6805 (tpp)
REVERT: C   85 GLU cc_start: 0.7500 (mp0) cc_final: 0.7126 (mp0)
REVERT: C  108 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6791 (tm-30)
REVERT: C  130 ILE cc_start: 0.8703 (mp) cc_final: 0.8442 (mm)
REVERT: C  154 VAL cc_start: 0.7896 (t) cc_final: 0.7695 (p)
REVERT: C  165 LYS cc_start: 0.7988 (pttp) cc_final: 0.7353 (ptpt)
REVERT: C  171 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7220 (mm-30)
REVERT: C  205 LEU cc_start: 0.8269 (mt) cc_final: 0.7964 (tp)
REVERT: C  209 LYS cc_start: 0.8152 (ptmm) cc_final: 0.7793 (ttpp)
REVERT: C  215 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7828 (ttmm)
REVERT: C  230 MET cc_start: 0.5658 (mtm) cc_final: 0.5391 (mtm)
REVERT: E    6 ILE cc_start: 0.6747 (tp) cc_final: 0.6487 (tp)
REVERT: E   15 LYS cc_start: 0.8500 (mtmt) cc_final: 0.8147 (mmtp)
REVERT: E   36 THR cc_start: 0.7779 (p) cc_final: 0.7362 (p)
REVERT: E   93 GLU cc_start: 0.7994 (tp30) cc_final: 0.7725 (tp30)
REVERT: E  101 LYS cc_start: 0.8521 (pttm) cc_final: 0.8201 (pttm)
REVERT: E  126 SER cc_start: 0.8302 (t) cc_final: 0.7849 (p)
REVERT: E  127 THR cc_start: 0.8137 (m) cc_final: 0.7826 (p)
REVERT: E  135 THR cc_start: 0.7973 (m) cc_final: 0.7671 (p)
REVERT: E  174 ILE cc_start: 0.7966 (mm) cc_final: 0.7655 (tp)
REVERT: E  194 SER cc_start: 0.7917 (p) cc_final: 0.7591 (p)
REVERT: E  197 ILE cc_start: 0.7930 (mm) cc_final: 0.7561 (tp)
REVERT: E  223 LYS cc_start: 0.7443 (mmtp) cc_final: 0.7201 (mmtm)
REVERT: E  224 THR cc_start: 0.7084 (p) cc_final: 0.6875 (p)
REVERT: E  239 GLU cc_start: 0.7324 (tp30) cc_final: 0.6350 (mp0)
REVERT: E  265 ARG cc_start: 0.7733 (mtp180) cc_final: 0.7085 (mtp-110)
REVERT: E  270 LYS cc_start: 0.7309 (ttmt) cc_final: 0.7090 (ttmt)
REVERT: E  274 LYS cc_start: 0.7109 (mppt) cc_final: 0.6486 (mppt)
REVERT: E  290 PRO cc_start: 0.7961 (Cg_endo) cc_final: 0.7588 (Cg_exo)
REVERT: E  325 GLN cc_start: 0.7229 (tp40) cc_final: 0.6712 (tp40)
REVERT: E  326 GLU cc_start: 0.7622 (tp30) cc_final: 0.6367 (tp30)
REVERT: E  329 HIS cc_start: 0.7152 (m90) cc_final: 0.5910 (m90)
REVERT: E  363 LYS cc_start: 0.8316 (mmtt) cc_final: 0.8092 (mmtp)
REVERT: E  397 LYS cc_start: 0.7699 (mmmt) cc_final: 0.7398 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 335
  average time/residue: 0.3059
  time to fit residues: 133.0996
Evaluate side-chains
  313 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 313
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 110 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 115 optimal weight:    0.0970
   chunk 118 optimal weight:    0.7980
   chunk 121 optimal weight:    0.1980
   chunk 108 optimal weight:    0.5980
   chunk 119 optimal weight:    0.0980
   chunk 83 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.3578

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

Flipped N/Q/H residues before XYZ refinement:
B 157 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.138404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.117149 restraints weight = 19070.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.119825 restraints weight = 11900.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.121646 restraints weight = 8349.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3556
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3556 r_free = 0.3556    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 = 0.3556 r_free = 0.3556    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3556
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6908
moved from start:          0.3838

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= 0.115
  Angle     :  0.586  11.043  14963  Z= 0.309
  Chirality :  0.043   0.156   1723
  Planarity :  0.004   0.049   1683
  Dihedral  : 20.849 150.585   1931
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.25), residues: 1171
  helix: -0.25 (0.31), residues: 306
  sheet:  0.36 (0.32), residues: 319
  loop : -2.85 (0.23), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E  50 
 HIS   0.008   0.001   HIS B 157 
 PHE   0.016   0.001   PHE E  10 
 TYR   0.013   0.001   TYR C  59 
 ARG   0.004   0.000   ARG E  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03637 (  386)
  hydrogen bonds       : angle       4.91305 ( 1003)
  covalent geometry    : bond        0.00254 (10899)
  covalent geometry    : angle       0.58637 (14963)
  Misc. bond           : bond        0.00089 (    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
  331 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 331
  time to evaluate  : 1.019 
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: 0.5813 (t70) cc_final: 0.5416 (t0)
REVERT: A   57 LEU cc_start: 0.8034 (mt) cc_final: 0.7785 (mt)
REVERT: A   59 GLU cc_start: 0.8227 (tp30) cc_final: 0.7897 (tp30)
REVERT: A   69 LYS cc_start: 0.7769 (mppt) cc_final: 0.7290 (mmtm)
REVERT: A   91 LEU cc_start: 0.7922 (tp) cc_final: 0.7687 (tt)
REVERT: A   93 GLU cc_start: 0.8652 (pp20) cc_final: 0.8333 (pp20)
REVERT: A   99 LYS cc_start: 0.8049 (tppp) cc_final: 0.7769 (tppp)
REVERT: A  116 LYS cc_start: 0.8000 (mtmm) cc_final: 0.7769 (tppt)
REVERT: A  119 LYS cc_start: 0.7089 (mppt) cc_final: 0.6836 (mppt)
REVERT: A  206 LYS cc_start: 0.7899 (ttmm) cc_final: 0.7666 (ttmm)
REVERT: B   21 ASP cc_start: 0.7645 (t0) cc_final: 0.6649 (t0)
REVERT: B  107 THR cc_start: 0.8139 (p) cc_final: 0.7790 (t)
REVERT: B  132 LYS cc_start: 0.8082 (ttmt) cc_final: 0.7680 (ttmm)
REVERT: B  145 ASP cc_start: 0.6496 (m-30) cc_final: 0.6036 (t0)
REVERT: B  153 VAL cc_start: 0.8262 (t) cc_final: 0.7962 (p)
REVERT: B  162 LYS cc_start: 0.7653 (mttp) cc_final: 0.7279 (mttp)
REVERT: C    3 VAL cc_start: 0.8419 (t) cc_final: 0.7978 (p)
REVERT: C    7 ASP cc_start: 0.7648 (t70) cc_final: 0.7272 (t0)
REVERT: C   30 LYS cc_start: 0.7802 (mmtm) cc_final: 0.7357 (tppp)
REVERT: C   35 GLU cc_start: 0.6965 (mp0) cc_final: 0.6708 (pm20)
REVERT: C   76 LYS cc_start: 0.8005 (ttpt) cc_final: 0.7773 (ttpt)
REVERT: C   84 LYS cc_start: 0.7796 (tttt) cc_final: 0.7334 (tttt)
REVERT: C  108 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6671 (tm-30)
REVERT: C  109 PHE cc_start: 0.7951 (m-80) cc_final: 0.7648 (m-80)
REVERT: C  130 ILE cc_start: 0.8667 (mp) cc_final: 0.8451 (mm)
REVERT: C  154 VAL cc_start: 0.8040 (t) cc_final: 0.7678 (p)
REVERT: C  165 LYS cc_start: 0.7934 (pttp) cc_final: 0.7356 (ptpt)
REVERT: C  171 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7119 (mm-30)
REVERT: C  190 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8174 (mtpt)
REVERT: C  205 LEU cc_start: 0.8163 (mt) cc_final: 0.7889 (tp)
REVERT: C  209 LYS cc_start: 0.8130 (ptmm) cc_final: 0.7782 (ttpp)
REVERT: C  230 MET cc_start: 0.5728 (mtm) cc_final: 0.5411 (mtm)
REVERT: E    6 ILE cc_start: 0.6900 (tp) cc_final: 0.6507 (tp)
REVERT: E   15 LYS cc_start: 0.8381 (mtmt) cc_final: 0.8124 (mmtm)
REVERT: E   36 THR cc_start: 0.7856 (p) cc_final: 0.7411 (p)
REVERT: E   93 GLU cc_start: 0.7843 (tp30) cc_final: 0.7559 (tp30)
REVERT: E  101 LYS cc_start: 0.8457 (pttm) cc_final: 0.8176 (pttm)
REVERT: E  126 SER cc_start: 0.8208 (t) cc_final: 0.7855 (p)
REVERT: E  127 THR cc_start: 0.8077 (m) cc_final: 0.7765 (p)
REVERT: E  135 THR cc_start: 0.8296 (m) cc_final: 0.8021 (p)
REVERT: E  174 ILE cc_start: 0.7960 (mm) cc_final: 0.7607 (tp)
REVERT: E  194 SER cc_start: 0.7835 (p) cc_final: 0.6735 (p)
REVERT: E  197 ILE cc_start: 0.7936 (mm) cc_final: 0.7503 (tp)
REVERT: E  223 LYS cc_start: 0.7399 (mmtp) cc_final: 0.7064 (mmtm)
REVERT: E  265 ARG cc_start: 0.7776 (mtp180) cc_final: 0.7169 (mtp-110)
REVERT: E  274 LYS cc_start: 0.7113 (mppt) cc_final: 0.6503 (mppt)
REVERT: E  281 ARG cc_start: 0.6695 (mtm180) cc_final: 0.6344 (mtm110)
REVERT: E  283 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6921 (mp0)
REVERT: E  290 PRO cc_start: 0.7965 (Cg_endo) cc_final: 0.7623 (Cg_exo)
REVERT: E  325 GLN cc_start: 0.7198 (tp40) cc_final: 0.6699 (tp40)
REVERT: E  326 GLU cc_start: 0.7691 (tp30) cc_final: 0.6528 (tp30)
REVERT: E  329 HIS cc_start: 0.7140 (m90) cc_final: 0.5942 (m90)
REVERT: E  363 LYS cc_start: 0.8358 (mmtt) cc_final: 0.8103 (mmtp)
REVERT: E  397 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7370 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 331
  average time/residue: 0.3002
  time to fit residues: 129.1410
Evaluate side-chains
  309 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 309
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 36 optimal weight:    7.9990
   chunk 76 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 100 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 118 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
E 102 GLN
** 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 = 0.3715 r_free = 0.3715 target = 0.132480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.111149 restraints weight = 19459.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.113680 restraints weight = 12217.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.115322 restraints weight = 8686.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3476
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3476 r_free = 0.3476    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3476 r_free = 0.3476    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3476
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7020
moved from start:          0.3905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.097  10900  Z= 0.229
  Angle     :  0.712  11.362  14963  Z= 0.380
  Chirality :  0.047   0.171   1723
  Planarity :  0.004   0.048   1683
  Dihedral  : 21.209 155.265   1931
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.42 %
    Favored  : 89.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.24), residues: 1171
  helix: -0.67 (0.30), residues: 305
  sheet:  0.26 (0.32), residues: 309
  loop : -3.01 (0.23), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.004   TRP E  50 
 HIS   0.003   0.001   HIS A  39 
 PHE   0.026   0.002   PHE E  10 
 TYR   0.028   0.002   TYR C  59 
 ARG   0.012   0.001   ARG E 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05573 (  386)
  hydrogen bonds       : angle       5.28993 ( 1003)
  covalent geometry    : bond        0.00510 (10899)
  covalent geometry    : angle       0.71225 (14963)
  Misc. bond           : bond        0.00173 (    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
  342 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 342
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ILE cc_start: 0.8274 (tp) cc_final: 0.8050 (mm)
REVERT: A   24 ASP cc_start: 0.5761 (t70) cc_final: 0.5415 (t0)
REVERT: A   57 LEU cc_start: 0.8111 (mt) cc_final: 0.7869 (mt)
REVERT: A   59 GLU cc_start: 0.8202 (tp30) cc_final: 0.7977 (tp30)
REVERT: A   65 PRO cc_start: 0.6661 (Cg_exo) cc_final: 0.6363 (Cg_endo)
REVERT: A   69 LYS cc_start: 0.7711 (mppt) cc_final: 0.7283 (mmtp)
REVERT: A   99 LYS cc_start: 0.8046 (tppp) cc_final: 0.7707 (tppp)
REVERT: A  116 LYS cc_start: 0.8028 (mtmm) cc_final: 0.7764 (tptt)
REVERT: A  119 LYS cc_start: 0.7083 (mppt) cc_final: 0.6818 (mppt)
REVERT: A  164 ASP cc_start: 0.6483 (t70) cc_final: 0.6238 (t0)
REVERT: A  206 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7771 (ttmm)
REVERT: A  229 MET cc_start: 0.5858 (ttp) cc_final: 0.5562 (ttp)
REVERT: A  231 ILE cc_start: 0.8172 (mp) cc_final: 0.7821 (mt)
REVERT: B   21 ASP cc_start: 0.7544 (t0) cc_final: 0.6528 (t0)
REVERT: B   35 ILE cc_start: 0.8500 (mm) cc_final: 0.8257 (tp)
REVERT: B  132 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7879 (ttmm)
REVERT: B  162 LYS cc_start: 0.7732 (mttp) cc_final: 0.7393 (mttp)
REVERT: C    3 VAL cc_start: 0.8728 (t) cc_final: 0.8345 (p)
REVERT: C    7 ASP cc_start: 0.7675 (t70) cc_final: 0.7143 (t0)
REVERT: C   28 LYS cc_start: 0.8198 (mttp) cc_final: 0.7014 (mttm)
REVERT: C   30 LYS cc_start: 0.7890 (mmtm) cc_final: 0.7492 (mmmm)
REVERT: C   35 GLU cc_start: 0.6949 (mp0) cc_final: 0.6387 (mp0)
REVERT: C   72 GLN cc_start: 0.7542 (tt0) cc_final: 0.7324 (mt0)
REVERT: C   75 MET cc_start: 0.7610 (tpp) cc_final: 0.7224 (tpp)
REVERT: C   85 GLU cc_start: 0.7518 (mp0) cc_final: 0.7062 (mp0)
REVERT: C  108 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6846 (tm-30)
REVERT: C  154 VAL cc_start: 0.8295 (t) cc_final: 0.7955 (p)
REVERT: C  165 LYS cc_start: 0.8019 (pttp) cc_final: 0.7508 (ptpt)
REVERT: C  171 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7195 (mm-30)
REVERT: C  205 LEU cc_start: 0.8406 (mt) cc_final: 0.8123 (tp)
REVERT: C  209 LYS cc_start: 0.8157 (ptmm) cc_final: 0.7846 (ttpp)
REVERT: C  215 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7744 (ttmm)
REVERT: E    1 MET cc_start: 0.7293 (mtm) cc_final: 0.6968 (mtm)
REVERT: E   46 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7608 (tm-30)
REVERT: E   49 LEU cc_start: 0.7292 (mt) cc_final: 0.7051 (mt)
REVERT: E   86 LYS cc_start: 0.7948 (tptm) cc_final: 0.7647 (mmmm)
REVERT: E  101 LYS cc_start: 0.8658 (pttm) cc_final: 0.8254 (pttm)
REVERT: E  102 GLN cc_start: 0.6461 (pt0) cc_final: 0.6179 (pt0)
REVERT: E  126 SER cc_start: 0.8346 (t) cc_final: 0.7858 (p)
REVERT: E  174 ILE cc_start: 0.7986 (mm) cc_final: 0.7716 (tp)
REVERT: E  198 GLU cc_start: 0.6374 (pm20) cc_final: 0.6122 (pm20)
REVERT: E  203 LEU cc_start: 0.7846 (mt) cc_final: 0.7610 (mt)
REVERT: E  226 LYS cc_start: 0.6751 (tptt) cc_final: 0.6519 (tppt)
REVERT: E  236 MET cc_start: 0.7503 (ptp) cc_final: 0.7262 (ptp)
REVERT: E  239 GLU cc_start: 0.7336 (tp30) cc_final: 0.6258 (mp0)
REVERT: E  248 LEU cc_start: 0.6723 (mp) cc_final: 0.6428 (mp)
REVERT: E  274 LYS cc_start: 0.7128 (mppt) cc_final: 0.6637 (mppt)
REVERT: E  281 ARG cc_start: 0.6884 (mtm180) cc_final: 0.6449 (mtm110)
REVERT: E  283 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6703 (mp0)
REVERT: E  290 PRO cc_start: 0.7967 (Cg_endo) cc_final: 0.7569 (Cg_exo)
REVERT: E  325 GLN cc_start: 0.7327 (tp40) cc_final: 0.6938 (tp-100)
REVERT: E  326 GLU cc_start: 0.7788 (tp30) cc_final: 0.6513 (tp30)
REVERT: E  329 HIS cc_start: 0.7161 (m90) cc_final: 0.5787 (m90)
REVERT: E  360 TYR cc_start: 0.7248 (m-80) cc_final: 0.6841 (m-80)
REVERT: E  363 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8233 (mmtp)
REVERT: E  397 LYS cc_start: 0.7807 (mmmt) cc_final: 0.7472 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 342
  average time/residue: 0.2983
  time to fit residues: 132.2477
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  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 101 optimal weight:    0.0980
   chunk 74 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 115 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3755 r_free = 0.3755 target = 0.135291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.113952 restraints weight = 18980.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.116533 restraints weight = 12017.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.118311 restraints weight = 8547.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3521
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3521 r_free = 0.3521    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3521 r_free = 0.3521    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3521
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.4088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10900  Z= 0.144
  Angle     :  0.651  10.920  14963  Z= 0.343
  Chirality :  0.045   0.178   1723
  Planarity :  0.004   0.049   1683
  Dihedral  : 21.057 150.863   1931
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.24), residues: 1171
  helix: -0.42 (0.31), residues: 306
  sheet:  0.17 (0.31), residues: 320
  loop : -2.96 (0.23), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP E  50 
 HIS   0.004   0.001   HIS A  39 
 PHE   0.035   0.002   PHE A  30 
 TYR   0.018   0.001   TYR E 381 
 ARG   0.005   0.000   ARG E 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04280 (  386)
  hydrogen bonds       : angle       5.00129 ( 1003)
  covalent geometry    : bond        0.00322 (10899)
  covalent geometry    : angle       0.65109 (14963)
  Misc. bond           : bond        0.00117 (    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
  331 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 331
  time to evaluate  : 1.107 
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: 0.5934 (t70) cc_final: 0.5565 (t0)
REVERT: A   57 LEU cc_start: 0.8150 (mt) cc_final: 0.7922 (mt)
REVERT: A   69 LYS cc_start: 0.7705 (mppt) cc_final: 0.7161 (mmtm)
REVERT: A   91 LEU cc_start: 0.8041 (tp) cc_final: 0.7628 (tt)
REVERT: A  116 LYS cc_start: 0.7999 (mtmm) cc_final: 0.7737 (tptt)
REVERT: A  119 LYS cc_start: 0.7072 (mppt) cc_final: 0.6867 (mppt)
REVERT: A  164 ASP cc_start: 0.6406 (t70) cc_final: 0.6182 (t0)
REVERT: A  165 LYS cc_start: 0.7564 (mmpt) cc_final: 0.7259 (mmpt)
REVERT: A  206 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7755 (ttmm)
REVERT: A  229 MET cc_start: 0.5830 (ttp) cc_final: 0.5541 (ttp)
REVERT: B   21 ASP cc_start: 0.7412 (t0) cc_final: 0.6398 (t0)
REVERT: B   35 ILE cc_start: 0.8435 (mm) cc_final: 0.8157 (tp)
REVERT: B  107 THR cc_start: 0.8008 (p) cc_final: 0.7588 (t)
REVERT: B  132 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7673 (ttmm)
REVERT: B  162 LYS cc_start: 0.7777 (mttp) cc_final: 0.7401 (mttp)
REVERT: B  207 LYS cc_start: 0.8930 (ptpp) cc_final: 0.8717 (ptmm)
REVERT: C    3 VAL cc_start: 0.8551 (t) cc_final: 0.7989 (p)
REVERT: C    7 ASP cc_start: 0.7647 (t70) cc_final: 0.7204 (t0)
REVERT: C   28 LYS cc_start: 0.8150 (mttp) cc_final: 0.6700 (mttm)
REVERT: C   30 LYS cc_start: 0.7879 (mmtm) cc_final: 0.7531 (mmmm)
REVERT: C   35 GLU cc_start: 0.7047 (mp0) cc_final: 0.6463 (mp0)
REVERT: C   72 GLN cc_start: 0.7550 (tt0) cc_final: 0.7300 (mt0)
REVERT: C   75 MET cc_start: 0.7493 (tpp) cc_final: 0.7161 (tpp)
REVERT: C   77 ILE cc_start: 0.8288 (pt) cc_final: 0.8063 (tt)
REVERT: C   84 LYS cc_start: 0.7943 (tttt) cc_final: 0.7542 (tttt)
REVERT: C   88 GLU cc_start: 0.7061 (pp20) cc_final: 0.6188 (pm20)
REVERT: C  108 GLU cc_start: 0.7002 (tm-30) cc_final: 0.6648 (tm-30)
REVERT: C  109 PHE cc_start: 0.8003 (m-80) cc_final: 0.7672 (m-80)
REVERT: C  130 ILE cc_start: 0.8732 (mp) cc_final: 0.8490 (mm)
REVERT: C  165 LYS cc_start: 0.7919 (pttp) cc_final: 0.7508 (ptpt)
REVERT: C  171 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7221 (mm-30)
REVERT: C  205 LEU cc_start: 0.8253 (mt) cc_final: 0.7904 (tp)
REVERT: C  209 LYS cc_start: 0.8135 (ptmm) cc_final: 0.7656 (ptmm)
REVERT: E    1 MET cc_start: 0.7222 (mtm) cc_final: 0.6995 (mtm)
REVERT: E   15 LYS cc_start: 0.8418 (mtmm) cc_final: 0.7964 (mmtm)
REVERT: E   36 THR cc_start: 0.7657 (p) cc_final: 0.7276 (p)
REVERT: E   49 LEU cc_start: 0.7181 (mt) cc_final: 0.6930 (mt)
REVERT: E   86 LYS cc_start: 0.7839 (tptm) cc_final: 0.7602 (mmmm)
REVERT: E  101 LYS cc_start: 0.8538 (pttm) cc_final: 0.8255 (pttm)
REVERT: E  126 SER cc_start: 0.8327 (t) cc_final: 0.7816 (p)
REVERT: E  127 THR cc_start: 0.8005 (m) cc_final: 0.7753 (m)
REVERT: E  141 ASP cc_start: 0.7328 (m-30) cc_final: 0.7055 (m-30)
REVERT: E  174 ILE cc_start: 0.8016 (mm) cc_final: 0.7639 (tp)
REVERT: E  194 SER cc_start: 0.7402 (p) cc_final: 0.6303 (p)
REVERT: E  198 GLU cc_start: 0.6362 (pm20) cc_final: 0.5987 (pm20)
REVERT: E  203 LEU cc_start: 0.7717 (mt) cc_final: 0.7439 (mt)
REVERT: E  224 THR cc_start: 0.7155 (p) cc_final: 0.6946 (p)
REVERT: E  226 LYS cc_start: 0.6761 (tptt) cc_final: 0.6515 (tppt)
REVERT: E  239 GLU cc_start: 0.7301 (tp30) cc_final: 0.6297 (mp0)
REVERT: E  265 ARG cc_start: 0.7736 (mtp180) cc_final: 0.7125 (mtp180)
REVERT: E  274 LYS cc_start: 0.7242 (mppt) cc_final: 0.6735 (mppt)
REVERT: E  281 ARG cc_start: 0.6882 (mtm180) cc_final: 0.6471 (mtm110)
REVERT: E  290 PRO cc_start: 0.7951 (Cg_endo) cc_final: 0.7598 (Cg_exo)
REVERT: E  325 GLN cc_start: 0.7201 (tp40) cc_final: 0.6953 (tp40)
REVERT: E  363 LYS cc_start: 0.8387 (mmtt) cc_final: 0.8168 (mmtp)
REVERT: E  397 LYS cc_start: 0.7782 (mmmt) cc_final: 0.7451 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 331
  average time/residue: 0.2918
  time to fit residues: 125.8943
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  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 92 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 29 optimal weight:    0.2980
   chunk 119 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 99 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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
** C  72 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 = 0.3763 r_free = 0.3763 target = 0.135742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.114381 restraints weight = 19327.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.116902 restraints weight = 12237.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.118624 restraints weight = 8739.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3527
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3527 r_free = 0.3527    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3527 r_free = 0.3527    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3527
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.4192

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= 0.142
  Angle     :  0.655  10.748  14963  Z= 0.347
  Chirality :  0.045   0.167   1723
  Planarity :  0.004   0.048   1683
  Dihedral  : 21.047 150.534   1931
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.31 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.24), residues: 1171
  helix: -0.32 (0.31), residues: 306
  sheet:  0.16 (0.31), residues: 323
  loop : -2.98 (0.23), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP E  50 
 HIS   0.008   0.001   HIS B 157 
 PHE   0.024   0.002   PHE A  30 
 TYR   0.015   0.001   TYR C  59 
 ARG   0.005   0.000   ARG A 248 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04237 (  386)
  hydrogen bonds       : angle       4.91889 ( 1003)
  covalent geometry    : bond        0.00319 (10899)
  covalent geometry    : angle       0.65485 (14963)
  Misc. bond           : bond        0.00115 (    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
  322 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 322
  time to evaluate  : 1.109 
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: 0.5959 (t70) cc_final: 0.5557 (t0)
REVERT: A   69 LYS cc_start: 0.7749 (mppt) cc_final: 0.7133 (mmtm)
REVERT: A   93 GLU cc_start: 0.8674 (pp20) cc_final: 0.8287 (pp20)
REVERT: A  116 LYS cc_start: 0.8034 (mtmm) cc_final: 0.7775 (tptt)
REVERT: A  119 LYS cc_start: 0.7065 (mppt) cc_final: 0.6836 (mppt)
REVERT: A  165 LYS cc_start: 0.7583 (mmpt) cc_final: 0.7280 (mmpt)
REVERT: A  206 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7748 (ttmm)
REVERT: A  229 MET cc_start: 0.5801 (ttp) cc_final: 0.5550 (ttp)
REVERT: B   21 ASP cc_start: 0.7373 (t0) cc_final: 0.6327 (t0)
REVERT: B   22 PHE cc_start: 0.7484 (m-10) cc_final: 0.7213 (m-10)
REVERT: B   35 ILE cc_start: 0.8386 (mm) cc_final: 0.8094 (tp)
REVERT: B   67 GLU cc_start: 0.5925 (mp0) cc_final: 0.5704 (mp0)
REVERT: B  107 THR cc_start: 0.8047 (p) cc_final: 0.7633 (t)
REVERT: B  132 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7694 (ttmm)
REVERT: B  149 ASP cc_start: 0.7843 (t70) cc_final: 0.7581 (t0)
REVERT: B  162 LYS cc_start: 0.7718 (mttp) cc_final: 0.7395 (mttp)
REVERT: C    3 VAL cc_start: 0.8463 (t) cc_final: 0.7929 (p)
REVERT: C    7 ASP cc_start: 0.7656 (t70) cc_final: 0.7243 (t0)
REVERT: C   30 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7664 (tppp)
REVERT: C   65 PHE cc_start: 0.7943 (t80) cc_final: 0.7735 (t80)
REVERT: C   75 MET cc_start: 0.7396 (tpp) cc_final: 0.7096 (tpp)
REVERT: C   77 ILE cc_start: 0.8275 (pt) cc_final: 0.8053 (tt)
REVERT: C   84 LYS cc_start: 0.8041 (tttt) cc_final: 0.7729 (tttt)
REVERT: C   85 GLU cc_start: 0.7557 (mp0) cc_final: 0.7310 (mp0)
REVERT: C   88 GLU cc_start: 0.7032 (pp20) cc_final: 0.6557 (pp20)
REVERT: C  109 PHE cc_start: 0.8064 (m-80) cc_final: 0.7555 (m-80)
REVERT: C  130 ILE cc_start: 0.8752 (mp) cc_final: 0.8537 (mm)
REVERT: C  165 LYS cc_start: 0.7923 (pttp) cc_final: 0.7499 (ptpt)
REVERT: C  171 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7084 (mm-30)
REVERT: C  205 LEU cc_start: 0.8232 (mt) cc_final: 0.7938 (tp)
REVERT: C  209 LYS cc_start: 0.8138 (ptmm) cc_final: 0.7821 (ttpp)
REVERT: E    1 MET cc_start: 0.7312 (mtm) cc_final: 0.7081 (mtm)
REVERT: E   32 LYS cc_start: 0.7720 (mtmm) cc_final: 0.7496 (mtmm)
REVERT: E   34 ASP cc_start: 0.7940 (t0) cc_final: 0.7714 (t0)
REVERT: E   36 THR cc_start: 0.7640 (p) cc_final: 0.7185 (p)
REVERT: E   86 LYS cc_start: 0.7798 (tptm) cc_final: 0.7588 (mmmm)
REVERT: E  101 LYS cc_start: 0.8538 (pttm) cc_final: 0.8242 (pttm)
REVERT: E  126 SER cc_start: 0.8306 (t) cc_final: 0.7836 (p)
REVERT: E  127 THR cc_start: 0.8032 (m) cc_final: 0.7738 (m)
REVERT: E  140 ARG cc_start: 0.6700 (ptm160) cc_final: 0.6499 (mtp-110)
REVERT: E  141 ASP cc_start: 0.7357 (m-30) cc_final: 0.7054 (m-30)
REVERT: E  174 ILE cc_start: 0.8048 (mm) cc_final: 0.7629 (tp)
REVERT: E  194 SER cc_start: 0.7395 (p) cc_final: 0.6314 (p)
REVERT: E  198 GLU cc_start: 0.6379 (pm20) cc_final: 0.5905 (pm20)
REVERT: E  203 LEU cc_start: 0.7689 (mt) cc_final: 0.7454 (mt)
REVERT: E  209 ASN cc_start: 0.7828 (p0) cc_final: 0.7627 (p0)
REVERT: E  224 THR cc_start: 0.7224 (p) cc_final: 0.7000 (p)
REVERT: E  226 LYS cc_start: 0.6738 (tptt) cc_final: 0.6526 (tppt)
REVERT: E  234 ARG cc_start: 0.7669 (mtm180) cc_final: 0.7465 (ttm110)
REVERT: E  239 GLU cc_start: 0.7322 (tp30) cc_final: 0.6357 (mp0)
REVERT: E  274 LYS cc_start: 0.7236 (mppt) cc_final: 0.6798 (mppt)
REVERT: E  281 ARG cc_start: 0.6747 (mtm180) cc_final: 0.6485 (mtm110)
REVERT: E  290 PRO cc_start: 0.7991 (Cg_endo) cc_final: 0.7583 (Cg_exo)
REVERT: E  325 GLN cc_start: 0.7244 (tp40) cc_final: 0.6772 (tp40)
REVERT: E  326 GLU cc_start: 0.7789 (tp30) cc_final: 0.6684 (tp30)
REVERT: E  329 HIS cc_start: 0.6997 (m90) cc_final: 0.5695 (m90)
REVERT: E  363 LYS cc_start: 0.8429 (mmtt) cc_final: 0.8219 (mmtp)
REVERT: E  397 LYS cc_start: 0.7782 (mmmt) cc_final: 0.7436 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 322
  average time/residue: 0.2960
  time to fit residues: 124.7585
Evaluate side-chains
  301 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 301
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 57 optimal weight:    0.2980
   chunk 95 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 10 optimal weight:    0.4980
   chunk 28 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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
** C  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 100 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.136054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.114701 restraints weight = 19254.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.117253 restraints weight = 12301.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.119002 restraints weight = 8794.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3524
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3524 r_free = 0.3524    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3524 r_free = 0.3524    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3524
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          0.4317

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= 0.139
  Angle     :  0.659  10.684  14963  Z= 0.349
  Chirality :  0.044   0.167   1723
  Planarity :  0.004   0.047   1683
  Dihedral  : 21.044 149.817   1931
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.24), residues: 1171
  helix: -0.46 (0.30), residues: 309
  sheet:  0.20 (0.31), residues: 323
  loop : -2.92 (0.23), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP E  50 
 HIS   0.004   0.001   HIS A  39 
 PHE   0.024   0.002   PHE E  10 
 TYR   0.023   0.001   TYR B 197 
 ARG   0.006   0.000   ARG A 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04158 (  386)
  hydrogen bonds       : angle       4.92239 ( 1003)
  covalent geometry    : bond        0.00314 (10899)
  covalent geometry    : angle       0.65879 (14963)
  Misc. bond           : bond        0.00113 (    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
  322 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 322
  time to evaluate  : 1.055 
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: 0.5874 (t70) cc_final: 0.5510 (t0)
REVERT: A   69 LYS cc_start: 0.7770 (mppt) cc_final: 0.7175 (mmtm)
REVERT: A   93 GLU cc_start: 0.8587 (pp20) cc_final: 0.8318 (pp20)
REVERT: A  116 LYS cc_start: 0.8002 (mtmm) cc_final: 0.7770 (tptt)
REVERT: A  119 LYS cc_start: 0.7045 (mppt) cc_final: 0.6832 (mppt)
REVERT: A  165 LYS cc_start: 0.7514 (mmpt) cc_final: 0.7246 (mmpt)
REVERT: A  206 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7713 (ttmm)
REVERT: A  229 MET cc_start: 0.5822 (ttp) cc_final: 0.5547 (ttp)
REVERT: B   21 ASP cc_start: 0.7317 (t0) cc_final: 0.6234 (t0)
REVERT: B   22 PHE cc_start: 0.7491 (m-10) cc_final: 0.7220 (m-10)
REVERT: B   35 ILE cc_start: 0.8380 (mm) cc_final: 0.8075 (tp)
REVERT: B  107 THR cc_start: 0.8059 (p) cc_final: 0.7651 (t)
REVERT: B  132 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7639 (ttmm)
REVERT: B  149 ASP cc_start: 0.7792 (t70) cc_final: 0.7564 (t0)
REVERT: B  162 LYS cc_start: 0.7806 (mttp) cc_final: 0.7461 (mttp)
REVERT: B  200 GLU cc_start: 0.6853 (tm-30) cc_final: 0.6629 (tm-30)
REVERT: C    3 VAL cc_start: 0.8416 (t) cc_final: 0.7906 (p)
REVERT: C    7 ASP cc_start: 0.7660 (t70) cc_final: 0.7260 (t0)
REVERT: C   28 LYS cc_start: 0.8321 (mttp) cc_final: 0.7776 (mtmm)
REVERT: C   75 MET cc_start: 0.7348 (tpp) cc_final: 0.7043 (tpt)
REVERT: C   77 ILE cc_start: 0.8305 (pt) cc_final: 0.8047 (tt)
REVERT: C   84 LYS cc_start: 0.7998 (tttt) cc_final: 0.7700 (tttt)
REVERT: C  100 ASN cc_start: 0.7509 (m110) cc_final: 0.7215 (m-40)
REVERT: C  130 ILE cc_start: 0.8772 (mp) cc_final: 0.8532 (mm)
REVERT: C  140 LYS cc_start: 0.8051 (ttpt) cc_final: 0.7726 (tttm)
REVERT: C  165 LYS cc_start: 0.7908 (pttp) cc_final: 0.7449 (ptpt)
REVERT: C  171 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7144 (mm-30)
REVERT: C  209 LYS cc_start: 0.8147 (ptmm) cc_final: 0.7789 (ttpp)
REVERT: C  222 LYS cc_start: 0.7266 (mmtt) cc_final: 0.6958 (mmtm)
REVERT: E   15 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7942 (mmtm)
REVERT: E   36 THR cc_start: 0.7823 (p) cc_final: 0.7463 (p)
REVERT: E   86 LYS cc_start: 0.7746 (tptm) cc_final: 0.7534 (mmmm)
REVERT: E  101 LYS cc_start: 0.8498 (pttm) cc_final: 0.8196 (pttm)
REVERT: E  126 SER cc_start: 0.8294 (t) cc_final: 0.7821 (p)
REVERT: E  127 THR cc_start: 0.8007 (m) cc_final: 0.7731 (m)
REVERT: E  140 ARG cc_start: 0.6625 (ptm160) cc_final: 0.6281 (ttp-110)
REVERT: E  141 ASP cc_start: 0.7225 (m-30) cc_final: 0.6948 (m-30)
REVERT: E  174 ILE cc_start: 0.8036 (mm) cc_final: 0.7623 (tt)
REVERT: E  194 SER cc_start: 0.7273 (p) cc_final: 0.6410 (p)
REVERT: E  198 GLU cc_start: 0.6308 (pm20) cc_final: 0.5943 (pm20)
REVERT: E  203 LEU cc_start: 0.7676 (mt) cc_final: 0.7421 (mt)
REVERT: E  209 ASN cc_start: 0.7792 (p0) cc_final: 0.7564 (p0)
REVERT: E  236 MET cc_start: 0.7473 (ptp) cc_final: 0.7254 (ptp)
REVERT: E  239 GLU cc_start: 0.7321 (tp30) cc_final: 0.6377 (mp0)
REVERT: E  274 LYS cc_start: 0.7294 (mppt) cc_final: 0.6863 (mppt)
REVERT: E  290 PRO cc_start: 0.7937 (Cg_endo) cc_final: 0.7568 (Cg_exo)
REVERT: E  299 TYR cc_start: 0.6525 (m-10) cc_final: 0.6211 (m-10)
REVERT: E  325 GLN cc_start: 0.7207 (tp40) cc_final: 0.6810 (tp40)
REVERT: E  326 GLU cc_start: 0.7737 (tp30) cc_final: 0.6646 (tp30)
REVERT: E  329 HIS cc_start: 0.7071 (m90) cc_final: 0.5754 (m90)
REVERT: E  363 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8201 (mmtp)
REVERT: E  397 LYS cc_start: 0.7756 (mmmt) cc_final: 0.7427 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 322
  average time/residue: 0.2997
  time to fit residues: 125.9695
Evaluate side-chains
  296 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 296
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 98 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 69 optimal weight:    0.2980
   chunk 61 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0870
   chunk 55 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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
** C  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 100 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.136934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.115567 restraints weight = 19085.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.118110 restraints weight = 12167.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.119872 restraints weight = 8721.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3539
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3539 r_free = 0.3539    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 = 0.3539 r_free = 0.3539    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3539
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6929
moved from start:          0.4418

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= 0.134
  Angle     :  0.669  10.503  14963  Z= 0.352
  Chirality :  0.044   0.157   1723
  Planarity :  0.004   0.048   1683
  Dihedral  : 21.026 149.996   1931
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.24), residues: 1171
  helix: -0.38 (0.30), residues: 309
  sheet:  0.29 (0.31), residues: 316
  loop : -2.88 (0.23), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP E  50 
 HIS   0.007   0.001   HIS B 157 
 PHE   0.022   0.002   PHE A  30 
 TYR   0.019   0.001   TYR B 197 
 ARG   0.006   0.000   ARG A 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04003 (  386)
  hydrogen bonds       : angle       4.88414 ( 1003)
  covalent geometry    : bond        0.00303 (10899)
  covalent geometry    : angle       0.66866 (14963)
  Misc. bond           : bond        0.00097 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4135.69 seconds
wall clock time: 71 minutes 56.60 seconds (4316.60 seconds total)