Starting phenix.real_space_refine
on Fri Feb 14 21:07:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rpo_24618/02_2025/7rpo_24618.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rpo_24618/02_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_24618/02_2025/7rpo_24618.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rpo_24618/02_2025/7rpo_24618.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rpo_24618/02_2025/7rpo_24618.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rpo_24618/02_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-5592/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}
          Classifications: {'RNA': 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: 5.86, per 1000 atoms: 0.55
  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: 2.44
  Conformation dependent library (CDL) restraints added in 1.3 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: 3.59
  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: 3.63

  Time building geometry restraints manager: 2.77 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=" C4' AMP E 701 "
       pdb=" O4' AMP E 701 "
    ideal  model  delta    sigma   weight residual
    1.454  1.429  0.025 1.50e-02 4.44e+03 2.72e+00
  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
  ... (remaining 10894 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 14616
        1.45 -     2.91: 307
        2.91 -     4.36: 30
        4.36 -     5.81: 8
        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=" C1' AMP E 701 "
        pdb=" C2' AMP E 701 "
        pdb=" C3' AMP E 701 "
      ideal   model   delta    sigma   weight residual
     101.50  105.65   -4.15 1.00e+00 1.00e+00 1.73e+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=" C2' AMP E 701 "
        pdb=" C3' AMP E 701 "
        pdb=" C4' AMP E 701 "
      ideal   model   delta    sigma   weight residual
     102.60  106.06   -3.46 1.00e+00 1.00e+00 1.20e+01
  angle pdb=" C3' AMP E 701 "
        pdb=" C4' AMP E 701 "
        pdb=" C5' AMP E 701 "
      ideal   model   delta    sigma   weight residual
     115.20  110.34    4.86 1.50e+00 4.44e-01 1.05e+01
  ... (remaining 14958 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.40: 6078
       30.40 -    60.80: 380
       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 -    0.030: 1111
       0.030 -    0.060: 401
       0.060 -    0.089: 100
       0.089 -    0.119: 96
       0.119 -    0.149: 15
  Chirality restraints: 1723
  Sorted by residual:
  chirality pdb=" C3' AMP E 701 "
            pdb=" C2' AMP E 701 "
            pdb=" C4' AMP E 701 "
            pdb=" O3' AMP E 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.60   -0.15 2.00e-01 2.50e+01 5.53e-01
  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
  ... (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:                  0.010
  Normalize map: mean=0, sd=1:             0.290
  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:                     27.410
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.360
-------------------------------------------------------------------------------
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   0.044  10899  Z= 0.153
  Angle     :  0.505   7.267  14963  Z= 0.288
  Chirality :  0.040   0.149   1723
  Planarity :  0.003   0.034   1683
  Dihedral  : 16.976 151.990   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 

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

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  414 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 397
  time to evaluate  : 0.997 
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: 0.2938
  time to fit residues: 159.3895
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  : 1.049 
-------------------------------------------------------------------------------
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 = 0.137978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.115601 restraints weight = 18451.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.118477 restraints weight = 11393.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.120452 restraints weight = 7953.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3542
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3542 r_free = 0.3542    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.50   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: 0.6938
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10899  Z= 0.201
  Angle     :  0.595   7.198  14963  Z= 0.326
  Chirality :  0.044   0.161   1723
  Planarity :  0.004   0.051   1683
  Dihedral  : 20.788 151.948   1931
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.51 %
    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: -2.04 (0.24), residues: 1171
  helix: -0.21 (0.31), residues: 299
  sheet:  0.04 (0.32), residues: 321
  loop : -2.98 (0.23), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E  50 
 HIS   0.003   0.001   HIS A 240 
 PHE   0.021   0.002   PHE C 228 
 TYR   0.011   0.001   TYR E 259 
 ARG   0.005   0.001   ARG E 427 

*********************** 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  : 1.132 
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: 0.5619 (t70) cc_final: 0.5242 (t0)
REVERT: A   47 MET cc_start: 0.7219 (ttt) cc_final: 0.6985 (ttt)
REVERT: A   57 LEU cc_start: 0.8203 (mt) cc_final: 0.7898 (mt)
REVERT: A   59 GLU cc_start: 0.8336 (tp30) cc_final: 0.8118 (tp30)
REVERT: A   70 LEU cc_start: 0.7415 (mt) cc_final: 0.7128 (mt)
REVERT: A  110 LYS cc_start: 0.7222 (ttmt) cc_final: 0.6957 (ttmm)
REVERT: A  116 LYS cc_start: 0.8011 (mtmm) cc_final: 0.7687 (tptt)
REVERT: A  159 ILE cc_start: 0.8081 (mt) cc_final: 0.7714 (mm)
REVERT: A  212 LEU cc_start: 0.7407 (mt) cc_final: 0.7107 (tp)
REVERT: A  213 ARG cc_start: 0.6929 (mtt90) cc_final: 0.6580 (mtt90)
REVERT: A  229 MET cc_start: 0.6527 (ttt) cc_final: 0.6094 (ttt)
REVERT: B   21 ASP cc_start: 0.7603 (t0) cc_final: 0.6742 (t0)
REVERT: B   33 GLU cc_start: 0.7503 (pm20) cc_final: 0.7297 (pm20)
REVERT: B  132 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8081 (ttmm)
REVERT: B  159 LYS cc_start: 0.7877 (ttpp) cc_final: 0.7615 (ttmm)
REVERT: C    3 VAL cc_start: 0.8325 (t) cc_final: 0.7841 (p)
REVERT: C    6 ASP cc_start: 0.7451 (t0) cc_final: 0.7238 (t0)
REVERT: C    7 ASP cc_start: 0.7752 (t70) cc_final: 0.7341 (t0)
REVERT: C   75 MET cc_start: 0.7019 (tmm) cc_final: 0.6788 (tpp)
REVERT: C   76 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7875 (ttpt)
REVERT: C   77 ILE cc_start: 0.8311 (pt) cc_final: 0.8016 (tt)
REVERT: C   95 ASP cc_start: 0.8207 (t70) cc_final: 0.7537 (t70)
REVERT: C  100 ASN cc_start: 0.7612 (m-40) cc_final: 0.7404 (m-40)
REVERT: C  108 GLU cc_start: 0.7093 (pp20) cc_final: 0.6751 (tm-30)
REVERT: C  112 ARG cc_start: 0.8254 (tpp80) cc_final: 0.7932 (tpp80)
REVERT: C  140 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7604 (tttm)
REVERT: C  165 LYS cc_start: 0.7822 (pttp) cc_final: 0.7253 (ptpt)
REVERT: C  171 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7158 (mm-30)
REVERT: C  205 LEU cc_start: 0.8195 (mt) cc_final: 0.7925 (tp)
REVERT: C  209 LYS cc_start: 0.8115 (ptmm) cc_final: 0.7605 (ptmm)
REVERT: C  215 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7801 (ttmm)
REVERT: C  230 MET cc_start: 0.5445 (mtm) cc_final: 0.5175 (mtm)
REVERT: E    6 ILE cc_start: 0.6499 (tp) cc_final: 0.6229 (tp)
REVERT: E   46 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7513 (tm-30)
REVERT: E   86 LYS cc_start: 0.7703 (tppt) cc_final: 0.7495 (mmmm)
REVERT: E  101 LYS cc_start: 0.8663 (pttm) cc_final: 0.8207 (pttm)
REVERT: E  117 GLU cc_start: 0.5076 (mp0) cc_final: 0.4661 (mp0)
REVERT: E  126 SER cc_start: 0.8352 (t) cc_final: 0.7923 (p)
REVERT: E  127 THR cc_start: 0.8170 (m) cc_final: 0.7782 (p)
REVERT: E  135 THR cc_start: 0.8030 (m) cc_final: 0.7770 (p)
REVERT: E  174 ILE cc_start: 0.7955 (mm) cc_final: 0.7646 (tp)
REVERT: E  194 SER cc_start: 0.7854 (p) cc_final: 0.7583 (p)
REVERT: E  197 ILE cc_start: 0.8043 (mm) cc_final: 0.7716 (tp)
REVERT: E  239 GLU cc_start: 0.7561 (tp30) cc_final: 0.6351 (mp0)
REVERT: E  274 LYS cc_start: 0.6933 (mppt) cc_final: 0.6596 (mppt)
REVERT: E  277 ILE cc_start: 0.8560 (mp) cc_final: 0.8341 (mt)
REVERT: E  290 PRO cc_start: 0.8007 (Cg_endo) cc_final: 0.7714 (Cg_exo)
REVERT: E  325 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6936 (tp-100)
REVERT: E  326 GLU cc_start: 0.7543 (tp30) cc_final: 0.6739 (tp30)
REVERT: E  328 MET cc_start: 0.7530 (mtm) cc_final: 0.7242 (mtm)
REVERT: E  329 HIS cc_start: 0.7228 (m90) cc_final: 0.5939 (m90)
REVERT: E  360 TYR cc_start: 0.7392 (m-80) cc_final: 0.6584 (m-80)
REVERT: E  363 LYS cc_start: 0.8339 (mmtt) cc_final: 0.8062 (mmtp)
REVERT: E  397 LYS cc_start: 0.7778 (mmmt) cc_final: 0.7487 (mmtp)
REVERT: E  434 LEU cc_start: 0.8477 (tp) cc_final: 0.7953 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 357
  average time/residue: 0.2981
  time to fit residues: 138.7937
Evaluate side-chains
  314 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 314
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 50 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 98 optimal weight:    0.0770
   chunk 43 optimal weight:    0.6980
   chunk 95 optimal weight:    0.1980
   chunk 112 optimal weight:    6.9990
   chunk 69 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.4138

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.136877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.115321 restraints weight = 19248.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.117989 restraints weight = 12144.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.119818 restraints weight = 8620.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3549
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3549 r_free = 0.3549    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 = 0.3549 r_free = 0.3549    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3549
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6919
moved from start:          0.3082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10899  Z= 0.163
  Angle     :  0.571   9.881  14963  Z= 0.308
  Chirality :  0.043   0.171   1723
  Planarity :  0.004   0.050   1683
  Dihedral  : 20.791 149.626   1931
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  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: -1.99 (0.25), residues: 1171
  helix: -0.27 (0.31), residues: 309
  sheet:  0.23 (0.32), residues: 314
  loop : -3.01 (0.23), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  50 
 HIS   0.003   0.001   HIS A  39 
 PHE   0.017   0.001   PHE E  10 
 TYR   0.018   0.001   TYR C  59 
 ARG   0.007   0.000   ARG E 234 

*********************** 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  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.5565 (t70) cc_final: 0.5223 (t0)
REVERT: A   57 LEU cc_start: 0.8087 (mt) cc_final: 0.7811 (mt)
REVERT: A   65 PRO cc_start: 0.6647 (Cg_exo) cc_final: 0.6396 (Cg_endo)
REVERT: A   91 LEU cc_start: 0.8095 (tp) cc_final: 0.7866 (tt)
REVERT: A  110 LYS cc_start: 0.7151 (ttmt) cc_final: 0.6876 (ttmm)
REVERT: A  116 LYS cc_start: 0.8027 (mtmm) cc_final: 0.7657 (tppt)
REVERT: A  119 LYS cc_start: 0.7074 (mppt) cc_final: 0.6707 (mppt)
REVERT: A  156 GLU cc_start: 0.7962 (mp0) cc_final: 0.7738 (mm-30)
REVERT: A  212 LEU cc_start: 0.7353 (mt) cc_final: 0.7091 (tp)
REVERT: A  213 ARG cc_start: 0.6782 (mtt90) cc_final: 0.6550 (mtt90)
REVERT: A  220 MET cc_start: 0.7586 (tmm) cc_final: 0.7070 (ttp)
REVERT: A  229 MET cc_start: 0.6340 (ttt) cc_final: 0.6084 (ttt)
REVERT: B   21 ASP cc_start: 0.7549 (t0) cc_final: 0.6706 (t0)
REVERT: B  103 ASP cc_start: 0.6917 (m-30) cc_final: 0.6713 (m-30)
REVERT: B  107 THR cc_start: 0.8066 (p) cc_final: 0.7780 (t)
REVERT: B  132 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7815 (ttmm)
REVERT: B  153 VAL cc_start: 0.7832 (t) cc_final: 0.7506 (p)
REVERT: B  159 LYS cc_start: 0.7892 (ttpp) cc_final: 0.7572 (ttmm)
REVERT: B  162 LYS cc_start: 0.8007 (mttp) cc_final: 0.7767 (mttp)
REVERT: C    3 VAL cc_start: 0.8317 (t) cc_final: 0.7901 (p)
REVERT: C    6 ASP cc_start: 0.7317 (t0) cc_final: 0.7079 (t0)
REVERT: C    7 ASP cc_start: 0.7782 (t70) cc_final: 0.7407 (t0)
REVERT: C   23 ASP cc_start: 0.7740 (m-30) cc_final: 0.7527 (m-30)
REVERT: C   75 MET cc_start: 0.6896 (tmm) cc_final: 0.6671 (tpp)
REVERT: C   77 ILE cc_start: 0.8302 (pt) cc_final: 0.8051 (tt)
REVERT: C   84 LYS cc_start: 0.7804 (mttp) cc_final: 0.7508 (mttp)
REVERT: C   85 GLU cc_start: 0.7442 (mp0) cc_final: 0.7071 (mp0)
REVERT: C   95 ASP cc_start: 0.8245 (t70) cc_final: 0.7756 (t70)
REVERT: C  109 PHE cc_start: 0.8010 (m-80) cc_final: 0.7754 (m-80)
REVERT: C  112 ARG cc_start: 0.8244 (tpp80) cc_final: 0.7927 (tpp80)
REVERT: C  130 ILE cc_start: 0.8649 (mp) cc_final: 0.8400 (mm)
REVERT: C  165 LYS cc_start: 0.7960 (pttp) cc_final: 0.7341 (ptpt)
REVERT: C  171 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7151 (mm-30)
REVERT: C  205 LEU cc_start: 0.8243 (mt) cc_final: 0.7932 (tp)
REVERT: C  209 LYS cc_start: 0.8115 (ptmm) cc_final: 0.7555 (ptmm)
REVERT: C  215 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7880 (ttmm)
REVERT: E    6 ILE cc_start: 0.6813 (tp) cc_final: 0.6493 (tp)
REVERT: E   15 LYS cc_start: 0.8425 (mtmt) cc_final: 0.8101 (mmtm)
REVERT: E   36 THR cc_start: 0.7868 (p) cc_final: 0.7445 (p)
REVERT: E   46 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7550 (tm-30)
REVERT: E   86 LYS cc_start: 0.7664 (tppt) cc_final: 0.7435 (mmmm)
REVERT: E   93 GLU cc_start: 0.7925 (tp30) cc_final: 0.7704 (tp30)
REVERT: E  101 LYS cc_start: 0.8613 (pttm) cc_final: 0.8185 (pttm)
REVERT: E  117 GLU cc_start: 0.4969 (mp0) cc_final: 0.4597 (mp0)
REVERT: E  126 SER cc_start: 0.8268 (t) cc_final: 0.7824 (p)
REVERT: E  127 THR cc_start: 0.8067 (m) cc_final: 0.7783 (p)
REVERT: E  135 THR cc_start: 0.7817 (m) cc_final: 0.7532 (p)
REVERT: E  171 ARG cc_start: 0.8169 (mtm-85) cc_final: 0.7857 (mtm-85)
REVERT: E  174 ILE cc_start: 0.7932 (mm) cc_final: 0.7650 (tp)
REVERT: E  197 ILE cc_start: 0.7991 (mm) cc_final: 0.7748 (tp)
REVERT: E  209 ASN cc_start: 0.6527 (m-40) cc_final: 0.6036 (m-40)
REVERT: E  239 GLU cc_start: 0.7573 (tp30) cc_final: 0.6424 (mp0)
REVERT: E  274 LYS cc_start: 0.6957 (mppt) cc_final: 0.6549 (mppt)
REVERT: E  277 ILE cc_start: 0.8489 (mp) cc_final: 0.8280 (mt)
REVERT: E  290 PRO cc_start: 0.7955 (Cg_endo) cc_final: 0.7648 (Cg_exo)
REVERT: E  326 GLU cc_start: 0.7613 (tp30) cc_final: 0.6687 (tp30)
REVERT: E  328 MET cc_start: 0.7371 (mtm) cc_final: 0.7076 (mmp)
REVERT: E  329 HIS cc_start: 0.7236 (m90) cc_final: 0.5862 (m90)
REVERT: E  363 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8205 (mmtp)
REVERT: E  397 LYS cc_start: 0.7761 (mmmt) cc_final: 0.7419 (mmtp)
REVERT: E  434 LEU cc_start: 0.8473 (tp) cc_final: 0.7932 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 349
  average time/residue: 0.2998
  time to fit residues: 136.1551
Evaluate side-chains
  321 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 321
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 67 optimal weight:    0.0970
   chunk 37 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 117 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
B 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 = 0.3762 r_free = 0.3762 target = 0.135253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.113643 restraints weight = 18922.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.116219 restraints weight = 11931.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.118125 restraints weight = 8444.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3522
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3522 r_free = 0.3522    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 = 0.3522 r_free = 0.3522    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3522
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10899  Z= 0.208
  Angle     :  0.606   9.449  14963  Z= 0.326
  Chirality :  0.044   0.175   1723
  Planarity :  0.004   0.047   1683
  Dihedral  : 20.910 148.894   1931
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.22 %
    Favored  : 90.78 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.90 %
    Favored  : 97.00 %
  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 (0.24), residues: 1171
  helix: -0.33 (0.31), residues: 306
  sheet:  0.20 (0.32), residues: 317
  loop : -2.99 (0.23), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E  50 
 HIS   0.003   0.001   HIS A 240 
 PHE   0.017   0.002   PHE E  10 
 TYR   0.019   0.001   TYR C  59 
 ARG   0.009   0.001   ARG E 265 

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

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 343
  time to evaluate  : 1.106 
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   10 LYS cc_start: 0.7495 (mttt) cc_final: 0.7249 (mttt)
REVERT: A   24 ASP cc_start: 0.5667 (t70) cc_final: 0.5256 (t0)
REVERT: A   57 LEU cc_start: 0.8090 (mt) cc_final: 0.7883 (mt)
REVERT: A   69 LYS cc_start: 0.7707 (mppt) cc_final: 0.7246 (mmtm)
REVERT: A   91 LEU cc_start: 0.8137 (tp) cc_final: 0.7893 (tt)
REVERT: A   99 LYS cc_start: 0.7915 (tptt) cc_final: 0.7668 (ttmm)
REVERT: A  116 LYS cc_start: 0.8010 (mtmm) cc_final: 0.7695 (tptt)
REVERT: A  136 PHE cc_start: 0.6871 (p90) cc_final: 0.6588 (p90)
REVERT: A  156 GLU cc_start: 0.7936 (mp0) cc_final: 0.7712 (mm-30)
REVERT: A  210 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7928 (mtpp)
REVERT: A  213 ARG cc_start: 0.6738 (mtt90) cc_final: 0.6524 (mtt90)
REVERT: A  227 LEU cc_start: 0.7491 (tp) cc_final: 0.7070 (tt)
REVERT: A  229 MET cc_start: 0.6409 (ttt) cc_final: 0.6135 (ttt)
REVERT: B   21 ASP cc_start: 0.7487 (t0) cc_final: 0.6655 (t0)
REVERT: B  107 THR cc_start: 0.8024 (p) cc_final: 0.7776 (t)
REVERT: B  132 LYS cc_start: 0.8191 (ttmt) cc_final: 0.7844 (ttmm)
REVERT: B  139 THR cc_start: 0.7790 (p) cc_final: 0.7587 (p)
REVERT: B  145 ASP cc_start: 0.6287 (m-30) cc_final: 0.5706 (t70)
REVERT: B  153 VAL cc_start: 0.8241 (t) cc_final: 0.8002 (p)
REVERT: B  162 LYS cc_start: 0.7993 (mttp) cc_final: 0.7542 (mttp)
REVERT: C    3 VAL cc_start: 0.8543 (t) cc_final: 0.8111 (p)
REVERT: C    7 ASP cc_start: 0.7850 (t70) cc_final: 0.7469 (t0)
REVERT: C   23 ASP cc_start: 0.7947 (m-30) cc_final: 0.7529 (m-30)
REVERT: C   28 LYS cc_start: 0.8109 (mttp) cc_final: 0.7345 (mttm)
REVERT: C   30 LYS cc_start: 0.7646 (mmmm) cc_final: 0.7322 (tppp)
REVERT: C   35 GLU cc_start: 0.6890 (mp0) cc_final: 0.6543 (pm20)
REVERT: C   75 MET cc_start: 0.7051 (tmm) cc_final: 0.6781 (tpp)
REVERT: C   76 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7881 (ttpt)
REVERT: C   84 LYS cc_start: 0.7703 (mttp) cc_final: 0.7498 (mttp)
REVERT: C   85 GLU cc_start: 0.7315 (mp0) cc_final: 0.6734 (mp0)
REVERT: C  112 ARG cc_start: 0.8185 (tpp80) cc_final: 0.7969 (tpp80)
REVERT: C  130 ILE cc_start: 0.8685 (mp) cc_final: 0.8416 (mm)
REVERT: C  154 VAL cc_start: 0.7913 (t) cc_final: 0.7558 (p)
REVERT: C  165 LYS cc_start: 0.8004 (pttp) cc_final: 0.7320 (ptpt)
REVERT: C  171 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7073 (mm-30)
REVERT: C  175 GLU cc_start: 0.6863 (pt0) cc_final: 0.6626 (pt0)
REVERT: C  205 LEU cc_start: 0.8259 (mt) cc_final: 0.7957 (tp)
REVERT: C  209 LYS cc_start: 0.8160 (ptmm) cc_final: 0.7798 (ttpp)
REVERT: C  215 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7838 (ttmm)
REVERT: E    6 ILE cc_start: 0.6828 (tp) cc_final: 0.6461 (tp)
REVERT: E   46 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7626 (tm-30)
REVERT: E   49 LEU cc_start: 0.7278 (mt) cc_final: 0.6968 (mt)
REVERT: E   93 GLU cc_start: 0.7972 (tp30) cc_final: 0.7691 (tp30)
REVERT: E  110 PHE cc_start: 0.5948 (m-10) cc_final: 0.5726 (m-10)
REVERT: E  117 GLU cc_start: 0.5031 (mp0) cc_final: 0.4642 (mp0)
REVERT: E  126 SER cc_start: 0.8313 (t) cc_final: 0.7814 (p)
REVERT: E  135 THR cc_start: 0.8284 (m) cc_final: 0.8039 (p)
REVERT: E  142 LEU cc_start: 0.8140 (mt) cc_final: 0.7895 (mt)
REVERT: E  174 ILE cc_start: 0.7920 (mm) cc_final: 0.7590 (tt)
REVERT: E  194 SER cc_start: 0.7913 (p) cc_final: 0.7410 (p)
REVERT: E  197 ILE cc_start: 0.7983 (mm) cc_final: 0.7545 (tp)
REVERT: E  198 GLU cc_start: 0.6929 (tt0) cc_final: 0.6689 (pt0)
REVERT: E  223 LYS cc_start: 0.7526 (mmtp) cc_final: 0.7267 (mmtm)
REVERT: E  239 GLU cc_start: 0.7579 (tp30) cc_final: 0.6477 (mp0)
REVERT: E  274 LYS cc_start: 0.7036 (mppt) cc_final: 0.6612 (mppt)
REVERT: E  277 ILE cc_start: 0.8471 (mp) cc_final: 0.8252 (mt)
REVERT: E  281 ARG cc_start: 0.6818 (mtm180) cc_final: 0.6573 (mtm180)
REVERT: E  290 PRO cc_start: 0.7992 (Cg_endo) cc_final: 0.7646 (Cg_exo)
REVERT: E  325 GLN cc_start: 0.7258 (tp40) cc_final: 0.6891 (tp-100)
REVERT: E  326 GLU cc_start: 0.7661 (tp30) cc_final: 0.6567 (tp30)
REVERT: E  329 HIS cc_start: 0.7230 (m90) cc_final: 0.5870 (m90)
REVERT: E  363 LYS cc_start: 0.8276 (mmtt) cc_final: 0.8049 (mmtp)
REVERT: E  397 LYS cc_start: 0.7753 (mmmt) cc_final: 0.7408 (mmtp)
  outliers start: 1
  outliers final: 1
  residues processed: 344
  average time/residue: 0.3070
  time to fit residues: 137.3627
Evaluate side-chains
  316 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 315
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 38 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0980
   chunk 77 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3765 r_free = 0.3765 target = 0.135777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.114365 restraints weight = 18885.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.116906 restraints weight = 11931.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.118689 restraints weight = 8551.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3531
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3531 r_free = 0.3531    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 = 0.3531 r_free = 0.3531    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3531
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.3558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10899  Z= 0.192
  Angle     :  0.601   8.985  14963  Z= 0.322
  Chirality :  0.044   0.167   1723
  Planarity :  0.004   0.051   1683
  Dihedral  : 20.918 149.281   1931
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    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: -1.96 (0.24), residues: 1171
  helix: -0.32 (0.31), residues: 305
  sheet:  0.24 (0.32), residues: 321
  loop : -2.96 (0.23), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E  50 
 HIS   0.007   0.001   HIS B 157 
 PHE   0.030   0.002   PHE A  30 
 TYR   0.018   0.002   TYR C  59 
 ARG   0.009   0.000   ARG E 234 

*********************** 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
  333 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 333
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.5675 (t70) cc_final: 0.5313 (t0)
REVERT: A   57 LEU cc_start: 0.8094 (mt) cc_final: 0.7876 (mt)
REVERT: A   59 GLU cc_start: 0.8247 (tp30) cc_final: 0.7993 (tp30)
REVERT: A   69 LYS cc_start: 0.7723 (mppt) cc_final: 0.7197 (mmtm)
REVERT: A   91 LEU cc_start: 0.8050 (tp) cc_final: 0.7734 (tt)
REVERT: A  116 LYS cc_start: 0.8076 (mtmm) cc_final: 0.7708 (tptt)
REVERT: A  136 PHE cc_start: 0.7200 (p90) cc_final: 0.6920 (p90)
REVERT: A  156 GLU cc_start: 0.7911 (mp0) cc_final: 0.7694 (mm-30)
REVERT: A  229 MET cc_start: 0.6365 (ttt) cc_final: 0.6101 (ttt)
REVERT: B   21 ASP cc_start: 0.7647 (t0) cc_final: 0.6717 (t0)
REVERT: B  107 THR cc_start: 0.8307 (p) cc_final: 0.7884 (t)
REVERT: B  132 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7716 (ttmm)
REVERT: B  153 VAL cc_start: 0.8318 (t) cc_final: 0.8027 (p)
REVERT: B  162 LYS cc_start: 0.7821 (mttp) cc_final: 0.7431 (mttp)
REVERT: C    3 VAL cc_start: 0.8523 (t) cc_final: 0.8063 (p)
REVERT: C    7 ASP cc_start: 0.7855 (t70) cc_final: 0.7439 (t0)
REVERT: C   23 ASP cc_start: 0.7916 (m-30) cc_final: 0.7491 (m-30)
REVERT: C   35 GLU cc_start: 0.6921 (mp0) cc_final: 0.6368 (mp0)
REVERT: C   75 MET cc_start: 0.7085 (tmm) cc_final: 0.6795 (tpp)
REVERT: C   85 GLU cc_start: 0.7285 (mp0) cc_final: 0.6950 (mp0)
REVERT: C  112 ARG cc_start: 0.8185 (tpp80) cc_final: 0.7975 (tpp80)
REVERT: C  130 ILE cc_start: 0.8680 (mp) cc_final: 0.8427 (mm)
REVERT: C  165 LYS cc_start: 0.7966 (pttp) cc_final: 0.7317 (ptpt)
REVERT: C  171 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7193 (mm-30)
REVERT: C  195 SER cc_start: 0.8422 (m) cc_final: 0.8158 (p)
REVERT: C  205 LEU cc_start: 0.8226 (mt) cc_final: 0.7939 (tp)
REVERT: C  209 LYS cc_start: 0.8150 (ptmm) cc_final: 0.7803 (ttpp)
REVERT: C  215 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7885 (ttmm)
REVERT: E    6 ILE cc_start: 0.6808 (tp) cc_final: 0.6416 (tp)
REVERT: E   36 THR cc_start: 0.7773 (p) cc_final: 0.7381 (p)
REVERT: E   46 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7602 (tm-30)
REVERT: E   86 LYS cc_start: 0.7763 (tptm) cc_final: 0.7540 (mmmm)
REVERT: E   93 GLU cc_start: 0.8024 (tp30) cc_final: 0.7728 (tp30)
REVERT: E  101 LYS cc_start: 0.8595 (pttm) cc_final: 0.8240 (pttm)
REVERT: E  126 SER cc_start: 0.8341 (t) cc_final: 0.7880 (p)
REVERT: E  127 THR cc_start: 0.8007 (m) cc_final: 0.7680 (p)
REVERT: E  135 THR cc_start: 0.7946 (m) cc_final: 0.7582 (p)
REVERT: E  142 LEU cc_start: 0.8092 (mt) cc_final: 0.7861 (mt)
REVERT: E  174 ILE cc_start: 0.7978 (mm) cc_final: 0.7679 (tp)
REVERT: E  194 SER cc_start: 0.7908 (p) cc_final: 0.6769 (p)
REVERT: E  197 ILE cc_start: 0.7906 (mm) cc_final: 0.7514 (tp)
REVERT: E  203 LEU cc_start: 0.7781 (mt) cc_final: 0.7523 (mt)
REVERT: E  239 GLU cc_start: 0.7316 (tp30) cc_final: 0.6316 (mp0)
REVERT: E  248 LEU cc_start: 0.6754 (mp) cc_final: 0.6514 (mp)
REVERT: E  274 LYS cc_start: 0.7052 (mppt) cc_final: 0.6612 (mppt)
REVERT: E  277 ILE cc_start: 0.8453 (mp) cc_final: 0.8241 (mt)
REVERT: E  290 PRO cc_start: 0.8013 (Cg_endo) cc_final: 0.7664 (Cg_exo)
REVERT: E  325 GLN cc_start: 0.7244 (tp40) cc_final: 0.6698 (tp40)
REVERT: E  326 GLU cc_start: 0.7652 (tp30) cc_final: 0.6390 (tp30)
REVERT: E  329 HIS cc_start: 0.7126 (m90) cc_final: 0.5892 (m90)
REVERT: E  363 LYS cc_start: 0.8313 (mmtt) cc_final: 0.8100 (mmtp)
REVERT: E  397 LYS cc_start: 0.7743 (mmmt) cc_final: 0.7346 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 333
  average time/residue: 0.2913
  time to fit residues: 126.1139
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  : 1.262 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 115 optimal weight:    0.9990
   chunk 118 optimal weight:    0.7980
   chunk 121 optimal weight:    0.5980
   chunk 108 optimal weight:    2.9990
   chunk 119 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0870
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
B 157 HIS
C  72 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.136152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.114736 restraints weight = 18983.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.117309 restraints weight = 12081.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.119105 restraints weight = 8599.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3532
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3532 r_free = 0.3532    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 = 0.3532 r_free = 0.3532    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3532
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6946
moved from start:          0.3754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10899  Z= 0.184
  Angle     :  0.601  10.104  14963  Z= 0.321
  Chirality :  0.044   0.164   1723
  Planarity :  0.004   0.050   1683
  Dihedral  : 20.944 148.398   1931
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  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: -1.96 (0.25), residues: 1171
  helix: -0.30 (0.31), residues: 309
  sheet:  0.17 (0.31), residues: 325
  loop : -2.96 (0.23), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E  50 
 HIS   0.006   0.001   HIS B 157 
 PHE   0.023   0.002   PHE E  10 
 TYR   0.017   0.001   TYR C  59 
 ARG   0.004   0.000   ARG E 265 

*********************** 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
  334 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 334
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.5802 (t70) cc_final: 0.5415 (t0)
REVERT: A   57 LEU cc_start: 0.8131 (mt) cc_final: 0.7861 (mt)
REVERT: A   65 PRO cc_start: 0.6618 (Cg_exo) cc_final: 0.6316 (Cg_endo)
REVERT: A   69 LYS cc_start: 0.7741 (mppt) cc_final: 0.7221 (mmtm)
REVERT: A   91 LEU cc_start: 0.8007 (tp) cc_final: 0.7373 (tt)
REVERT: A   99 LYS cc_start: 0.8007 (tppp) cc_final: 0.7771 (tppp)
REVERT: A  116 LYS cc_start: 0.8060 (mtmm) cc_final: 0.7770 (tppt)
REVERT: A  119 LYS cc_start: 0.7083 (mppt) cc_final: 0.6838 (mppt)
REVERT: A  206 LYS cc_start: 0.7991 (ttmm) cc_final: 0.7772 (ttmm)
REVERT: A  229 MET cc_start: 0.6372 (ttt) cc_final: 0.6095 (ttt)
REVERT: B   21 ASP cc_start: 0.7642 (t0) cc_final: 0.6669 (t0)
REVERT: B  107 THR cc_start: 0.8247 (p) cc_final: 0.7838 (t)
REVERT: B  132 LYS cc_start: 0.7942 (ttmt) cc_final: 0.7681 (ttmm)
REVERT: B  153 VAL cc_start: 0.8344 (t) cc_final: 0.8081 (p)
REVERT: B  162 LYS cc_start: 0.7718 (mttp) cc_final: 0.7318 (mttp)
REVERT: C    3 VAL cc_start: 0.8505 (t) cc_final: 0.8047 (p)
REVERT: C    7 ASP cc_start: 0.7877 (t70) cc_final: 0.7407 (t0)
REVERT: C   23 ASP cc_start: 0.7910 (m-30) cc_final: 0.7537 (m-30)
REVERT: C   30 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7390 (tppp)
REVERT: C   35 GLU cc_start: 0.6921 (mp0) cc_final: 0.6587 (pm20)
REVERT: C   75 MET cc_start: 0.7058 (tmm) cc_final: 0.6802 (tpp)
REVERT: C   76 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7856 (ttpt)
REVERT: C   84 LYS cc_start: 0.7679 (mttm) cc_final: 0.7232 (mttm)
REVERT: C  109 PHE cc_start: 0.8466 (m-80) cc_final: 0.7850 (m-80)
REVERT: C  130 ILE cc_start: 0.8685 (mp) cc_final: 0.8424 (mm)
REVERT: C  165 LYS cc_start: 0.7783 (pttp) cc_final: 0.7468 (ptpt)
REVERT: C  171 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7018 (mm-30)
REVERT: C  205 LEU cc_start: 0.8217 (mt) cc_final: 0.7951 (tp)
REVERT: C  209 LYS cc_start: 0.8117 (ptmm) cc_final: 0.7797 (ttpp)
REVERT: E    1 MET cc_start: 0.7267 (mtm) cc_final: 0.7030 (mtm)
REVERT: E    6 ILE cc_start: 0.6836 (tp) cc_final: 0.6539 (tp)
REVERT: E   15 LYS cc_start: 0.8507 (mtmt) cc_final: 0.8061 (mmtm)
REVERT: E   32 LYS cc_start: 0.7693 (mmmm) cc_final: 0.7404 (ttmm)
REVERT: E   36 THR cc_start: 0.7747 (p) cc_final: 0.7317 (p)
REVERT: E   86 LYS cc_start: 0.7735 (tptm) cc_final: 0.7530 (mmmm)
REVERT: E   93 GLU cc_start: 0.7967 (tp30) cc_final: 0.7655 (tp30)
REVERT: E  101 LYS cc_start: 0.8519 (pttm) cc_final: 0.8227 (pttm)
REVERT: E  126 SER cc_start: 0.8286 (t) cc_final: 0.7876 (p)
REVERT: E  127 THR cc_start: 0.8011 (m) cc_final: 0.7650 (p)
REVERT: E  135 THR cc_start: 0.8312 (m) cc_final: 0.8023 (p)
REVERT: E  142 LEU cc_start: 0.8093 (mt) cc_final: 0.7878 (mt)
REVERT: E  174 ILE cc_start: 0.8014 (mm) cc_final: 0.7649 (tp)
REVERT: E  194 SER cc_start: 0.7918 (p) cc_final: 0.7454 (p)
REVERT: E  197 ILE cc_start: 0.7955 (mm) cc_final: 0.7688 (tp)
REVERT: E  198 GLU cc_start: 0.7019 (pt0) cc_final: 0.6745 (pt0)
REVERT: E  203 LEU cc_start: 0.7734 (mt) cc_final: 0.7521 (mt)
REVERT: E  206 ASP cc_start: 0.7807 (t70) cc_final: 0.7319 (t70)
REVERT: E  209 ASN cc_start: 0.7995 (p0) cc_final: 0.7382 (p0)
REVERT: E  239 GLU cc_start: 0.7333 (tp30) cc_final: 0.6335 (mp0)
REVERT: E  248 LEU cc_start: 0.6797 (mp) cc_final: 0.6534 (mp)
REVERT: E  274 LYS cc_start: 0.7090 (mppt) cc_final: 0.6614 (mppt)
REVERT: E  277 ILE cc_start: 0.8441 (mp) cc_final: 0.8202 (mt)
REVERT: E  281 ARG cc_start: 0.6743 (mtm180) cc_final: 0.6315 (mtm110)
REVERT: E  283 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6927 (mp0)
REVERT: E  290 PRO cc_start: 0.7960 (Cg_endo) cc_final: 0.7641 (Cg_exo)
REVERT: E  325 GLN cc_start: 0.7223 (tp40) cc_final: 0.6711 (tp40)
REVERT: E  326 GLU cc_start: 0.7665 (tp30) cc_final: 0.6418 (tp30)
REVERT: E  329 HIS cc_start: 0.7179 (m90) cc_final: 0.5929 (m90)
REVERT: E  363 LYS cc_start: 0.8320 (mmtt) cc_final: 0.8105 (mmtp)
REVERT: E  394 GLU cc_start: 0.7309 (pm20) cc_final: 0.6890 (tp30)
REVERT: E  397 LYS cc_start: 0.7698 (mmmt) cc_final: 0.7368 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 334
  average time/residue: 0.2923
  time to fit residues: 127.7041
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  : 1.143 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 118 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    1.7990

-------------------------------------------------------------------------------
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 = 0.3709 r_free = 0.3709 target = 0.132091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.110725 restraints weight = 19451.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.113276 restraints weight = 12374.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.115032 restraints weight = 8822.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.105  10899  Z= 0.352
  Angle     :  0.721  11.242  14963  Z= 0.387
  Chirality :  0.047   0.190   1723
  Planarity :  0.004   0.056   1683
  Dihedral  : 21.277 155.958   1931
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.93 %
    Favored  : 89.07 %
  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: -2.32 (0.24), residues: 1171
  helix: -0.76 (0.30), residues: 306
  sheet:  0.04 (0.31), residues: 315
  loop : -3.06 (0.22), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.004   TRP E  50 
 HIS   0.004   0.001   HIS A  39 
 PHE   0.030   0.003   PHE B  71 
 TYR   0.028   0.002   TYR C  59 
 ARG   0.008   0.001   ARG E 265 

*********************** 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
  337 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 337
  time to evaluate  : 1.247 
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   19 ILE cc_start: 0.8320 (tp) cc_final: 0.8091 (mm)
REVERT: A   24 ASP cc_start: 0.5814 (t70) cc_final: 0.5521 (t0)
REVERT: A   57 LEU cc_start: 0.8061 (mt) cc_final: 0.7764 (mt)
REVERT: A   59 GLU cc_start: 0.8314 (tp30) cc_final: 0.8034 (tp30)
REVERT: A   69 LYS cc_start: 0.7671 (mppt) cc_final: 0.7152 (pttm)
REVERT: A  116 LYS cc_start: 0.8017 (mtmm) cc_final: 0.7750 (tppt)
REVERT: A  206 LYS cc_start: 0.8017 (ttmm) cc_final: 0.7758 (ttmm)
REVERT: B   21 ASP cc_start: 0.7395 (t0) cc_final: 0.6305 (t0)
REVERT: B  107 THR cc_start: 0.7925 (p) cc_final: 0.7627 (t)
REVERT: B  132 LYS cc_start: 0.8402 (ttmt) cc_final: 0.7872 (ttmm)
REVERT: B  162 LYS cc_start: 0.7784 (mttp) cc_final: 0.7422 (mttp)
REVERT: B  200 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6744 (tm-30)
REVERT: B  218 TYR cc_start: 0.7942 (m-80) cc_final: 0.7721 (m-80)
REVERT: C    3 VAL cc_start: 0.8811 (t) cc_final: 0.8493 (p)
REVERT: C    7 ASP cc_start: 0.7729 (t70) cc_final: 0.7156 (t0)
REVERT: C   23 ASP cc_start: 0.7529 (m-30) cc_final: 0.7089 (m-30)
REVERT: C   28 LYS cc_start: 0.8155 (mttp) cc_final: 0.7036 (mttm)
REVERT: C   30 LYS cc_start: 0.7783 (mmtp) cc_final: 0.7424 (mmmm)
REVERT: C   35 GLU cc_start: 0.6982 (mp0) cc_final: 0.6413 (mp0)
REVERT: C   72 GLN cc_start: 0.7707 (tt0) cc_final: 0.7286 (mt0)
REVERT: C   75 MET cc_start: 0.6992 (tmm) cc_final: 0.6751 (tpp)
REVERT: C   85 GLU cc_start: 0.7468 (mp0) cc_final: 0.7139 (mp0)
REVERT: C  165 LYS cc_start: 0.7848 (pttp) cc_final: 0.7524 (ptpt)
REVERT: C  171 GLU cc_start: 0.7550 (mt-10) cc_final: 0.6839 (mm-30)
REVERT: C  205 LEU cc_start: 0.8458 (mt) cc_final: 0.8139 (tp)
REVERT: C  209 LYS cc_start: 0.8169 (ptmm) cc_final: 0.7705 (ptmm)
REVERT: C  215 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7775 (ttmm)
REVERT: E    1 MET cc_start: 0.7166 (mtm) cc_final: 0.6910 (mtm)
REVERT: E    6 ILE cc_start: 0.6877 (tp) cc_final: 0.6614 (tp)
REVERT: E   32 LYS cc_start: 0.8001 (mmmm) cc_final: 0.7653 (ttmm)
REVERT: E   46 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7571 (tm-30)
REVERT: E   49 LEU cc_start: 0.7252 (mt) cc_final: 0.6998 (mt)
REVERT: E   86 LYS cc_start: 0.7871 (tptm) cc_final: 0.7587 (mmmm)
REVERT: E  101 LYS cc_start: 0.8657 (pttm) cc_final: 0.8231 (pttm)
REVERT: E  126 SER cc_start: 0.8397 (t) cc_final: 0.7883 (p)
REVERT: E  127 THR cc_start: 0.8039 (m) cc_final: 0.7774 (m)
REVERT: E  141 ASP cc_start: 0.7251 (m-30) cc_final: 0.7049 (m-30)
REVERT: E  142 LEU cc_start: 0.8157 (mt) cc_final: 0.7869 (mt)
REVERT: E  174 ILE cc_start: 0.8038 (mm) cc_final: 0.7683 (tt)
REVERT: E  194 SER cc_start: 0.7973 (p) cc_final: 0.7260 (p)
REVERT: E  197 ILE cc_start: 0.7973 (mm) cc_final: 0.7711 (tp)
REVERT: E  198 GLU cc_start: 0.7043 (pt0) cc_final: 0.6754 (pt0)
REVERT: E  224 THR cc_start: 0.7207 (p) cc_final: 0.6948 (p)
REVERT: E  226 LYS cc_start: 0.6533 (tptt) cc_final: 0.6001 (tptt)
REVERT: E  239 GLU cc_start: 0.7348 (tp30) cc_final: 0.6289 (mp0)
REVERT: E  248 LEU cc_start: 0.6731 (mp) cc_final: 0.6511 (mp)
REVERT: E  274 LYS cc_start: 0.7173 (mppt) cc_final: 0.6575 (mppt)
REVERT: E  281 ARG cc_start: 0.6783 (mtm180) cc_final: 0.6375 (mtm110)
REVERT: E  283 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6764 (mp0)
REVERT: E  290 PRO cc_start: 0.7943 (Cg_endo) cc_final: 0.7441 (Cg_exo)
REVERT: E  291 ASP cc_start: 0.7503 (p0) cc_final: 0.7081 (p0)
REVERT: E  325 GLN cc_start: 0.7343 (tp40) cc_final: 0.6968 (tp-100)
REVERT: E  326 GLU cc_start: 0.7739 (tp30) cc_final: 0.6436 (tp30)
REVERT: E  329 HIS cc_start: 0.7156 (m90) cc_final: 0.5916 (m90)
REVERT: E  363 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8223 (mmtp)
REVERT: E  394 GLU cc_start: 0.7321 (pm20) cc_final: 0.7058 (tp30)
REVERT: E  397 LYS cc_start: 0.7818 (mmmt) cc_final: 0.7491 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 337
  average time/residue: 0.3058
  time to fit residues: 134.9242
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  : 1.123 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 32 optimal weight:    0.0470
   chunk 15 optimal weight:    2.9990
   chunk 101 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 115 optimal weight:    5.9990
   chunk 46 optimal weight:    0.2980
   chunk 61 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    1.4482

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

Flipped N/Q/H residues before XYZ refinement:
A 135 ASN
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 102 GLN
** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.135957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.112921 restraints weight = 18941.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.115732 restraints weight = 11858.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.117689 restraints weight = 8415.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3502
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3502 r_free = 0.3502    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3501 r_free = 0.3501    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3501
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.4026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  10899  Z= 0.291
  Angle     :  0.702  12.206  14963  Z= 0.377
  Chirality :  0.047   0.196   1723
  Planarity :  0.004   0.053   1683
  Dihedral  : 21.307 156.218   1931
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.59 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  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: -2.31 (0.24), residues: 1171
  helix: -0.77 (0.30), residues: 305
  sheet:  0.04 (0.31), residues: 314
  loop : -3.04 (0.22), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP E  50 
 HIS   0.006   0.001   HIS B 157 
 PHE   0.038   0.003   PHE C  65 
 TYR   0.021   0.002   TYR C  59 
 ARG   0.006   0.001   ARG E 265 

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

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 337
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.5897 (t70) cc_final: 0.5559 (t0)
REVERT: A   57 LEU cc_start: 0.8021 (mt) cc_final: 0.7773 (mt)
REVERT: A   59 GLU cc_start: 0.8379 (tp30) cc_final: 0.8062 (tp30)
REVERT: A   69 LYS cc_start: 0.7660 (mppt) cc_final: 0.7230 (mmtp)
REVERT: A  116 LYS cc_start: 0.8013 (mtmm) cc_final: 0.7769 (tptt)
REVERT: A  119 LYS cc_start: 0.6969 (mppt) cc_final: 0.6759 (mppt)
REVERT: A  165 LYS cc_start: 0.7473 (mmpt) cc_final: 0.7183 (mmpt)
REVERT: B   21 ASP cc_start: 0.7435 (t0) cc_final: 0.6402 (t0)
REVERT: B  132 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7756 (ttmm)
REVERT: B  162 LYS cc_start: 0.7892 (mttp) cc_final: 0.7564 (mttp)
REVERT: C    2 LYS cc_start: 0.7346 (tppt) cc_final: 0.7074 (tppt)
REVERT: C    7 ASP cc_start: 0.7702 (t70) cc_final: 0.7172 (t0)
REVERT: C   72 GLN cc_start: 0.7747 (tt0) cc_final: 0.7298 (mt0)
REVERT: C   75 MET cc_start: 0.7047 (tmm) cc_final: 0.6828 (tpp)
REVERT: C   76 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8116 (ttpt)
REVERT: C   85 GLU cc_start: 0.7514 (mp0) cc_final: 0.7129 (mp0)
REVERT: C   88 GLU cc_start: 0.7375 (pp20) cc_final: 0.7051 (pp20)
REVERT: C  112 ARG cc_start: 0.8153 (tpp80) cc_final: 0.7783 (tpp80)
REVERT: C  130 ILE cc_start: 0.8833 (mp) cc_final: 0.8541 (mm)
REVERT: C  165 LYS cc_start: 0.7772 (pttp) cc_final: 0.7478 (ptpt)
REVERT: C  171 GLU cc_start: 0.7605 (mt-10) cc_final: 0.6868 (mm-30)
REVERT: C  205 LEU cc_start: 0.8421 (mt) cc_final: 0.8122 (tp)
REVERT: C  215 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7800 (ttmm)
REVERT: E    1 MET cc_start: 0.7066 (mtm) cc_final: 0.6858 (mtm)
REVERT: E    6 ILE cc_start: 0.6804 (tp) cc_final: 0.6510 (tp)
REVERT: E   32 LYS cc_start: 0.8052 (mmmm) cc_final: 0.7697 (ttmm)
REVERT: E   36 THR cc_start: 0.7540 (p) cc_final: 0.7116 (p)
REVERT: E   46 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7588 (tm-30)
REVERT: E   49 LEU cc_start: 0.7134 (mt) cc_final: 0.6887 (mt)
REVERT: E   86 LYS cc_start: 0.7833 (tptm) cc_final: 0.7566 (mmmm)
REVERT: E  101 LYS cc_start: 0.8653 (pttm) cc_final: 0.8239 (pttm)
REVERT: E  126 SER cc_start: 0.8380 (t) cc_final: 0.7887 (p)
REVERT: E  127 THR cc_start: 0.8038 (m) cc_final: 0.7778 (m)
REVERT: E  141 ASP cc_start: 0.7217 (m-30) cc_final: 0.6981 (m-30)
REVERT: E  142 LEU cc_start: 0.8144 (mt) cc_final: 0.7861 (mt)
REVERT: E  174 ILE cc_start: 0.8043 (mm) cc_final: 0.7661 (tt)
REVERT: E  194 SER cc_start: 0.7940 (p) cc_final: 0.7194 (p)
REVERT: E  197 ILE cc_start: 0.7979 (mm) cc_final: 0.7728 (tp)
REVERT: E  198 GLU cc_start: 0.7043 (pt0) cc_final: 0.6736 (pt0)
REVERT: E  203 LEU cc_start: 0.7806 (mt) cc_final: 0.7569 (mt)
REVERT: E  224 THR cc_start: 0.7191 (p) cc_final: 0.6967 (p)
REVERT: E  239 GLU cc_start: 0.7358 (tp30) cc_final: 0.6845 (mp0)
REVERT: E  248 LEU cc_start: 0.6706 (mp) cc_final: 0.6491 (mp)
REVERT: E  265 ARG cc_start: 0.7857 (ttm170) cc_final: 0.7521 (ttm170)
REVERT: E  274 LYS cc_start: 0.7238 (mppt) cc_final: 0.6714 (mppt)
REVERT: E  281 ARG cc_start: 0.6924 (mtm180) cc_final: 0.6490 (mtm110)
REVERT: E  290 PRO cc_start: 0.7949 (Cg_endo) cc_final: 0.7514 (Cg_exo)
REVERT: E  291 ASP cc_start: 0.7712 (p0) cc_final: 0.7278 (p0)
REVERT: E  320 GLU cc_start: 0.6153 (tp30) cc_final: 0.5903 (tp30)
REVERT: E  363 LYS cc_start: 0.8484 (mmtt) cc_final: 0.8219 (mmtp)
REVERT: E  394 GLU cc_start: 0.7336 (pm20) cc_final: 0.7071 (tp30)
REVERT: E  397 LYS cc_start: 0.7814 (mmmt) cc_final: 0.7480 (mmtp)
REVERT: E  409 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6861 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 337
  average time/residue: 0.2966
  time to fit residues: 130.4396
Evaluate side-chains
  307 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 307
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 92 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 119 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
B 157 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.138276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.115214 restraints weight = 19169.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.118059 restraints weight = 11935.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.120041 restraints weight = 8464.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3534
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3534 r_free = 0.3534    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3534 r_free = 0.3534    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3534
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.4149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  10899  Z= 0.205
  Angle     :  0.654  11.080  14963  Z= 0.350
  Chirality :  0.045   0.173   1723
  Planarity :  0.004   0.051   1683
  Dihedral  : 21.172 153.924   1931
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.39 %
    Favored  : 90.61 %
  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: -2.17 (0.24), residues: 1171
  helix: -0.56 (0.30), residues: 305
  sheet:  0.12 (0.31), residues: 316
  loop : -3.02 (0.23), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP E  50 
 HIS   0.007   0.001   HIS B 157 
 PHE   0.025   0.002   PHE E  10 
 TYR   0.018   0.001   TYR C  59 
 ARG   0.008   0.000   ARG E 234 

*********************** 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
  338 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 338
  time to evaluate  : 1.165 
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: 0.5996 (t70) cc_final: 0.5570 (t0)
REVERT: A   57 LEU cc_start: 0.8058 (mt) cc_final: 0.7740 (mt)
REVERT: A   59 GLU cc_start: 0.8321 (tp30) cc_final: 0.8012 (tp30)
REVERT: A   65 PRO cc_start: 0.6704 (Cg_exo) cc_final: 0.6337 (Cg_endo)
REVERT: A   69 LYS cc_start: 0.7693 (mppt) cc_final: 0.7288 (mmtp)
REVERT: A  116 LYS cc_start: 0.7987 (mtmm) cc_final: 0.7785 (tptt)
REVERT: A  165 LYS cc_start: 0.7538 (mmpt) cc_final: 0.7244 (mmpt)
REVERT: B   21 ASP cc_start: 0.7421 (t0) cc_final: 0.6294 (t0)
REVERT: B  107 THR cc_start: 0.8097 (p) cc_final: 0.7676 (t)
REVERT: B  132 LYS cc_start: 0.8098 (ttmt) cc_final: 0.7734 (ttmm)
REVERT: B  162 LYS cc_start: 0.7719 (mttp) cc_final: 0.7439 (mttp)
REVERT: B  207 LYS cc_start: 0.9026 (ptpt) cc_final: 0.8761 (ptpp)
REVERT: C    3 VAL cc_start: 0.8615 (t) cc_final: 0.8151 (p)
REVERT: C    6 ASP cc_start: 0.7485 (t0) cc_final: 0.7229 (t0)
REVERT: C    7 ASP cc_start: 0.7878 (t70) cc_final: 0.7512 (t0)
REVERT: C   23 ASP cc_start: 0.7832 (m-30) cc_final: 0.7370 (m-30)
REVERT: C   28 LYS cc_start: 0.8252 (mttt) cc_final: 0.7812 (mtmt)
REVERT: C   85 GLU cc_start: 0.7574 (mp0) cc_final: 0.7225 (mp0)
REVERT: C   88 GLU cc_start: 0.7323 (pp20) cc_final: 0.7081 (pp20)
REVERT: C  109 PHE cc_start: 0.7864 (m-80) cc_final: 0.7623 (m-80)
REVERT: C  112 ARG cc_start: 0.8114 (tpp80) cc_final: 0.7765 (tpp80)
REVERT: C  130 ILE cc_start: 0.8806 (mp) cc_final: 0.8577 (mm)
REVERT: C  165 LYS cc_start: 0.7733 (pttp) cc_final: 0.7472 (ptpt)
REVERT: C  171 GLU cc_start: 0.7598 (mt-10) cc_final: 0.6908 (mm-30)
REVERT: C  195 SER cc_start: 0.8507 (m) cc_final: 0.8120 (p)
REVERT: C  205 LEU cc_start: 0.8234 (mt) cc_final: 0.7887 (tp)
REVERT: C  209 LYS cc_start: 0.8180 (ptmm) cc_final: 0.7933 (ttpp)
REVERT: E    6 ILE cc_start: 0.6734 (tp) cc_final: 0.6445 (tp)
REVERT: E   15 LYS cc_start: 0.8102 (mtmt) cc_final: 0.7854 (mmtp)
REVERT: E   32 LYS cc_start: 0.8006 (mmmm) cc_final: 0.7751 (ttmm)
REVERT: E   36 THR cc_start: 0.7747 (p) cc_final: 0.7315 (p)
REVERT: E   86 LYS cc_start: 0.7794 (tptm) cc_final: 0.7534 (mmmm)
REVERT: E  101 LYS cc_start: 0.8551 (pttm) cc_final: 0.8203 (pttm)
REVERT: E  126 SER cc_start: 0.8340 (t) cc_final: 0.7836 (p)
REVERT: E  127 THR cc_start: 0.7995 (m) cc_final: 0.7714 (m)
REVERT: E  142 LEU cc_start: 0.8118 (mt) cc_final: 0.7839 (mt)
REVERT: E  174 ILE cc_start: 0.8066 (mm) cc_final: 0.7647 (tt)
REVERT: E  194 SER cc_start: 0.7892 (p) cc_final: 0.7074 (p)
REVERT: E  197 ILE cc_start: 0.7982 (mm) cc_final: 0.7695 (tp)
REVERT: E  198 GLU cc_start: 0.7016 (pt0) cc_final: 0.6698 (pt0)
REVERT: E  203 LEU cc_start: 0.7778 (mt) cc_final: 0.7516 (mt)
REVERT: E  206 ASP cc_start: 0.7629 (t0) cc_final: 0.7095 (t0)
REVERT: E  224 THR cc_start: 0.7034 (p) cc_final: 0.6822 (p)
REVERT: E  265 ARG cc_start: 0.7751 (ttm170) cc_final: 0.7439 (ttm170)
REVERT: E  274 LYS cc_start: 0.7259 (mppt) cc_final: 0.6740 (mppt)
REVERT: E  290 PRO cc_start: 0.8026 (Cg_endo) cc_final: 0.7507 (Cg_exo)
REVERT: E  291 ASP cc_start: 0.7617 (p0) cc_final: 0.7162 (p0)
REVERT: E  325 GLN cc_start: 0.7393 (tp-100) cc_final: 0.7092 (tp-100)
REVERT: E  363 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8234 (mmtp)
REVERT: E  394 GLU cc_start: 0.7341 (pm20) cc_final: 0.7011 (tp30)
REVERT: E  397 LYS cc_start: 0.7782 (mmmt) cc_final: 0.7483 (mmtp)
REVERT: E  409 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6312 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 338
  average time/residue: 0.2993
  time to fit residues: 132.1330
Evaluate side-chains
  303 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 303
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
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:    0.0370
   chunk 45 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.7058

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

Flipped N/Q/H residues before XYZ refinement:
B 157 HIS
C 100 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.138791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.115490 restraints weight = 19021.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.118409 restraints weight = 11892.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.120414 restraints weight = 8386.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
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:        5 |
|-----------------------------------------------------------------------------|
|-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:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3539
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.4230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10899  Z= 0.198
  Angle     :  0.663  10.459  14963  Z= 0.354
  Chirality :  0.045   0.181   1723
  Planarity :  0.004   0.051   1683
  Dihedral  : 21.160 153.076   1931
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.74 %
    Favored  : 90.26 %
  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: -2.12 (0.24), residues: 1171
  helix: -0.60 (0.30), residues: 313
  sheet:  0.02 (0.30), residues: 330
  loop : -2.95 (0.24), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP E  50 
 HIS   0.004   0.001   HIS A  39 
 PHE   0.027   0.002   PHE E  10 
 TYR   0.017   0.001   TYR B 218 
 ARG   0.006   0.000   ARG A 103 

********************** 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
  338 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 338
  time to evaluate  : 1.115 
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: 0.5955 (t70) cc_final: 0.5557 (t0)
REVERT: A   69 LYS cc_start: 0.7701 (mppt) cc_final: 0.7281 (mmtp)
REVERT: B   21 ASP cc_start: 0.7413 (t0) cc_final: 0.6317 (t0)
REVERT: B   67 GLU cc_start: 0.5869 (mp0) cc_final: 0.5575 (mp0)
REVERT: B  107 THR cc_start: 0.8027 (p) cc_final: 0.7677 (t)
REVERT: B  132 LYS cc_start: 0.8131 (ttmt) cc_final: 0.7602 (ttmm)
REVERT: B  162 LYS cc_start: 0.7826 (mttp) cc_final: 0.7495 (mttp)
REVERT: B  207 LYS cc_start: 0.8993 (ptpt) cc_final: 0.8668 (ptpp)
REVERT: C    3 VAL cc_start: 0.8548 (t) cc_final: 0.8049 (p)
REVERT: C    7 ASP cc_start: 0.7888 (t70) cc_final: 0.7508 (t0)
REVERT: C   23 ASP cc_start: 0.7752 (m-30) cc_final: 0.7418 (m-30)
REVERT: C   28 LYS cc_start: 0.7823 (mttt) cc_final: 0.7619 (mtmm)
REVERT: C   72 GLN cc_start: 0.7478 (tt0) cc_final: 0.7056 (mt0)
REVERT: C   75 MET cc_start: 0.7483 (tpp) cc_final: 0.7076 (tpp)
REVERT: C   76 LYS cc_start: 0.7934 (ttpt) cc_final: 0.7651 (ttmm)
REVERT: C   77 ILE cc_start: 0.8335 (pt) cc_final: 0.8089 (tt)
REVERT: C   85 GLU cc_start: 0.7585 (mp0) cc_final: 0.7197 (mp0)
REVERT: C   88 GLU cc_start: 0.7162 (pp20) cc_final: 0.6865 (pp20)
REVERT: C  112 ARG cc_start: 0.8077 (tpp80) cc_final: 0.7770 (tpp80)
REVERT: C  130 ILE cc_start: 0.8820 (mp) cc_final: 0.8557 (mm)
REVERT: C  140 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7717 (tttm)
REVERT: C  165 LYS cc_start: 0.7736 (pttp) cc_final: 0.7516 (ptpt)
REVERT: C  171 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6738 (mm-30)
REVERT: C  195 SER cc_start: 0.8482 (m) cc_final: 0.8107 (p)
REVERT: C  205 LEU cc_start: 0.8248 (mt) cc_final: 0.7941 (tp)
REVERT: C  209 LYS cc_start: 0.8119 (ptmm) cc_final: 0.7829 (ttpp)
REVERT: C  215 LYS cc_start: 0.8092 (ttmt) cc_final: 0.7759 (ttmm)
REVERT: C  222 LYS cc_start: 0.7209 (mmtt) cc_final: 0.6975 (mmtm)
REVERT: E   36 THR cc_start: 0.7714 (p) cc_final: 0.7279 (p)
REVERT: E   86 LYS cc_start: 0.7765 (tptm) cc_final: 0.7557 (mmmm)
REVERT: E   93 GLU cc_start: 0.7845 (tp30) cc_final: 0.7603 (tp30)
REVERT: E  101 LYS cc_start: 0.8537 (pttm) cc_final: 0.8167 (pttm)
REVERT: E  126 SER cc_start: 0.8320 (t) cc_final: 0.7830 (p)
REVERT: E  127 THR cc_start: 0.8003 (m) cc_final: 0.7720 (m)
REVERT: E  142 LEU cc_start: 0.8128 (mt) cc_final: 0.7823 (mt)
REVERT: E  174 ILE cc_start: 0.8052 (mm) cc_final: 0.7631 (tt)
REVERT: E  194 SER cc_start: 0.7904 (p) cc_final: 0.7103 (p)
REVERT: E  197 ILE cc_start: 0.7962 (mm) cc_final: 0.7687 (tp)
REVERT: E  198 GLU cc_start: 0.7066 (pt0) cc_final: 0.6773 (pt0)
REVERT: E  203 LEU cc_start: 0.7712 (mt) cc_final: 0.7467 (mt)
REVERT: E  224 THR cc_start: 0.7101 (p) cc_final: 0.6836 (p)
REVERT: E  239 GLU cc_start: 0.7346 (tp30) cc_final: 0.6336 (mp0)
REVERT: E  265 ARG cc_start: 0.7698 (ttm170) cc_final: 0.7383 (ttm170)
REVERT: E  274 LYS cc_start: 0.7220 (mppt) cc_final: 0.6792 (mppt)
REVERT: E  285 ILE cc_start: 0.8665 (pt) cc_final: 0.8369 (tt)
REVERT: E  290 PRO cc_start: 0.7948 (Cg_endo) cc_final: 0.7491 (Cg_exo)
REVERT: E  291 ASP cc_start: 0.7531 (p0) cc_final: 0.7073 (p0)
REVERT: E  325 GLN cc_start: 0.7340 (tp-100) cc_final: 0.7115 (tp40)
REVERT: E  363 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8246 (mmtp)
REVERT: E  394 GLU cc_start: 0.7399 (pm20) cc_final: 0.7075 (tp30)
REVERT: E  397 LYS cc_start: 0.7772 (mmmt) cc_final: 0.7421 (mmtp)
REVERT: E  409 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6358 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 338
  average time/residue: 0.2994
  time to fit residues: 131.6890
Evaluate side-chains
  305 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 305
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 98 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0670
   chunk 61 optimal weight:    1.9990
   chunk 14 optimal weight:    0.3980
   chunk 55 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 102 optimal weight:    3.9990
   overall best weight:    0.6118

-------------------------------------------------------------------------------
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 100 ASN
** E 288 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 = 0.3822 r_free = 0.3822 target = 0.139804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.116400 restraints weight = 18942.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.119352 restraints weight = 11841.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.121383 restraints weight = 8330.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3549
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3549 r_free = 0.3549    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3549 r_free = 0.3549    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3549
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.4302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10899  Z= 0.193
  Angle     :  0.659  11.358  14963  Z= 0.349
  Chirality :  0.044   0.167   1723
  Planarity :  0.004   0.046   1683
  Dihedral  : 21.142 152.059   1931
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  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: -2.10 (0.24), residues: 1171
  helix: -0.53 (0.30), residues: 310
  sheet:  0.08 (0.31), residues: 325
  loop : -2.97 (0.23), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP E  50 
 HIS   0.008   0.001   HIS B 157 
 PHE   0.028   0.002   PHE E  10 
 TYR   0.025   0.001   TYR B 197 
 ARG   0.006   0.000   ARG A 103 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3782.01 seconds
wall clock time: 68 minutes 2.71 seconds (4082.71 seconds total)