Starting phenix.real_space_refine
on Mon Apr 28 20:07:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6iac_4435/04_2025/6iac_4435.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6iac_4435/04_2025/6iac_4435.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6iac_4435/04_2025/6iac_4435.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6iac_4435/04_2025/6iac_4435.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6iac_4435/04_2025/6iac_4435.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6iac_4435/04_2025/6iac_4435.cif"
  }
  resolution = 3.9
  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
-------------------------------------------------------------------------------
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=   0.010
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: 4
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    5208      2.51       5
     N    1384      2.21       5
     O    1595      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8210
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 2353
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2353
          Classifications: {'peptide': 301}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 9, 'TRANS': 291}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 111
          Unresolved non-hydrogen dihedrals: 76
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 66
    Chain: "B"
      Number of atoms: 1763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1763
          Classifications: {'peptide': 220}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "D"
      Number of atoms: 1164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1164
          Classifications: {'peptide': 139}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 3, 'TRANS': 135}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 31
          Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 27
    Chain: "E"
      Number of atoms: 1259
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1259
          Classifications: {'peptide': 146}
          Link IDs: {'PTRANS': 3, 'TRANS': 142}
    Chain: "F"
      Number of atoms: 1019
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 1019
          Classifications: {'peptide': 121}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "G"
      Number of atoms: 90
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 90
          Classifications: {'peptide': 18}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'TRANS': 17}
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "H"
      Number of atoms: 90
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 90
          Classifications: {'peptide': 18}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'TRANS': 17}
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "I"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 120
          Classifications: {'peptide': 24}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'TRANS': 23}
          Unresolved non-hydrogen bonds: 73
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 43
    Chain: "J"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 120
          Classifications: {'peptide': 24}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'TRANS': 23}
          Unresolved non-hydrogen bonds: 73
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 43
    Chain: "K"
      Number of atoms: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 112
          Classifications: {'peptide': 22}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'TRANS': 21}
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 48
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 35
    Chain: "L"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 120
          Classifications: {'peptide': 24}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'TRANS': 23}
          Unresolved non-hydrogen bonds: 73
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 43
  Time building chain proxies: 5.99, per 1000 atoms: 0.73
  Number of scatterers: 8210
  At special positions: 0
  Unit cell: (126.497, 184.962, 255.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      23     16.00
     O    1595      8.00
     N    1384      7.00
     C    5208      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.89
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2056

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 7 sheets defined
      61.3% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 39
      removed outlier: 4.322A  pdb=" N   VAL A  21 " --> pdb=" O   SER A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 63
    Processing helix  chain 'A' and resid 152 through 177
      removed outlier: 3.960A  pdb=" N   ILE A 156 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLU A 158 " --> pdb=" O   ILE A 154 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ASP A 162 " --> pdb=" O   GLU A 158 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   GLU A 163 " --> pdb=" O   HIS A 159 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLN A 177 " --> pdb=" O   SER A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 200
    Processing helix  chain 'A' and resid 227 through 247
      removed outlier: 4.174A  pdb=" N   THR A 232 " --> pdb=" O   ILE A 228 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   GLU A 233 " --> pdb=" O   PRO A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 261
      removed outlier: 3.522A  pdb=" N   GLY A 261 " --> pdb=" O   ASP A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 285
      removed outlier: 3.567A  pdb=" N   THR A 274 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   SER A 276 " --> pdb=" O   GLY A 272 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ASN A 279 " --> pdb=" O   THR A 275 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE A 280 " --> pdb=" O   SER A 276 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   TYR A 281 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   LEU A 282 " --> pdb=" O   SER A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 295
      removed outlier: 3.653A  pdb=" N   PHE A 290 " --> pdb=" O   GLU A 286 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ARG A 294 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TYR A 295 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 315
    Processing helix  chain 'A' and resid 320 through 327
      removed outlier: 3.721A  pdb=" N   ASP A 324 " --> pdb=" O   ASP A 320 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASN A 326 " --> pdb=" O   SER A 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 19
      removed outlier: 3.583A  pdb=" N   LYS B  19 " --> pdb=" O   GLU B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 46
      removed outlier: 3.585A  pdb=" N   LYS B  42 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 58
    Processing helix  chain 'B' and resid 68 through 79
      removed outlier: 3.651A  pdb=" N   LEU B  72 " --> pdb=" O   LEU B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 102
      removed outlier: 3.562A  pdb=" N   ILE B  99 " --> pdb=" O   GLY B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 231
      removed outlier: 3.567A  pdb=" N   LYS B 230 " --> pdb=" O   ASP B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 246
      removed outlier: 4.109A  pdb=" N   GLU B 241 " --> pdb=" O   LYS B 237 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   PHE B 242 " --> pdb=" O   ILE B 238 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ASP B 243 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 14 through 19
      removed outlier: 3.626A  pdb=" N   LEU D  18 " --> pdb=" O   ILE D  14 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASP D  19 " --> pdb=" O   ARG D  15 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 14 through 19'
    Processing helix  chain 'D' and resid 20 through 23
      removed outlier: 3.840A  pdb=" N   LYS D  23 " --> pdb=" O   GLU D  20 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 20 through 23'
    Processing helix  chain 'D' and resid 42 through 53
      removed outlier: 3.550A  pdb=" N   ARG D  51 " --> pdb=" O   ASP D  47 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 54 through 84
      removed outlier: 4.089A  pdb=" N   ALA D  60 " --> pdb=" O   ILE D  56 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 98
      removed outlier: 4.946A  pdb=" N   ASP D  90 " --> pdb=" O   GLU D  86 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   ARG D  93 " --> pdb=" O   LYS D  89 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASP D  98 " --> pdb=" O   GLY D  94 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 141
      removed outlier: 3.939A  pdb=" N   ILE D 104 " --> pdb=" O   THR D 100 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   HIS D 106 " --> pdb=" O   ASP D 102 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   LYS D 111 " --> pdb=" O   ASP D 107 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   TYR D 112 " --> pdb=" O   GLU D 108 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ASP D 140 " --> pdb=" O   SER D 136 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU D 141 " --> pdb=" O   GLU D 137 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 142 through 146
      removed outlier: 4.335A  pdb=" N   ILE D 145 " --> pdb=" O   ILE D 142 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ASP D 146 " --> pdb=" O   LYS D 143 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 142 through 146'
    Processing helix  chain 'E' and resid 14 through 17
    Processing helix  chain 'E' and resid 18 through 27
      removed outlier: 3.772A  pdb=" N   TYR E  22 " --> pdb=" O   LEU E  18 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   GLU E  26 " --> pdb=" O   TYR E  22 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ARG E  27 " --> pdb=" O   LYS E  23 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 65
      removed outlier: 3.722A  pdb=" N   LYS E  54 " --> pdb=" O   SER E  50 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   LEU E  55 " --> pdb=" O   ARG E  51 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU E  59 " --> pdb=" O   LEU E  55 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ARG E  62 " --> pdb=" O   VAL E  58 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 65 through 74
      removed outlier: 4.097A  pdb=" N   GLU E  69 " --> pdb=" O   ASP E  65 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 74 through 104
      removed outlier: 4.129A  pdb=" N   ASP E  78 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
      Proline residue:  E  85  - end of helix
      removed outlier: 3.719A  pdb=" N   TRP E  95 " --> pdb=" O   LEU E  91 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU E  96 " --> pdb=" O   PHE E  92 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ASN E  97 " --> pdb=" O   ARG E  93 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ASP E  98 " --> pdb=" O   GLY E  94 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ILE E 101 " --> pdb=" O   ASN E  97 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ASP E 102 " --> pdb=" O   ASP E  98 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   SER E 103 " --> pdb=" O   GLY E  99 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 107 through 146
      removed outlier: 3.670A  pdb=" N   LYS E 111 " --> pdb=" O   ASP E 107 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ALA E 119 " --> pdb=" O   GLY E 115 " (cutoff:3.500A)
      removed outlier: 5.091A  pdb=" N   PHE E 120 " --> pdb=" O   LEU E 116 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   LEU E 141 " --> pdb=" O   GLU E 137 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ASP E 144 " --> pdb=" O   ASP E 140 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASP E 146 " --> pdb=" O   ILE E 142 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 147 through 149
      No H-bonds generated for 'chain 'E' and resid 147 through 149'
    Processing helix  chain 'F' and resid 44 through 83
      removed outlier: 3.960A  pdb=" N   LYS F  72 " --> pdb=" O   ASN F  68 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ASP F  79 " --> pdb=" O   LYS F  75 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU F  80 " --> pdb=" O   ASN F  76 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 93
      removed outlier: 3.713A  pdb=" N   PHE F  92 " --> pdb=" O   ALA F  88 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ARG F  93 " --> pdb=" O   LYS F  89 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 96 through 106
    Processing helix  chain 'F' and resid 110 through 135
      removed outlier: 3.517A  pdb=" N   ALA F 114 " --> pdb=" O   LYS F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 136 through 139
      removed outlier: 3.923A  pdb=" N   LYS F 139 " --> pdb=" O   SER F 136 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 136 through 139'
    Processing helix  chain 'G' and resid 78 through 94
    Processing helix  chain 'H' and resid 78 through 94
    Processing helix  chain 'I' and resid 78 through 98
    Processing helix  chain 'J' and resid 78 through 97
      removed outlier: 3.599A  pdb=" N   GLN J  97 " --> pdb=" O   PHE J  93 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 78 through 94
    Processing helix  chain 'L' and resid 78 through 95
      removed outlier: 3.508A  pdb=" N   PHE L  93 " --> pdb=" O   GLN L  89 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81
      removed outlier: 3.984A  pdb=" N   VAL A  68 " --> pdb=" O   MET A 143 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183
      removed outlier: 4.017A  pdb=" N   SER A 181 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 118
    Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 127
      removed outlier: 3.779A  pdb=" N   GLN B 125 " --> pdb=" O   GLY B 212 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 132
      removed outlier: 3.500A  pdb=" N   ARG B 206 " --> pdb=" O   ASN B 131 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 135 through 139
    Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 150

    435 hydrogen bonds defined for protein.
    1278 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.92

  Time building geometry restraints manager: 2.24 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2182
        1.33 -     1.45: 1673
        1.45 -     1.57: 4450
        1.57 -     1.69: 0
        1.69 -     1.81: 43
  Bond restraints: 8348
  Sorted by residual:
  bond pdb=" C   ARG D  15 "
       pdb=" N   PRO D  16 "
    ideal  model  delta    sigma   weight residual
    1.334  1.368 -0.035 8.40e-03 1.42e+04 1.71e+01
  bond pdb=" C   GLU A 286 "
       pdb=" N   PRO A 287 "
    ideal  model  delta    sigma   weight residual
    1.336  1.379 -0.043 1.08e-02 8.57e+03 1.58e+01
  bond pdb=" CA  ASP A 153 "
       pdb=" C   ASP A 153 "
    ideal  model  delta    sigma   weight residual
    1.523  1.570 -0.046 1.80e-02 3.09e+03 6.65e+00
  bond pdb=" CB  MET B   6 "
       pdb=" CG  MET B   6 "
    ideal  model  delta    sigma   weight residual
    1.520  1.446  0.074 3.00e-02 1.11e+03 6.09e+00
  bond pdb=" CB  TYR A  45 "
       pdb=" CG  TYR A  45 "
    ideal  model  delta    sigma   weight residual
    1.512  1.461  0.051 2.20e-02 2.07e+03 5.44e+00
  ... (remaining 8343 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.58: 10997
        3.58 -     7.16: 225
        7.16 -    10.74: 42
       10.74 -    14.32: 5
       14.32 -    17.90: 2
  Bond angle restraints: 11271
  Sorted by residual:
  angle pdb=" C   THR A 308 "
        pdb=" N   SER A 309 "
        pdb=" CA  SER A 309 "
      ideal   model   delta    sigma   weight residual
     121.54  132.39  -10.85 1.91e+00 2.74e-01 3.23e+01
  angle pdb=" C   LYS D  89 "
        pdb=" N   ASP D  90 "
        pdb=" CA  ASP D  90 "
      ideal   model   delta    sigma   weight residual
     121.54  132.27  -10.73 1.91e+00 2.74e-01 3.15e+01
  angle pdb=" CA  TYR A  45 "
        pdb=" CB  TYR A  45 "
        pdb=" CG  TYR A  45 "
      ideal   model   delta    sigma   weight residual
     113.90  123.83   -9.93 1.80e+00 3.09e-01 3.04e+01
  angle pdb=" C   ASP A 153 "
        pdb=" CA  ASP A 153 "
        pdb=" CB  ASP A 153 "
      ideal   model   delta    sigma   weight residual
     110.36  100.37    9.99 1.85e+00 2.92e-01 2.92e+01
  angle pdb=" C   ASP A 264 "
        pdb=" N   GLU A 265 "
        pdb=" CA  GLU A 265 "
      ideal   model   delta    sigma   weight residual
     121.54  131.79  -10.25 1.91e+00 2.74e-01 2.88e+01
  ... (remaining 11266 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.07: 4589
       16.07 -    32.14: 371
       32.14 -    48.21: 78
       48.21 -    64.28: 1
       64.28 -    80.34: 6
  Dihedral angle restraints: 5045
    sinusoidal: 1896
      harmonic: 3149
  Sorted by residual:
  dihedral pdb=" CA  GLU A 187 "
           pdb=" C   GLU A 187 "
           pdb=" N   ILE A 188 "
           pdb=" CA  ILE A 188 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -139.12  -40.88     0      5.00e+00 4.00e-02 6.68e+01
  dihedral pdb=" CA  SER B 114 "
           pdb=" C   SER B 114 "
           pdb=" N   SER B 115 "
           pdb=" CA  SER B 115 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.37  -38.63     0      5.00e+00 4.00e-02 5.97e+01
  dihedral pdb=" CA  TYR B 113 "
           pdb=" C   TYR B 113 "
           pdb=" N   SER B 114 "
           pdb=" CA  SER B 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.38   36.62     0      5.00e+00 4.00e-02 5.36e+01
  ... (remaining 5042 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 997
       0.079 -    0.158: 210
       0.158 -    0.237: 40
       0.237 -    0.316: 6
       0.316 -    0.395: 2
  Chirality restraints: 1255
  Sorted by residual:
  chirality pdb=" CA  TYR A  45 "
            pdb=" N   TYR A  45 "
            pdb=" C   TYR A  45 "
            pdb=" CB  TYR A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.90e+00
  chirality pdb=" CG  LEU A   8 "
            pdb=" CB  LEU A   8 "
            pdb=" CD1 LEU A   8 "
            pdb=" CD2 LEU A   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.24   -0.35 2.00e-01 2.50e+01 2.98e+00
  chirality pdb=" CB  THR A  46 "
            pdb=" CA  THR A  46 "
            pdb=" OG1 THR A  46 "
            pdb=" CG2 THR A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.26    0.29 2.00e-01 2.50e+01 2.16e+00
  ... (remaining 1252 not shown)

  Planarity restraints: 1460
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP D  90 "    0.020 2.00e-02 2.50e+03   4.02e-02 1.61e+01
        pdb=" C   ASP D  90 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   ASP D  90 "    0.026 2.00e-02 2.50e+03
        pdb=" N   LEU D  91 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F  46 "   -0.034 2.00e-02 2.50e+03   2.77e-02 1.53e+01
        pdb=" CG  TYR F  46 "    0.064 2.00e-02 2.50e+03
        pdb=" CD1 TYR F  46 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR F  46 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR F  46 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE2 TYR F  46 "   -0.024 2.00e-02 2.50e+03
        pdb=" CZ  TYR F  46 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR F  46 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  45 "   -0.035 2.00e-02 2.50e+03   2.73e-02 1.49e+01
        pdb=" CG  TYR A  45 "    0.066 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  45 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  45 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  45 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  45 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  45 "   -0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR A  45 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1457 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2080
        2.78 -     3.31: 7828
        3.31 -     3.84: 12670
        3.84 -     4.37: 13537
        4.37 -     4.90: 22438
  Nonbonded interactions: 58553
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 157 "
            pdb=" OG1 THR A 161 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OG  SER A 292 "
            pdb=" O   LEU A 297 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   PHE A 273 "
            pdb=" OG  SER A 276 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OH  TYR D  66 "
            pdb=" OD1 ASP F  67 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   THR A 108 "
            pdb=" OH  TYR A 132 "
     model   vdw
     2.318 3.040
  ... (remaining 58548 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'D' and (resid 24 through 25 or (resid 26 through 27 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 28 or (resid 29 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 30 through 34 or (resid 35 throu \ 
gh 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throu \ 
gh 144))
  selection = (chain 'E' and (resid 24 through 25 or (resid 26 through 27 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 28 or (resid 29 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 30 through 34 or (resid 35 throu \ 
gh 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throu \ 
gh 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 52 through 105 or (resid 106 through 107 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 108 through 110 or (resid 111 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 112 through 144))
  selection = (chain 'F' and (resid 24 through 26 or (resid 27 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 28 through 50 or (resid 51 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 52 through 105 or (resid 106 thr \ 
ough 107 and (name N or name CA or name C or name O or name CB )) or resid 108 t \ 
hrough 110 or (resid 111 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 112 through 144))
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'I' and resid 77 through 98)
  selection = (chain 'J' and resid 77 through 98)
  selection = (chain 'K' and (name N or name CA or name C or name O or name CB ))
  selection = (chain 'L' and resid 77 through 98)
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.300
  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:          0.400
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.400
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
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      :  0.009   0.082   8348  Z= 0.426
  Angle     :  1.315  17.897  11271  Z= 0.721
  Chirality :  0.069   0.395   1255
  Planarity :  0.007   0.073   1460
  Dihedral  : 12.355  80.344   2989
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 11.95 %
    Favored  : 87.85 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  6.11 %
    Favored  : 92.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.78 %

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: -4.54 (0.20), residues: 1029
  helix: -2.28 (0.16), residues: 582
  sheet: -3.46 (0.43), residues: 84
  loop : -3.95 (0.27), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.004   TRP F  95 
 HIS   0.021   0.006   HIS E 106 
 PHE   0.064   0.005   PHE D  31 
 TYR   0.066   0.005   TYR A  45 
 ARG   0.014   0.001   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16551 (  435)
  hydrogen bonds       : angle       7.28134 ( 1278)
  covalent geometry    : bond        0.00943 ( 8348)
  covalent geometry    : angle       1.31470 (11271)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  426 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 417
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8464 (tm-30)
REVERT: A   77 GLN cc_start: 0.9381 (mp10) cc_final: 0.9033 (mp10)
REVERT: A  185 LYS cc_start: 0.8027 (ttmt) cc_final: 0.7669 (ttmt)
REVERT: A  201 TYR cc_start: 0.9084 (t80) cc_final: 0.8456 (t80)
REVERT: A  241 LYS cc_start: 0.8972 (ttmm) cc_final: 0.8346 (tppt)
REVERT: A  244 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7958 (tm-30)
REVERT: A  248 TYR cc_start: 0.8663 (t80) cc_final: 0.8438 (t80)
REVERT: A  259 GLU cc_start: 0.7944 (mp0) cc_final: 0.7744 (mp0)
REVERT: A  303 TYR cc_start: 0.8185 (t80) cc_final: 0.7853 (t80)
REVERT: A  306 GLU cc_start: 0.6681 (pt0) cc_final: 0.6439 (pt0)
REVERT: B   18 LYS cc_start: 0.9060 (tmmm) cc_final: 0.8796 (ttpt)
REVERT: B   47 ASP cc_start: 0.8620 (p0) cc_final: 0.8159 (p0)
REVERT: B   51 LEU cc_start: 0.9506 (tp) cc_final: 0.9250 (tp)
REVERT: B  125 GLN cc_start: 0.8587 (tm-30) cc_final: 0.7909 (tm-30)
REVERT: B  145 ASN cc_start: 0.8448 (t0) cc_final: 0.8204 (t0)
REVERT: B  188 ASP cc_start: 0.8873 (p0) cc_final: 0.8222 (m-30)
REVERT: B  250 ILE cc_start: 0.8450 (tp) cc_final: 0.8177 (tt)
REVERT: D   25 ARG cc_start: 0.8125 (ttt180) cc_final: 0.7589 (mpp-170)
REVERT: D   47 ASP cc_start: 0.7655 (t0) cc_final: 0.7420 (t0)
REVERT: D   75 LYS cc_start: 0.8163 (tmtt) cc_final: 0.7704 (mmpt)
REVERT: D   87 GLN cc_start: 0.9137 (mt0) cc_final: 0.8898 (mt0)
REVERT: D   89 LYS cc_start: 0.8266 (tmmt) cc_final: 0.7979 (tmtt)
REVERT: D   90 ASP cc_start: 0.7751 (t0) cc_final: 0.7397 (p0)
REVERT: D  133 ASP cc_start: 0.8682 (t0) cc_final: 0.8155 (t70)
REVERT: E   14 ILE cc_start: 0.8274 (mm) cc_final: 0.7959 (pt)
REVERT: E   17 PHE cc_start: 0.9141 (m-80) cc_final: 0.8862 (m-10)
REVERT: E   22 TYR cc_start: 0.8511 (t80) cc_final: 0.7943 (t80)
REVERT: E   23 LYS cc_start: 0.9392 (tptp) cc_final: 0.9189 (tptt)
REVERT: E   51 ARG cc_start: 0.7862 (tpt-90) cc_final: 0.7402 (tmt170)
REVERT: E   86 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8593 (tm-30)
REVERT: E   90 ASP cc_start: 0.8850 (t0) cc_final: 0.8376 (m-30)
REVERT: E  104 ILE cc_start: 0.8808 (mt) cc_final: 0.8007 (mm)
REVERT: F   27 ARG cc_start: 0.8032 (ptp90) cc_final: 0.7752 (tpt-90)
REVERT: F   43 LYS cc_start: 0.8892 (mtpm) cc_final: 0.8338 (mptt)
REVERT: F   54 LYS cc_start: 0.6338 (tmmt) cc_final: 0.5470 (mttt)
REVERT: F   57 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8379 (tm-30)
REVERT: F   68 ASN cc_start: 0.8697 (t0) cc_final: 0.8439 (t0)
REVERT: F   87 GLN cc_start: 0.8538 (tp-100) cc_final: 0.8150 (tp-100)
REVERT: F   91 LEU cc_start: 0.7608 (pp) cc_final: 0.6593 (pp)
REVERT: F  123 PHE cc_start: 0.7056 (t80) cc_final: 0.6732 (t80)
REVERT: F  125 VAL cc_start: 0.9406 (t) cc_final: 0.9038 (p)
REVERT: F  131 MET cc_start: 0.7930 (mmt) cc_final: 0.7729 (mmm)
REVERT: F  143 LYS cc_start: 0.5689 (mppt) cc_final: 0.4091 (mmtt)
  outliers start: 9
  outliers final: 2
  residues processed: 420
  average time/residue: 0.2212
  time to fit residues: 120.6300
Evaluate side-chains
  310 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 308
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  239 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    4.9990
   chunk 76 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 40 optimal weight:    7.9990
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 91 optimal weight:   20.0000
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 HIS
E   6 ASN
E 130 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.151724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.127487 restraints weight = 18677.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.129791 restraints weight = 9383.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.131163 restraints weight = 5694.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8348  Z= 0.175
  Angle     :  0.778  12.452  11271  Z= 0.415
  Chirality :  0.048   0.230   1255
  Planarity :  0.005   0.048   1460
  Dihedral  :  6.697  35.671   1138
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 16.99 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -2.59 (0.24), residues: 1029
  helix: -0.37 (0.20), residues: 594
  sheet: -3.36 (0.47), residues: 69
  loop : -3.66 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP F  95 
 HIS   0.004   0.001   HIS E 106 
 PHE   0.027   0.002   PHE F  84 
 TYR   0.025   0.002   TYR A  45 
 ARG   0.006   0.001   ARG A 285 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04001 (  435)
  hydrogen bonds       : angle       4.81029 ( 1278)
  covalent geometry    : bond        0.00381 ( 8348)
  covalent geometry    : angle       0.77750 (11271)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  395 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 354
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8181 (tp)
REVERT: A   45 TYR cc_start: 0.8860 (p90) cc_final: 0.7402 (p90)
REVERT: A   55 PHE cc_start: 0.8695 (m-80) cc_final: 0.8446 (m-80)
REVERT: A   57 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8206 (tm-30)
REVERT: A   74 ARG cc_start: 0.6901 (mmp-170) cc_final: 0.6607 (tpt-90)
REVERT: A   76 LYS cc_start: 0.8625 (pttt) cc_final: 0.8056 (ptmt)
REVERT: A   77 GLN cc_start: 0.9225 (mp10) cc_final: 0.8715 (mp10)
REVERT: A  160 TYR cc_start: 0.8747 (m-80) cc_final: 0.8417 (m-80)
REVERT: A  163 GLU cc_start: 0.7893 (tt0) cc_final: 0.7596 (tt0)
REVERT: A  185 LYS cc_start: 0.7185 (ttmt) cc_final: 0.6568 (tmtt)
REVERT: A  248 TYR cc_start: 0.8511 (t80) cc_final: 0.8225 (t80)
REVERT: A  251 ILE cc_start: 0.9323 (pp) cc_final: 0.8902 (pp)
REVERT: A  303 TYR cc_start: 0.7885 (t80) cc_final: 0.7482 (t80)
REVERT: B   38 GLN cc_start: 0.7882 (pm20) cc_final: 0.7393 (pt0)
REVERT: B  229 ASP cc_start: 0.7838 (t0) cc_final: 0.7603 (t0)
REVERT: B  245 LYS cc_start: 0.8391 (mttt) cc_final: 0.8133 (mttt)
REVERT: D   25 ARG cc_start: 0.8110 (ttt180) cc_final: 0.7407 (mpp-170)
REVERT: D   96 LEU cc_start: 0.7156 (pp) cc_final: 0.5885 (pp)
REVERT: D  122 LEU cc_start: 0.9081 (pp) cc_final: 0.8661 (mp)
REVERT: D  141 LEU cc_start: 0.8856 (mt) cc_final: 0.8561 (pp)
REVERT: E   17 PHE cc_start: 0.9046 (m-80) cc_final: 0.8836 (m-10)
REVERT: E   22 TYR cc_start: 0.8517 (t80) cc_final: 0.7952 (t80)
REVERT: E   46 TYR cc_start: 0.9207 (t80) cc_final: 0.8667 (t80)
REVERT: E   78 ASP cc_start: 0.8577 (m-30) cc_final: 0.8016 (t0)
REVERT: E   86 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8509 (tm-30)
REVERT: F   27 ARG cc_start: 0.8228 (ptp90) cc_final: 0.7621 (tpt-90)
REVERT: F   43 LYS cc_start: 0.8608 (mtpm) cc_final: 0.8338 (mptt)
REVERT: F   54 LYS cc_start: 0.6877 (tmmt) cc_final: 0.6229 (mttt)
REVERT: F   57 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8140 (tm-30)
REVERT: F   78 ASP cc_start: 0.7974 (m-30) cc_final: 0.7610 (m-30)
REVERT: F   87 GLN cc_start: 0.8492 (tp-100) cc_final: 0.8045 (tp-100)
REVERT: F   91 LEU cc_start: 0.7595 (pp) cc_final: 0.6620 (pp)
REVERT: F  116 LEU cc_start: 0.9187 (mt) cc_final: 0.8926 (mt)
REVERT: F  143 LYS cc_start: 0.5669 (mppt) cc_final: 0.3676 (mmtt)
  outliers start: 41
  outliers final: 24
  residues processed: 371
  average time/residue: 0.2126
  time to fit residues: 103.7933
Evaluate side-chains
  334 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 309
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   35 TYR
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  148 ILE
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  130 HIS
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   74 PHE
Chi-restraints excluded: chain E residue   79 ASP
Chi-restraints excluded: chain E residue   97 ASN
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue  122 LEU
Chi-restraints excluded: chain F residue  141 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 26 optimal weight:    0.4980
   chunk 87 optimal weight:    9.9990
   chunk 85 optimal weight:    3.9990
   chunk 77 optimal weight:    9.9990
   chunk 72 optimal weight:    5.9990
   chunk 86 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 10 optimal weight:    0.3980
   chunk 73 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  39 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.148908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.125032 restraints weight = 19020.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.127172 restraints weight = 9732.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.128452 restraints weight = 5987.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.4195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8348  Z= 0.201
  Angle     :  0.784   9.554  11271  Z= 0.415
  Chirality :  0.049   0.205   1255
  Planarity :  0.004   0.040   1460
  Dihedral  :  6.253  37.729   1136
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  6.60 %
    Allowed  : 19.80 %
    Favored  : 73.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -1.83 (0.26), residues: 1029
  helix:  0.38 (0.22), residues: 597
  sheet: -3.23 (0.50), residues: 69
  loop : -3.62 (0.28), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP F  95 
 HIS   0.012   0.002   HIS B 130 
 PHE   0.026   0.003   PHE D 109 
 TYR   0.025   0.002   TYR E  45 
 ARG   0.007   0.001   ARG A 285 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03884 (  435)
  hydrogen bonds       : angle       4.61040 ( 1278)
  covalent geometry    : bond        0.00452 ( 8348)
  covalent geometry    : angle       0.78449 (11271)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  371 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 317
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ARG cc_start: 0.2696 (ptt-90) cc_final: 0.2387 (ptt-90)
REVERT: A   37 GLU cc_start: 0.6400 (tt0) cc_final: 0.5865 (tt0)
REVERT: A   39 LEU cc_start: 0.9615 (tt) cc_final: 0.9401 (tp)
REVERT: A   45 TYR cc_start: 0.8846 (p90) cc_final: 0.8603 (p90)
REVERT: A   57 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8187 (tm-30)
REVERT: A   74 ARG cc_start: 0.6784 (mmp-170) cc_final: 0.6537 (tpt-90)
REVERT: A   76 LYS cc_start: 0.8683 (pttt) cc_final: 0.7900 (ptmt)
REVERT: A   77 GLN cc_start: 0.9236 (mp10) cc_final: 0.8729 (mp10)
REVERT: A  155 GLU cc_start: 0.8287 (tp30) cc_final: 0.7985 (tp30)
REVERT: A  241 LYS cc_start: 0.9165 (tppp) cc_final: 0.8724 (tppp)
REVERT: B   23 GLU cc_start: 0.8270 (pm20) cc_final: 0.7276 (pt0)
REVERT: B   30 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8373 (mm)
REVERT: B   38 GLN cc_start: 0.7895 (pm20) cc_final: 0.7667 (pt0)
REVERT: B   47 ASP cc_start: 0.8635 (p0) cc_final: 0.8338 (p0)
REVERT: B  245 LYS cc_start: 0.8289 (mttt) cc_final: 0.8032 (mttt)
REVERT: D   25 ARG cc_start: 0.8144 (ttt180) cc_final: 0.7376 (mpp-170)
REVERT: D  122 LEU cc_start: 0.9095 (pp) cc_final: 0.8687 (mp)
REVERT: D  141 LEU cc_start: 0.8860 (mt) cc_final: 0.8649 (pp)
REVERT: F   27 ARG cc_start: 0.8176 (ptp90) cc_final: 0.7572 (tpt-90)
REVERT: F   54 LYS cc_start: 0.7070 (tmmt) cc_final: 0.6397 (mttm)
REVERT: F   57 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8117 (tm-30)
REVERT: F   78 ASP cc_start: 0.7902 (m-30) cc_final: 0.7632 (m-30)
REVERT: F   87 GLN cc_start: 0.8498 (tp-100) cc_final: 0.8069 (tp-100)
REVERT: F   91 LEU cc_start: 0.7667 (pp) cc_final: 0.6793 (pp)
REVERT: F  131 MET cc_start: 0.7875 (mmp) cc_final: 0.7602 (mmp)
  outliers start: 54
  outliers final: 36
  residues processed: 339
  average time/residue: 0.1945
  time to fit residues: 88.9840
Evaluate side-chains
  337 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 300
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 TYR
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  265 GLU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain D residue   59 LEU
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   74 PHE
Chi-restraints excluded: chain E residue   79 ASP
Chi-restraints excluded: chain E residue   80 LEU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue   97 ASN
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain F residue  122 LEU
Chi-restraints excluded: chain F residue  142 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0980
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0030
   chunk 68 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.2196

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

Flipped N/Q/H residues before XYZ refinement:
** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 HIS
F  39 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.151952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.128527 restraints weight = 18991.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.130721 restraints weight = 9532.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.132109 restraints weight = 5853.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.4795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8348  Z= 0.141
  Angle     :  0.742  10.384  11271  Z= 0.381
  Chirality :  0.047   0.182   1255
  Planarity :  0.004   0.034   1460
  Dihedral  :  5.768  35.887   1136
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  6.60 %
    Allowed  : 20.90 %
    Favored  : 72.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -1.33 (0.27), residues: 1029
  helix:  0.77 (0.22), residues: 596
  sheet: -2.61 (0.54), residues: 71
  loop : -3.46 (0.29), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  77 
 HIS   0.003   0.001   HIS E 106 
 PHE   0.018   0.002   PHE F 123 
 TYR   0.021   0.002   TYR F 112 
 ARG   0.005   0.001   ARG A 285 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03308 (  435)
  hydrogen bonds       : angle       4.38330 ( 1278)
  covalent geometry    : bond        0.00309 ( 8348)
  covalent geometry    : angle       0.74160 (11271)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  370 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 316
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 ARG cc_start: 0.2398 (ptt-90) cc_final: 0.2044 (ptt-90)
REVERT: A   37 GLU cc_start: 0.6021 (tt0) cc_final: 0.5497 (tt0)
REVERT: A   45 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8303 (p90)
REVERT: A   57 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8140 (tm-30)
REVERT: A   74 ARG cc_start: 0.6792 (mmp-170) cc_final: 0.6535 (tpt-90)
REVERT: A   77 GLN cc_start: 0.9153 (mp10) cc_final: 0.8674 (mp10)
REVERT: A  241 LYS cc_start: 0.9101 (tppp) cc_final: 0.8822 (tppp)
REVERT: A  242 ILE cc_start: 0.9192 (tt) cc_final: 0.8913 (tt)
REVERT: A  248 TYR cc_start: 0.8446 (t80) cc_final: 0.8173 (t80)
REVERT: B   23 GLU cc_start: 0.8243 (pm20) cc_final: 0.7267 (pt0)
REVERT: B   30 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8357 (mm)
REVERT: B   40 MET cc_start: 0.8759 (tpp) cc_final: 0.7384 (mtt)
REVERT: B   76 SER cc_start: 0.9429 (OUTLIER) cc_final: 0.8981 (m)
REVERT: B  125 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8090 (tm-30)
REVERT: B  188 ASP cc_start: 0.4786 (OUTLIER) cc_final: 0.4295 (m-30)
REVERT: D   25 ARG cc_start: 0.8076 (ttt180) cc_final: 0.7367 (mpp-170)
REVERT: D   87 GLN cc_start: 0.8885 (mt0) cc_final: 0.8664 (mp10)
REVERT: D   93 ARG cc_start: 0.7640 (mmp80) cc_final: 0.7269 (mmp80)
REVERT: D  122 LEU cc_start: 0.9056 (pp) cc_final: 0.8618 (mp)
REVERT: E   50 SER cc_start: 0.9138 (t) cc_final: 0.8901 (t)
REVERT: E   52 LEU cc_start: 0.9200 (tp) cc_final: 0.8867 (tt)
REVERT: E   78 ASP cc_start: 0.8541 (m-30) cc_final: 0.8017 (t0)
REVERT: E  120 PHE cc_start: 0.6544 (m-10) cc_final: 0.6164 (m-10)
REVERT: E  145 ILE cc_start: 0.7199 (pt) cc_final: 0.6913 (mm)
REVERT: F   27 ARG cc_start: 0.8238 (ptp90) cc_final: 0.7542 (tpt-90)
REVERT: F   38 TYR cc_start: 0.7882 (p90) cc_final: 0.7660 (p90)
REVERT: F   54 LYS cc_start: 0.6865 (tmmt) cc_final: 0.6301 (mttt)
REVERT: F   57 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8125 (tm-30)
REVERT: F   87 GLN cc_start: 0.8437 (tp-100) cc_final: 0.7995 (tp-100)
REVERT: F   91 LEU cc_start: 0.7669 (pp) cc_final: 0.6741 (pp)
REVERT: F  128 MET cc_start: 0.8665 (mmm) cc_final: 0.8426 (mmm)
REVERT: F  131 MET cc_start: 0.7919 (mmp) cc_final: 0.7493 (mmp)
  outliers start: 54
  outliers final: 40
  residues processed: 334
  average time/residue: 0.1900
  time to fit residues: 86.1130
Evaluate side-chains
  340 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 296
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   35 TYR
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue   45 TYR
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  148 ILE
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  265 GLU
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   76 SER
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  148 SER
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   41 ASN
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   74 PHE
Chi-restraints excluded: chain E residue   79 ASP
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue   97 ASN
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain F residue  141 LEU
Chi-restraints excluded: chain F residue  142 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 94 optimal weight:    6.9990
   chunk 76 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0570
   chunk 0 optimal weight:    5.9990
   chunk 60 optimal weight:    8.9990
   chunk 79 optimal weight:    5.9990
   overall best weight:    1.0102

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

Flipped N/Q/H residues before XYZ refinement:
B 145 ASN
F  39 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.153164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.129717 restraints weight = 18916.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.131927 restraints weight = 9465.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.133319 restraints weight = 5824.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.5112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8348  Z= 0.134
  Angle     :  0.733   9.264  11271  Z= 0.378
  Chirality :  0.047   0.217   1255
  Planarity :  0.004   0.035   1460
  Dihedral  :  5.506  35.590   1136
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  : 23.59 %
    Favored  : 70.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -1.07 (0.27), residues: 1029
  helix:  0.93 (0.22), residues: 599
  sheet: -2.31 (0.56), residues: 71
  loop : -3.33 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP E  95 
 HIS   0.003   0.001   HIS A 159 
 PHE   0.028   0.002   PHE E 109 
 TYR   0.018   0.002   TYR F 112 
 ARG   0.004   0.000   ARG D  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03153 (  435)
  hydrogen bonds       : angle       4.26696 ( 1278)
  covalent geometry    : bond        0.00298 ( 8348)
  covalent geometry    : angle       0.73335 (11271)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  367 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 315
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.4971 (tt0) cc_final: 0.4397 (tt0)
REVERT: A   45 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.7955 (p90)
REVERT: A   57 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8117 (tm-30)
REVERT: A   74 ARG cc_start: 0.6698 (mmp-170) cc_final: 0.6482 (tpt-90)
REVERT: A   77 GLN cc_start: 0.9146 (mp10) cc_final: 0.8676 (mp10)
REVERT: A  241 LYS cc_start: 0.9033 (tppp) cc_final: 0.8727 (tppt)
REVERT: A  242 ILE cc_start: 0.9138 (tt) cc_final: 0.8874 (tt)
REVERT: B   30 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8345 (mm)
REVERT: B   40 MET cc_start: 0.8738 (tpp) cc_final: 0.7361 (mtt)
REVERT: B   76 SER cc_start: 0.9394 (OUTLIER) cc_final: 0.9055 (m)
REVERT: B  125 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8102 (tm-30)
REVERT: B  149 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7372 (tm)
REVERT: B  243 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8653 (t0)
REVERT: D   25 ARG cc_start: 0.8081 (ttt180) cc_final: 0.7379 (mpp-170)
REVERT: D   38 TYR cc_start: 0.8784 (m-80) cc_final: 0.8534 (m-80)
REVERT: D   87 GLN cc_start: 0.8839 (mt0) cc_final: 0.8566 (mp10)
REVERT: D  122 LEU cc_start: 0.9090 (pp) cc_final: 0.8634 (mp)
REVERT: D  123 PHE cc_start: 0.9064 (t80) cc_final: 0.8744 (t80)
REVERT: E   50 SER cc_start: 0.9174 (t) cc_final: 0.8917 (t)
REVERT: E   52 LEU cc_start: 0.9197 (tp) cc_final: 0.8960 (tt)
REVERT: E   78 ASP cc_start: 0.8535 (m-30) cc_final: 0.8025 (t0)
REVERT: E  145 ILE cc_start: 0.7200 (pt) cc_final: 0.6913 (mm)
REVERT: F   27 ARG cc_start: 0.8274 (ptp90) cc_final: 0.7562 (tpt-90)
REVERT: F   54 LYS cc_start: 0.6931 (tmmt) cc_final: 0.6276 (mttt)
REVERT: F   57 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8094 (tm-30)
REVERT: F   70 LEU cc_start: 0.9481 (tp) cc_final: 0.9245 (tt)
REVERT: F   74 PHE cc_start: 0.8404 (m-80) cc_final: 0.8013 (m-80)
REVERT: F   87 GLN cc_start: 0.8432 (tp-100) cc_final: 0.7960 (tp-100)
REVERT: F   91 LEU cc_start: 0.7713 (pp) cc_final: 0.6768 (pp)
REVERT: F  128 MET cc_start: 0.8576 (mmm) cc_final: 0.8337 (mmm)
  outliers start: 52
  outliers final: 41
  residues processed: 334
  average time/residue: 0.1965
  time to fit residues: 88.3335
Evaluate side-chains
  350 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 304
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 TYR
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue   45 TYR
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  148 ILE
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  265 GLU
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   76 SER
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  199 GLU
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  120 PHE
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   74 PHE
Chi-restraints excluded: chain E residue   79 ASP
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue   97 ASN
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain F residue  122 LEU
Chi-restraints excluded: chain F residue  141 LEU
Chi-restraints excluded: chain F residue  142 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 92 optimal weight:    9.9990
   chunk 2 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0010
   chunk 94 optimal weight:    9.9990
   chunk 65 optimal weight:    0.0040
   chunk 8 optimal weight:    8.9990
   chunk 32 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
B 189 ASN
F  39 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.155349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.132407 restraints weight = 19023.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.134603 restraints weight = 9564.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.136020 restraints weight = 5743.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.5468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8348  Z= 0.125
  Angle     :  0.734   9.572  11271  Z= 0.371
  Chirality :  0.047   0.246   1255
  Planarity :  0.004   0.039   1460
  Dihedral  :  5.211  33.237   1136
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  6.23 %
    Allowed  : 24.08 %
    Favored  : 69.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.27), residues: 1029
  helix:  1.09 (0.22), residues: 600
  sheet: -1.95 (0.58), residues: 71
  loop : -3.22 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP E  95 
 HIS   0.004   0.001   HIS E 106 
 PHE   0.029   0.002   PHE E 109 
 TYR   0.022   0.001   TYR E  45 
 ARG   0.007   0.001   ARG D  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02885 (  435)
  hydrogen bonds       : angle       4.13358 ( 1278)
  covalent geometry    : bond        0.00268 ( 8348)
  covalent geometry    : angle       0.73445 (11271)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  365 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 314
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.5055 (tt0) cc_final: 0.4374 (tt0)
REVERT: A   45 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8016 (p90)
REVERT: A   57 GLN cc_start: 0.8377 (tm-30) cc_final: 0.8126 (tm-30)
REVERT: A   58 LEU cc_start: 0.9279 (tt) cc_final: 0.9056 (tp)
REVERT: A   77 GLN cc_start: 0.9086 (mp10) cc_final: 0.8627 (mp10)
REVERT: A  163 GLU cc_start: 0.7795 (tt0) cc_final: 0.7426 (tt0)
REVERT: A  241 LYS cc_start: 0.8965 (tppp) cc_final: 0.8694 (tppp)
REVERT: A  242 ILE cc_start: 0.9105 (tt) cc_final: 0.8850 (tt)
REVERT: B   30 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8304 (mm)
REVERT: B   40 MET cc_start: 0.8500 (tpp) cc_final: 0.7267 (mtt)
REVERT: B   97 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8356 (tm-30)
REVERT: B  244 LYS cc_start: 0.7375 (mptt) cc_final: 0.7174 (mmtt)
REVERT: D   25 ARG cc_start: 0.8085 (ttt180) cc_final: 0.7369 (mpp-170)
REVERT: D   87 GLN cc_start: 0.8788 (mt0) cc_final: 0.8495 (mp10)
REVERT: D  122 LEU cc_start: 0.9058 (pp) cc_final: 0.8595 (mp)
REVERT: E   43 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8394 (mmtm)
REVERT: F   27 ARG cc_start: 0.8353 (ptp90) cc_final: 0.7552 (tpt-90)
REVERT: F   43 LYS cc_start: 0.5897 (mptt) cc_final: 0.5602 (mptt)
REVERT: F   54 LYS cc_start: 0.6900 (tmmt) cc_final: 0.6341 (mttt)
REVERT: F   57 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7995 (tm-30)
REVERT: F   87 GLN cc_start: 0.8408 (tp-100) cc_final: 0.7922 (tp-100)
REVERT: F  128 MET cc_start: 0.8660 (mmm) cc_final: 0.8401 (mmm)
  outliers start: 51
  outliers final: 37
  residues processed: 331
  average time/residue: 0.2012
  time to fit residues: 89.6812
Evaluate side-chains
  333 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 294
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 TYR
Chi-restraints excluded: chain A residue   45 TYR
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  148 ILE
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  265 GLU
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  199 GLU
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain D residue   39 ASN
Chi-restraints excluded: chain D residue   40 THR
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   41 ASN
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   74 PHE
Chi-restraints excluded: chain E residue   79 ASP
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain F residue  141 LEU
Chi-restraints excluded: chain F residue  142 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 74 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 92 optimal weight:   10.0000
   chunk 48 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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 = 0.3816 r_free = 0.3816 target = 0.148969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.125463 restraints weight = 19065.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.127555 restraints weight = 9622.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.128904 restraints weight = 5907.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.5454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   8348  Z= 0.215
  Angle     :  0.830   9.297  11271  Z= 0.429
  Chirality :  0.050   0.225   1255
  Planarity :  0.005   0.061   1460
  Dihedral  :  5.784  39.603   1136
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.72 %
    Favored  : 90.28 %
  Rotamer:
    Outliers :  7.70 %
    Allowed  : 25.67 %
    Favored  : 66.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.28), residues: 1029
  helix:  1.05 (0.22), residues: 601
  sheet: -2.18 (0.54), residues: 81
  loop : -3.40 (0.30), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP E  95 
 HIS   0.004   0.001   HIS B 105 
 PHE   0.031   0.003   PHE F  74 
 TYR   0.032   0.002   TYR E  45 
 ARG   0.009   0.001   ARG D  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  435)
  hydrogen bonds       : angle       4.38091 ( 1278)
  covalent geometry    : bond        0.00491 ( 8348)
  covalent geometry    : angle       0.82976 (11271)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 313
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8708 (tpp) cc_final: 0.8453 (tpp)
REVERT: A   37 GLU cc_start: 0.5042 (tt0) cc_final: 0.4048 (tt0)
REVERT: A   45 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8166 (p90)
REVERT: A   74 ARG cc_start: 0.4046 (tpt170) cc_final: 0.3509 (tpt-90)
REVERT: A   77 GLN cc_start: 0.9233 (mp10) cc_final: 0.8893 (mp10)
REVERT: A  163 GLU cc_start: 0.7938 (tt0) cc_final: 0.7420 (tt0)
REVERT: A  166 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6362 (pp20)
REVERT: A  241 LYS cc_start: 0.9137 (tppp) cc_final: 0.8874 (tppt)
REVERT: A  242 ILE cc_start: 0.9326 (tt) cc_final: 0.9121 (tt)
REVERT: A  321 GLU cc_start: 0.8489 (tp30) cc_final: 0.7408 (tp30)
REVERT: B   18 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8896 (ttpt)
REVERT: B   76 SER cc_start: 0.9435 (OUTLIER) cc_final: 0.9103 (m)
REVERT: B  123 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7792 (tm-30)
REVERT: B  244 LYS cc_start: 0.7508 (mptt) cc_final: 0.6988 (tppt)
REVERT: D   25 ARG cc_start: 0.8126 (ttt180) cc_final: 0.7450 (mpp-170)
REVERT: D   67 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7836 (m-30)
REVERT: D   75 LYS cc_start: 0.8366 (tmtt) cc_final: 0.7845 (mmpt)
REVERT: D   87 GLN cc_start: 0.8849 (mt0) cc_final: 0.8567 (mp10)
REVERT: D  122 LEU cc_start: 0.9084 (pp) cc_final: 0.8607 (mp)
REVERT: E   46 TYR cc_start: 0.9175 (t80) cc_final: 0.8863 (t80)
REVERT: F   27 ARG cc_start: 0.8429 (ptp90) cc_final: 0.7636 (tpt-90)
REVERT: F   51 ARG cc_start: 0.8746 (mtp-110) cc_final: 0.8386 (ttm-80)
REVERT: F   54 LYS cc_start: 0.6849 (tmmt) cc_final: 0.6274 (mttt)
REVERT: F   57 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8137 (tm-30)
REVERT: F   87 GLN cc_start: 0.8439 (tp-100) cc_final: 0.7798 (tp-100)
  outliers start: 63
  outliers final: 44
  residues processed: 337
  average time/residue: 0.1901
  time to fit residues: 86.4141
Evaluate side-chains
  351 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 302
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 TYR
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue   45 TYR
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  148 ILE
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  265 GLU
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain B residue   18 LYS
Chi-restraints excluded: chain B residue   49 ASP
Chi-restraints excluded: chain B residue   76 SER
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  199 GLU
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain D residue   21 ILE
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain D residue   65 ASP
Chi-restraints excluded: chain D residue   67 ASP
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain E residue   18 LEU
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   79 ASP
Chi-restraints excluded: chain E residue   80 LEU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue   97 ASN
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain F residue  141 LEU
Chi-restraints excluded: chain F residue  142 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    0.0270
   chunk 25 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.7238

-------------------------------------------------------------------------------
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 = 0.3878 r_free = 0.3878 target = 0.153895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.131286 restraints weight = 19101.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.133492 restraints weight = 9401.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.134879 restraints weight = 5620.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.5799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8348  Z= 0.138
  Angle     :  0.793   9.754  11271  Z= 0.402
  Chirality :  0.047   0.186   1255
  Planarity :  0.004   0.070   1460
  Dihedral  :  5.362  35.416   1136
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 29.10 %
    Favored  : 65.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.27), residues: 1029
  helix:  1.15 (0.22), residues: 598
  sheet: -1.85 (0.55), residues: 81
  loop : -3.31 (0.30), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E  95 
 HIS   0.003   0.001   HIS A 159 
 PHE   0.032   0.002   PHE E 109 
 TYR   0.033   0.001   TYR E 112 
 ARG   0.010   0.001   ARG D  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03103 (  435)
  hydrogen bonds       : angle       4.25113 ( 1278)
  covalent geometry    : bond        0.00303 ( 8348)
  covalent geometry    : angle       0.79287 (11271)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 295
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8702 (tpp) cc_final: 0.8466 (tpp)
REVERT: A   37 GLU cc_start: 0.4765 (tt0) cc_final: 0.3916 (tt0)
REVERT: A   45 TYR cc_start: 0.9046 (OUTLIER) cc_final: 0.8210 (p90)
REVERT: A   77 GLN cc_start: 0.9071 (mp10) cc_final: 0.8588 (mp10)
REVERT: A  166 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6317 (pp20)
REVERT: A  217 ASP cc_start: 0.7562 (p0) cc_final: 0.7229 (p0)
REVERT: A  241 LYS cc_start: 0.9044 (tppp) cc_final: 0.8699 (tppt)
REVERT: B   18 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8856 (ttpt)
REVERT: B   40 MET cc_start: 0.8676 (tpp) cc_final: 0.6939 (mtt)
REVERT: B  123 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7207 (tm-30)
REVERT: B  199 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7896 (tt0)
REVERT: B  244 LYS cc_start: 0.7412 (mptt) cc_final: 0.7112 (mmtt)
REVERT: D   25 ARG cc_start: 0.8098 (ttt180) cc_final: 0.7437 (mpp-170)
REVERT: D   53 SER cc_start: 0.9188 (m) cc_final: 0.8731 (t)
REVERT: D   75 LYS cc_start: 0.8319 (tmtt) cc_final: 0.7781 (mmpt)
REVERT: D   87 GLN cc_start: 0.8828 (mt0) cc_final: 0.8531 (mp10)
REVERT: D  122 LEU cc_start: 0.9048 (pp) cc_final: 0.8547 (mp)
REVERT: E   46 TYR cc_start: 0.8993 (t80) cc_final: 0.8696 (t80)
REVERT: E   69 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8626 (tm-30)
REVERT: F   27 ARG cc_start: 0.8478 (ptp90) cc_final: 0.7663 (tpt-90)
REVERT: F   54 LYS cc_start: 0.6898 (tmmt) cc_final: 0.6291 (mttt)
REVERT: F   57 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8143 (tm-30)
REVERT: F   87 GLN cc_start: 0.8393 (tp-100) cc_final: 0.7729 (tp-100)
  outliers start: 41
  outliers final: 31
  residues processed: 313
  average time/residue: 0.1972
  time to fit residues: 83.2927
Evaluate side-chains
  326 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 291
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 TYR
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue   45 TYR
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  148 ILE
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  265 GLU
Chi-restraints excluded: chain B residue   18 LYS
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  188 ASP
Chi-restraints excluded: chain B residue  199 GLU
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain D residue   65 ASP
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain E residue   41 ASN
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   79 ASP
Chi-restraints excluded: chain E residue   80 LEU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain F residue  141 LEU
Chi-restraints excluded: chain F residue  142 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0050
   chunk 69 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 42 optimal weight:    9.9990
   chunk 64 optimal weight:    7.9990
   chunk 28 optimal weight:    0.0270
   overall best weight:    0.5654

-------------------------------------------------------------------------------
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 = 0.3903 r_free = 0.3903 target = 0.156012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.133692 restraints weight = 19258.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.135867 restraints weight = 9381.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.137259 restraints weight = 5579.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.6021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8348  Z= 0.139
  Angle     :  0.811  10.799  11271  Z= 0.405
  Chirality :  0.047   0.178   1255
  Planarity :  0.005   0.113   1460
  Dihedral  :  5.173  33.575   1136
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 30.20 %
    Favored  : 65.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.27), residues: 1029
  helix:  1.20 (0.22), residues: 600
  sheet: -1.56 (0.56), residues: 81
  loop : -3.33 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  77 
 HIS   0.003   0.000   HIS A 159 
 PHE   0.031   0.002   PHE D 109 
 TYR   0.047   0.001   TYR E 112 
 ARG   0.012   0.001   ARG D  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02957 (  435)
  hydrogen bonds       : angle       4.20895 ( 1278)
  covalent geometry    : bond        0.00298 ( 8348)
  covalent geometry    : angle       0.81134 (11271)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 310
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8713 (tpp) cc_final: 0.8479 (tpp)
REVERT: A   37 GLU cc_start: 0.4887 (tt0) cc_final: 0.3739 (tt0)
REVERT: A   45 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.8045 (p90)
REVERT: A   77 GLN cc_start: 0.9055 (mp10) cc_final: 0.8720 (mp10)
REVERT: A  166 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6368 (pp20)
REVERT: A  231 LEU cc_start: 0.9480 (tp) cc_final: 0.9270 (mt)
REVERT: B   23 GLU cc_start: 0.7928 (pm20) cc_final: 0.6984 (pt0)
REVERT: B   40 MET cc_start: 0.8676 (tpp) cc_final: 0.6740 (mtt)
REVERT: B  123 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7221 (tm-30)
REVERT: D   25 ARG cc_start: 0.8118 (ttt180) cc_final: 0.7393 (mpp-170)
REVERT: D   53 SER cc_start: 0.9150 (m) cc_final: 0.8760 (t)
REVERT: D   75 LYS cc_start: 0.8270 (tmtt) cc_final: 0.7633 (mmpt)
REVERT: D   87 GLN cc_start: 0.8781 (mt0) cc_final: 0.8463 (mp10)
REVERT: D  122 LEU cc_start: 0.9031 (pp) cc_final: 0.8531 (mp)
REVERT: E   22 TYR cc_start: 0.8198 (t80) cc_final: 0.7882 (t80)
REVERT: E   46 TYR cc_start: 0.8977 (t80) cc_final: 0.8726 (t80)
REVERT: F   27 ARG cc_start: 0.8432 (ptp90) cc_final: 0.7597 (tpt-90)
REVERT: F   54 LYS cc_start: 0.6884 (tmmt) cc_final: 0.6314 (mttt)
REVERT: F   57 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8107 (tm-30)
REVERT: F   87 GLN cc_start: 0.8416 (tp-100) cc_final: 0.7818 (tp-100)
  outliers start: 39
  outliers final: 31
  residues processed: 324
  average time/residue: 0.2070
  time to fit residues: 89.2479
Evaluate side-chains
  324 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 291
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 TYR
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue   45 TYR
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  148 ILE
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  265 GLU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   73 ARG
Chi-restraints excluded: chain E residue   79 ASP
Chi-restraints excluded: chain E residue   80 LEU
Chi-restraints excluded: chain E residue   81 MET
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain F residue  141 LEU
Chi-restraints excluded: chain F residue  142 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0870
   chunk 1 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 16 optimal weight:    0.2980
   chunk 89 optimal weight:    0.9980
   overall best weight:    0.6760

-------------------------------------------------------------------------------
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 = 0.3913 r_free = 0.3913 target = 0.156629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.134295 restraints weight = 18982.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.136516 restraints weight = 9270.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.137881 restraints weight = 5503.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.6229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8348  Z= 0.147
  Angle     :  0.855  12.446  11271  Z= 0.428
  Chirality :  0.047   0.226   1255
  Planarity :  0.006   0.143   1460
  Dihedral  :  5.140  32.780   1136
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 31.78 %
    Favored  : 63.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.28), residues: 1029
  helix:  1.27 (0.22), residues: 598
  sheet: -1.30 (0.57), residues: 83
  loop : -3.38 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E  95 
 HIS   0.003   0.001   HIS A 159 
 PHE   0.029   0.001   PHE B 127 
 TYR   0.045   0.001   TYR E 112 
 ARG   0.012   0.001   ARG E 147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03076 (  435)
  hydrogen bonds       : angle       4.28137 ( 1278)
  covalent geometry    : bond        0.00323 ( 8348)
  covalent geometry    : angle       0.85533 (11271)

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 302
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ARG cc_start: 0.2121 (ptt-90) cc_final: 0.1558 (ptt-90)
REVERT: A   31 MET cc_start: 0.8699 (tpp) cc_final: 0.8466 (tpp)
REVERT: A   37 GLU cc_start: 0.5006 (tt0) cc_final: 0.3688 (tt0)
REVERT: A   77 GLN cc_start: 0.8981 (mp10) cc_final: 0.8566 (mp10)
REVERT: A  166 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6385 (pp20)
REVERT: A  241 LYS cc_start: 0.9057 (tppt) cc_final: 0.8751 (tppt)
REVERT: B   23 GLU cc_start: 0.7918 (pm20) cc_final: 0.6961 (pt0)
REVERT: B   40 MET cc_start: 0.8680 (tpp) cc_final: 0.6684 (mtt)
REVERT: B  123 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7280 (tm-30)
REVERT: B  244 LYS cc_start: 0.8831 (tptt) cc_final: 0.8150 (mmtt)
REVERT: D   25 ARG cc_start: 0.8155 (ttt180) cc_final: 0.7481 (mpp-170)
REVERT: D   53 SER cc_start: 0.9137 (m) cc_final: 0.8773 (t)
REVERT: D   75 LYS cc_start: 0.8204 (tmtt) cc_final: 0.7621 (mmpt)
REVERT: D   87 GLN cc_start: 0.8746 (mt0) cc_final: 0.8399 (mp10)
REVERT: D  122 LEU cc_start: 0.9037 (pp) cc_final: 0.8524 (mp)
REVERT: E   46 TYR cc_start: 0.8959 (t80) cc_final: 0.8708 (t80)
REVERT: E   69 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8567 (tm-30)
REVERT: F   27 ARG cc_start: 0.8432 (ptp90) cc_final: 0.7562 (tpt-90)
REVERT: F   54 LYS cc_start: 0.6886 (tmmt) cc_final: 0.6249 (mttt)
REVERT: F   57 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8034 (tm-30)
REVERT: F   87 GLN cc_start: 0.8420 (tp-100) cc_final: 0.7800 (tp-100)
  outliers start: 36
  outliers final: 33
  residues processed: 315
  average time/residue: 0.1978
  time to fit residues: 83.9596
Evaluate side-chains
  333 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 299
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 TYR
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  148 ILE
Chi-restraints excluded: chain A residue  163 GLU
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  265 GLU
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  223 TYR
Chi-restraints excluded: chain D residue   39 ASN
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain E residue   58 VAL
Chi-restraints excluded: chain E residue   73 ARG
Chi-restraints excluded: chain E residue   79 ASP
Chi-restraints excluded: chain E residue   80 LEU
Chi-restraints excluded: chain E residue   81 MET
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  141 LEU
Chi-restraints excluded: chain F residue   42 SER
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain F residue  141 LEU
Chi-restraints excluded: chain F residue  142 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0070
   chunk 15 optimal weight:    0.0970
   chunk 97 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 40 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0770
   chunk 22 optimal weight:    0.9980
   chunk 89 optimal weight:   10.0000
   overall best weight:    0.3554

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

Flipped N/Q/H residues before XYZ refinement:
E 150 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.159529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.137460 restraints weight = 19205.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.139796 restraints weight = 9311.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.141198 restraints weight = 5432.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.6480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8348  Z= 0.142
  Angle     :  0.835  11.724  11271  Z= 0.416
  Chirality :  0.047   0.216   1255
  Planarity :  0.005   0.111   1460
  Dihedral  :  4.865  29.825   1136
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 32.40 %
    Favored  : 63.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.28), residues: 1029
  helix:  1.35 (0.23), residues: 598
  sheet: -0.79 (0.59), residues: 81
  loop : -3.29 (0.30), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E  95 
 HIS   0.004   0.001   HIS F 106 
 PHE   0.030   0.002   PHE D 109 
 TYR   0.041   0.001   TYR E 112 
 ARG   0.012   0.001   ARG D  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02943 (  435)
  hydrogen bonds       : angle       4.17588 ( 1278)
  covalent geometry    : bond        0.00305 ( 8348)
  covalent geometry    : angle       0.83527 (11271)

===============================================================================
Job complete
usr+sys time: 4132.49 seconds
wall clock time: 72 minutes 0.73 seconds (4320.73 seconds total)