Starting phenix.real_space_refine
on Thu Feb 13 10:55:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nhv_9374/02_2025/6nhv_9374.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nhv_9374/02_2025/6nhv_9374.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nhv_9374/02_2025/6nhv_9374.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nhv_9374/02_2025/6nhv_9374.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nhv_9374/02_2025/6nhv_9374.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nhv_9374/02_2025/6nhv_9374.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.934
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      31      5.16       5
     C    5653      2.51       5
     N    1546      2.21       5
     O    1718      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8948
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 470
          Classifications: {'peptide': 63}
          Link IDs: {'PTRANS': 4, 'TRANS': 58}
    Chain: "A"
      Number of atoms: 1358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 166, 1358
          Unusual residues: {'CRO': 1}
          Classifications: {'peptide': 165, 'undetermined': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 158, None: 1}
            Not linked:
              pdbres="CRO A  66 "
              pdbres="VAL A  68 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'CRO:plan-3': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "N"
      Number of atoms: 885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 885
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 1, 'TRANS': 116}
    Chain: "O"
      Number of atoms: 885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 885
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 1, 'TRANS': 116}
    Chain: "R"
      Number of atoms: 2251
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2251
          Classifications: {'peptide': 297}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 290}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "S"
      Number of atoms: 1107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1107
          Classifications: {'peptide': 143}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 2, 'TRANS': 140}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "T"
      Number of atoms: 1107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1107
          Classifications: {'peptide': 143}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 2, 'TRANS': 140}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "X"
      Number of atoms: 885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 885
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 1, 'TRANS': 116}
  Time building chain proxies: 5.60, per 1000 atoms: 0.63
  Number of scatterers: 8948
  At special positions: 0
  Unit cell: (119.78, 94.34, 115.54, 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      31     16.00
     O    1718      8.00
     N    1546      7.00
     C    5653      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.52
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2132

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 7 sheets defined
      51.2% alpha, 19.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 9
      removed outlier: 3.701A  pdb=" N   THR A   9 " --> pdb=" O   GLU A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 61
    Processing helix  chain 'A' and resid 68 through 72
    Processing helix  chain 'A' and resid 75 through 81
      removed outlier: 5.435A  pdb=" N   ARG A  80 " --> pdb=" O   HIS A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 87
    Processing helix  chain 'A' and resid 156 through 159
    Processing helix  chain 'N' and resid 17 through 31
      removed outlier: 3.737A  pdb=" N   LEU N  22 " --> pdb=" O   PRO N  18 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLU N  23 " --> pdb=" O   GLY N  19 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 73 through 89
      removed outlier: 3.748A  pdb=" N   ALA N  86 " --> pdb=" O   ALA N  82 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL N  87 " --> pdb=" O   SER N  83 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 17 through 31
      removed outlier: 3.707A  pdb=" N   LEU O  22 " --> pdb=" O   PRO O  18 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLU O  23 " --> pdb=" O   GLY O  19 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 73 through 89
      removed outlier: 3.820A  pdb=" N   ALA O  86 " --> pdb=" O   ALA O  82 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   VAL O  87 " --> pdb=" O   SER O  83 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 24 through 45
      removed outlier: 3.581A  pdb=" N   SER R  39 " --> pdb=" O   ASP R  35 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE R  40 " --> pdb=" O   GLU R  36 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY R  42 " --> pdb=" O   THR R  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 49 through 72
      removed outlier: 3.628A  pdb=" N   GLU R  58 " --> pdb=" O   GLY R  54 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ASN R  61 " --> pdb=" O   GLU R  57 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ASP R  62 " --> pdb=" O   GLU R  58 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLY R  68 " --> pdb=" O   TYR R  64 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 80 through 98
      removed outlier: 4.091A  pdb=" N   ILE R  84 " --> pdb=" O   SER R  80 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU R  88 " --> pdb=" O   ILE R  84 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LYS R  89 " --> pdb=" O   ALA R  85 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU R  92 " --> pdb=" O   LEU R  88 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   GLU R  96 " --> pdb=" O   LEU R  92 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   MET R  97 " --> pdb=" O   ARG R  93 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 110 through 137
      removed outlier: 3.581A  pdb=" N   LEU R 115 " --> pdb=" O   GLU R 111 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   THR R 120 " --> pdb=" O   ASP R 116 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG R 124 " --> pdb=" O   THR R 120 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   THR R 131 " --> pdb=" O   ARG R 127 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ARG R 134 " --> pdb=" O   LEU R 130 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 175
      removed outlier: 3.625A  pdb=" N   TYR R 145 " --> pdb=" O   GLU R 141 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ASP R 151 " --> pdb=" O   LEU R 147 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   PHE R 154 " --> pdb=" O   SER R 150 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   LEU R 155 " --> pdb=" O   ASP R 151 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLU R 161 " --> pdb=" O   ALA R 157 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE R 162 " --> pdb=" O   ARG R 158 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LYS R 167 " --> pdb=" O   GLU R 163 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU R 168 " --> pdb=" O   GLN R 164 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU R 169 " --> pdb=" O   GLY R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 176 through 186
      removed outlier: 3.789A  pdb=" N   VAL R 180 " --> pdb=" O   GLN R 176 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ARG R 181 " --> pdb=" O   ASP R 177 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASN R 186 " --> pdb=" O   ILE R 182 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 199 through 208
    Processing helix  chain 'R' and resid 209 through 220
      removed outlier: 3.711A  pdb=" N   CYS R 219 " --> pdb=" O   VAL R 215 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLY R 220 " --> pdb=" O   LEU R 216 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 232 through 240
    Processing helix  chain 'R' and resid 242 through 252
      removed outlier: 3.502A  pdb=" N   VAL R 246 " --> pdb=" O   HIS R 242 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 265 through 274
    Processing helix  chain 'R' and resid 275 through 285
      removed outlier: 3.628A  pdb=" N   VAL R 279 " --> pdb=" O   HIS R 275 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   TYR R 285 " --> pdb=" O   VAL R 281 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 298 through 307
    Processing helix  chain 'R' and resid 308 through 318
    Processing helix  chain 'S' and resid 24 through 45
      removed outlier: 3.593A  pdb=" N   SER S  39 " --> pdb=" O   ASP S  35 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   PHE S  40 " --> pdb=" O   GLU S  36 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLY S  42 " --> pdb=" O   THR S  38 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 49 through 72
      removed outlier: 3.597A  pdb=" N   GLU S  58 " --> pdb=" O   GLY S  54 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASP S  62 " --> pdb=" O   GLU S  58 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   GLY S  68 " --> pdb=" O   TYR S  64 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 80 through 98
      removed outlier: 4.167A  pdb=" N   ILE S  84 " --> pdb=" O   SER S  80 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU S  88 " --> pdb=" O   ILE S  84 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LYS S  89 " --> pdb=" O   ALA S  85 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU S  90 " --> pdb=" O   TRP S  86 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   GLU S  96 " --> pdb=" O   LEU S  92 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   MET S  97 " --> pdb=" O   ARG S  93 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 109 through 137
      removed outlier: 3.625A  pdb=" N   LEU S 115 " --> pdb=" O   GLU S 111 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL S 117 " --> pdb=" O   ALA S 113 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR S 120 " --> pdb=" O   ASP S 116 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ARG S 124 " --> pdb=" O   THR S 120 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR S 131 " --> pdb=" O   ARG S 127 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 139 through 165
      removed outlier: 3.689A  pdb=" N   TYR S 145 " --> pdb=" O   GLU S 141 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ALA S 148 " --> pdb=" O   ALA S 144 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ASP S 151 " --> pdb=" O   LEU S 147 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   PHE S 154 " --> pdb=" O   SER S 150 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU S 155 " --> pdb=" O   ASP S 151 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLU S 161 " --> pdb=" O   ALA S 157 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE S 162 " --> pdb=" O   ARG S 158 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 24 through 45
      removed outlier: 3.623A  pdb=" N   SER T  39 " --> pdb=" O   ASP T  35 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   PHE T  40 " --> pdb=" O   GLU T  36 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLY T  42 " --> pdb=" O   THR T  38 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 49 through 72
      removed outlier: 3.646A  pdb=" N   GLU T  58 " --> pdb=" O   GLY T  54 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ASP T  62 " --> pdb=" O   GLU T  58 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLY T  68 " --> pdb=" O   TYR T  64 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 80 through 98
      removed outlier: 4.129A  pdb=" N   ILE T  84 " --> pdb=" O   SER T  80 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU T  88 " --> pdb=" O   ILE T  84 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS T  89 " --> pdb=" O   ALA T  85 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU T  90 " --> pdb=" O   TRP T  86 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLU T  96 " --> pdb=" O   LEU T  92 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   MET T  97 " --> pdb=" O   ARG T  93 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 110 through 137
      removed outlier: 3.631A  pdb=" N   LEU T 115 " --> pdb=" O   GLU T 111 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASP T 116 " --> pdb=" O   SER T 112 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL T 117 " --> pdb=" O   ALA T 113 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   THR T 120 " --> pdb=" O   ASP T 116 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG T 124 " --> pdb=" O   THR T 120 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR T 131 " --> pdb=" O   ARG T 127 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ARG T 134 " --> pdb=" O   LEU T 130 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 139 through 165
      removed outlier: 3.689A  pdb=" N   TYR T 145 " --> pdb=" O   GLU T 141 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ALA T 148 " --> pdb=" O   ALA T 144 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ASP T 151 " --> pdb=" O   LEU T 147 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   PHE T 154 " --> pdb=" O   SER T 150 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LEU T 155 " --> pdb=" O   ASP T 151 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ARG T 158 " --> pdb=" O   PHE T 154 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE T 160 " --> pdb=" O   LEU T 156 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLU T 161 " --> pdb=" O   ALA T 157 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE T 162 " --> pdb=" O   ARG T 158 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 17 through 31
      removed outlier: 3.742A  pdb=" N   LEU X  22 " --> pdb=" O   PRO X  18 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLU X  23 " --> pdb=" O   GLY X  19 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 73 through 89
      removed outlier: 3.769A  pdb=" N   ALA X  86 " --> pdb=" O   ALA X  82 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   VAL X  87 " --> pdb=" O   SER X  83 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 22
      removed outlier: 6.191A  pdb=" N   ASN A 149 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   LYS A 166 " --> pdb=" O   ASN A 149 " (cutoff:3.500A)
      removed outlier: 8.671A  pdb=" N   LEU A 119 " --> pdb=" O   VAL A  11 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   ASN A 121 " --> pdb=" O   PRO A  13 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   LEU A  15 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   ILE A 123 " --> pdb=" O   LEU A  15 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   GLU A  17 " --> pdb=" O   ILE A 123 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   LEU A 125 " --> pdb=" O   GLU A  17 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ASP A  19 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   GLY A 127 " --> pdb=" O   ASP A  19 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   ASP A  21 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'O' and resid 49 through 52
      removed outlier: 4.470A  pdb=" N   ALA O  49 " --> pdb=" O   PHE N  44 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   LEU N   4 " --> pdb=" O   ARG N  43 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   VAL N  45 " --> pdb=" O   LEU N   4 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ILE N   6 " --> pdb=" O   VAL N  45 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   VAL N 100 " --> pdb=" O   VAL X 119 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'N' and resid 13 through 14
    Processing sheet with id=AA4, first strand: chain 'N' and resid 49 through 52
      removed outlier: 4.285A  pdb=" N   ALA N  49 " --> pdb=" O   PHE X  44 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   LEU X   4 " --> pdb=" O   ARG X  43 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   VAL X  45 " --> pdb=" O   LEU X   4 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   ILE X   6 " --> pdb=" O   VAL X  45 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL X 100 " --> pdb=" O   VAL O 119 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'N' and resid 115 through 119
      removed outlier: 3.792A  pdb=" N   VAL O 100 " --> pdb=" O   VAL N 119 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   LEU O   4 " --> pdb=" O   ARG O  43 " (cutoff:3.500A)
      removed outlier: 7.563A  pdb=" N   VAL O  45 " --> pdb=" O   LEU O   4 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   ILE O   6 " --> pdb=" O   VAL O  45 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ALA X  49 " --> pdb=" O   PHE O  44 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'O' and resid 13 through 14
    Processing sheet with id=AA7, first strand: chain 'X' and resid 13 through 14

    514 hydrogen bonds defined for protein.
    1458 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: 2.37

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1626
        1.29 -     1.42: 2012
        1.42 -     1.55: 5377
        1.55 -     1.68: 2
        1.68 -     1.81: 50
  Bond restraints: 9067
  Sorted by residual:
  bond pdb=" C   LEU R  90 "
       pdb=" N   ILE R  91 "
    ideal  model  delta    sigma   weight residual
    1.335  1.232  0.102 1.26e-02 6.30e+03 6.61e+01
  bond pdb=" C   PHE A 223 "
       pdb=" N   VAL A 224 "
    ideal  model  delta    sigma   weight residual
    1.331  1.250  0.081 1.24e-02 6.50e+03 4.23e+01
  bond pdb=" C   LYS A 156 "
       pdb=" O   LYS A 156 "
    ideal  model  delta    sigma   weight residual
    1.237  1.172  0.064 1.17e-02 7.31e+03 3.02e+01
  bond pdb=" C   VAL O   5 "
       pdb=" N   ILE O   6 "
    ideal  model  delta    sigma   weight residual
    1.330  1.262  0.068 1.25e-02 6.40e+03 2.95e+01
  bond pdb=" C   GLU R  81 "
       pdb=" N   GLU R  82 "
    ideal  model  delta    sigma   weight residual
    1.335  1.260  0.074 1.38e-02 5.25e+03 2.91e+01
  ... (remaining 9062 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 11398
        1.71 -     3.43: 753
        3.43 -     5.14: 79
        5.14 -     6.86: 11
        6.86 -     8.57: 3
  Bond angle restraints: 12244
  Sorted by residual:
  angle pdb=" C   VAL A 224 "
        pdb=" N   THR A 225 "
        pdb=" CA  THR A 225 "
      ideal   model   delta    sigma   weight residual
     122.73  114.16    8.57 1.62e+00 3.81e-01 2.80e+01
  angle pdb=" O   PHE A 223 "
        pdb=" C   PHE A 223 "
        pdb=" N   VAL A 224 "
      ideal   model   delta    sigma   weight residual
     123.23  117.38    5.85 1.30e+00 5.92e-01 2.02e+01
  angle pdb=" N   ILE A 123 "
        pdb=" CA  ILE A 123 "
        pdb=" C   ILE A 123 "
      ideal   model   delta    sigma   weight residual
     108.48  114.29   -5.81 1.44e+00 4.82e-01 1.63e+01
  angle pdb=" N   ILE R 162 "
        pdb=" CA  ILE R 162 "
        pdb=" C   ILE R 162 "
      ideal   model   delta    sigma   weight residual
     110.42  114.18   -3.76 9.60e-01 1.09e+00 1.53e+01
  angle pdb=" CA  PHE A 223 "
        pdb=" C   PHE A 223 "
        pdb=" N   VAL A 224 "
      ideal   model   delta    sigma   weight residual
     116.01  121.67   -5.66 1.49e+00 4.50e-01 1.45e+01
  ... (remaining 12239 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 5279
       17.67 -    35.34: 157
       35.34 -    53.02: 36
       53.02 -    70.69: 7
       70.69 -    88.36: 5
  Dihedral angle restraints: 5484
    sinusoidal: 2166
      harmonic: 3318
  Sorted by residual:
  dihedral pdb=" CA  ASP A 180 "
           pdb=" CB  ASP A 180 "
           pdb=" CG  ASP A 180 "
           pdb=" OD1 ASP A 180 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.07   58.07     1      2.00e+01 2.50e-03 1.13e+01
  dihedral pdb=" CA  PRO A 196 "
           pdb=" C   PRO A 196 "
           pdb=" N   ASP A 197 "
           pdb=" CA  ASP A 197 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.22   16.78     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  ARG A  96 "
           pdb=" C   ARG A  96 "
           pdb=" N   THR A  97 "
           pdb=" CA  THR A  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.28   16.72     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 5481 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 966
       0.044 -    0.088: 367
       0.088 -    0.133: 89
       0.133 -    0.177: 8
       0.177 -    0.221: 4
  Chirality restraints: 1434
  Sorted by residual:
  chirality pdb=" CA  GLU A   5 "
            pdb=" N   GLU A   5 "
            pdb=" C   GLU A   5 "
            pdb=" CB  GLU A   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CA  LYS A  41 "
            pdb=" N   LYS A  41 "
            pdb=" C   LYS A  41 "
            pdb=" CB  LYS A  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.74e-01
  chirality pdb=" CA  LYS A 156 "
            pdb=" N   LYS A 156 "
            pdb=" C   LYS A 156 "
            pdb=" CB  LYS A 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.42e-01
  ... (remaining 1431 not shown)

  Planarity restraints: 1579
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB2 CRO A  66 "   -0.040 2.00e-02 2.50e+03   3.40e-02 2.90e+01
        pdb=" CG2 CRO A  66 "    0.068 2.00e-02 2.50e+03
        pdb=" C1  CRO A  66 "   -0.033 2.00e-02 2.50e+03
        pdb=" C2  CRO A  66 "   -0.024 2.00e-02 2.50e+03
        pdb=" CA1 CRO A  66 "    0.011 2.00e-02 2.50e+03
        pdb=" CA2 CRO A  66 "   -0.015 2.00e-02 2.50e+03
        pdb=" CA3 CRO A  66 "    0.055 2.00e-02 2.50e+03
        pdb=" N2  CRO A  66 "   -0.017 2.00e-02 2.50e+03
        pdb=" N3  CRO A  66 "   -0.005 2.00e-02 2.50e+03
        pdb=" O2  CRO A  66 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB2 CRO A  66 "    0.014 2.00e-02 2.50e+03   2.55e-02 1.30e+01
        pdb=" CG2 CRO A  66 "   -0.060 2.00e-02 2.50e+03
        pdb=" CD1 CRO A  66 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 CRO A  66 "    0.018 2.00e-02 2.50e+03
        pdb=" CE1 CRO A  66 "    0.022 2.00e-02 2.50e+03
        pdb=" CE2 CRO A  66 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  CRO A  66 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  CRO A  66 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 162 "    0.015 2.00e-02 2.50e+03   3.14e-02 9.89e+00
        pdb=" C   ILE R 162 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   ILE R 162 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLU R 163 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1576 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 151
        2.68 -     3.23: 8286
        3.23 -     3.79: 12619
        3.79 -     4.34: 18591
        4.34 -     4.90: 30616
  Nonbonded interactions: 70263
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG X  77 "
            pdb=" OE2 GLU X 108 "
     model   vdw
     2.125 3.120
  nonbonded pdb=" NH1 ARG O  77 "
            pdb=" OE2 GLU O 108 "
     model   vdw
     2.153 3.120
  nonbonded pdb=" OD2 ASP T  62 "
            pdb=" OH  TYR T 145 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" NH1 ARG N  77 "
            pdb=" OE2 GLU N 108 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" OD2 ASP R  62 "
            pdb=" OH  TYR R 145 "
     model   vdw
     2.316 3.040
  ... (remaining 70258 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 'N'
  selection = chain 'O'
  selection = chain 'X'
}
ncs_group {
  reference = chain 'S'
  selection = chain 'T'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.870
  Find NCS groups from input model:        0.180
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6947
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      :  0.010   0.107   9067  Z= 0.665
  Angle     :  0.935   8.573  12244  Z= 0.597
  Chirality :  0.048   0.221   1434
  Planarity :  0.006   0.072   1579
  Dihedral  :  9.922  88.359   3352
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.83 %
    Favored  : 97.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -3.61 (0.20), residues: 1149
  helix: -4.05 (0.12), residues: 551
  sheet:  0.50 (0.33), residues: 205
  loop : -1.02 (0.25), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP S  86 
 HIS   0.008   0.002   HIS A 169 
 PHE   0.017   0.002   PHE A 165 
 TYR   0.012   0.002   TYR A 151 
 ARG   0.012   0.001   ARG O  43 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  399 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 397
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: N  105 GLU cc_start: 0.7812 (tt0) cc_final: 0.7511 (tt0)
REVERT: R   97 MET cc_start: 0.7590 (mtt) cc_final: 0.7274 (mtt)
REVERT: R  211 GLU cc_start: 0.8396 (pm20) cc_final: 0.7240 (pm20)
REVERT: T   67 MET cc_start: 0.7829 (mtp) cc_final: 0.7590 (mtp)
  outliers start: 2
  outliers final: 0
  residues processed: 398
  average time/residue: 0.2518
  time to fit residues: 130.3008
Evaluate side-chains
  272 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 272
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.5980
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 101 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN
** R 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 306 ASN
T  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.172109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.127905 restraints weight = 11577.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.131939 restraints weight = 6246.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.134643 restraints weight = 4013.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.3427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9067  Z= 0.201
  Angle     :  0.572   9.788  12244  Z= 0.302
  Chirality :  0.041   0.137   1434
  Planarity :  0.005   0.046   1579
  Dihedral  :  4.717  58.136   1254
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 12.67 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.22), residues: 1149
  helix: -1.44 (0.19), residues: 545
  sheet:  1.02 (0.31), residues: 224
  loop : -0.28 (0.28), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R  86 
 HIS   0.004   0.001   HIS R 202 
 PHE   0.019   0.002   PHE A 165 
 TYR   0.018   0.002   TYR A 200 
 ARG   0.007   0.001   ARG N  51 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 297
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 LYS cc_start: 0.6233 (tttm) cc_final: 0.5785 (tppt)
REVERT: A  114 PHE cc_start: 0.5111 (m-80) cc_final: 0.4267 (m-80)
REVERT: N   50 TYR cc_start: 0.9022 (p90) cc_final: 0.8674 (p90)
REVERT: O   13 ARG cc_start: 0.7447 (mpp80) cc_final: 0.7008 (mtm110)
REVERT: O   45 VAL cc_start: 0.8860 (t) cc_final: 0.8551 (m)
REVERT: R   35 ASP cc_start: 0.7392 (t0) cc_final: 0.7064 (t0)
REVERT: R  111 GLU cc_start: 0.8093 (mp0) cc_final: 0.7821 (mp0)
REVERT: R  262 ILE cc_start: 0.7670 (mm) cc_final: 0.7353 (mt)
REVERT: S  119 ARG cc_start: 0.8485 (ttp80) cc_final: 0.8169 (ttp80)
REVERT: S  155 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7896 (mt)
REVERT: X  105 GLU cc_start: 0.7714 (tt0) cc_final: 0.7476 (tt0)
  outliers start: 29
  outliers final: 21
  residues processed: 316
  average time/residue: 0.2224
  time to fit residues: 93.9308
Evaluate side-chains
  291 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 269
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   70 CYS
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain O residue   59 ARG
Chi-restraints excluded: chain R residue   28 ILE
Chi-restraints excluded: chain R residue  131 THR
Chi-restraints excluded: chain R residue  150 SER
Chi-restraints excluded: chain R residue  190 VAL
Chi-restraints excluded: chain R residue  252 ASN
Chi-restraints excluded: chain S residue  104 VAL
Chi-restraints excluded: chain S residue  109 THR
Chi-restraints excluded: chain S residue  131 THR
Chi-restraints excluded: chain S residue  155 LEU
Chi-restraints excluded: chain T residue   25 SER
Chi-restraints excluded: chain T residue   28 ILE
Chi-restraints excluded: chain T residue   63 ILE
Chi-restraints excluded: chain T residue   92 LEU
Chi-restraints excluded: chain T residue  112 SER
Chi-restraints excluded: chain T residue  131 THR
Chi-restraints excluded: chain T residue  138 ILE
Chi-restraints excluded: chain T residue  147 LEU
Chi-restraints excluded: chain X residue   54 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 49 optimal weight:    4.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
R 209 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.168247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.124027 restraints weight = 11534.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.128036 restraints weight = 6170.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.130807 restraints weight = 3957.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.4408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9067  Z= 0.226
  Angle     :  0.539   6.524  12244  Z= 0.285
  Chirality :  0.041   0.163   1434
  Planarity :  0.004   0.039   1579
  Dihedral  :  4.428  46.480   1254
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 16.11 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  0.26 (0.23), residues: 1149
  helix:  0.07 (0.21), residues: 548
  sheet:  1.31 (0.31), residues: 222
  loop : -0.14 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP T  86 
 HIS   0.006   0.001   HIS O   3 
 PHE   0.029   0.002   PHE A 145 
 TYR   0.013   0.001   TYR A 200 
 ARG   0.005   0.001   ARG N  77 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 267
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ARG cc_start: 0.8218 (mtt90) cc_final: 0.7947 (tmm160)
REVERT: A  101 LYS cc_start: 0.6156 (tttm) cc_final: 0.5803 (tppt)
REVERT: A  215 ARG cc_start: 0.8010 (mtp180) cc_final: 0.7470 (mtm180)
REVERT: N   50 TYR cc_start: 0.9135 (p90) cc_final: 0.8687 (p90)
REVERT: N   70 ASP cc_start: 0.7693 (p0) cc_final: 0.7412 (p0)
REVERT: O   45 VAL cc_start: 0.8941 (t) cc_final: 0.8671 (m)
REVERT: R   35 ASP cc_start: 0.7270 (t0) cc_final: 0.6621 (t0)
REVERT: R  173 ARG cc_start: 0.8391 (mtp85) cc_final: 0.7769 (ttm110)
REVERT: R  176 GLN cc_start: 0.8131 (mp10) cc_final: 0.7460 (mp10)
REVERT: R  189 ASP cc_start: 0.7905 (t0) cc_final: 0.7661 (t0)
REVERT: R  194 ASP cc_start: 0.8189 (t0) cc_final: 0.7960 (t0)
REVERT: S   65 LYS cc_start: 0.7692 (mmtp) cc_final: 0.7425 (mttm)
REVERT: X   15 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6981 (mm-30)
  outliers start: 35
  outliers final: 21
  residues processed: 283
  average time/residue: 0.2330
  time to fit residues: 88.3276
Evaluate side-chains
  275 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 254
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ASP
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain N residue   46 THR
Chi-restraints excluded: chain O residue   59 ARG
Chi-restraints excluded: chain R residue   72 SER
Chi-restraints excluded: chain R residue  131 THR
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  252 ASN
Chi-restraints excluded: chain R residue  298 THR
Chi-restraints excluded: chain S residue   77 GLU
Chi-restraints excluded: chain S residue  104 VAL
Chi-restraints excluded: chain S residue  128 LYS
Chi-restraints excluded: chain S residue  131 THR
Chi-restraints excluded: chain T residue   92 LEU
Chi-restraints excluded: chain T residue  100 LEU
Chi-restraints excluded: chain T residue  112 SER
Chi-restraints excluded: chain T residue  147 LEU
Chi-restraints excluded: chain X residue   74 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 3 optimal weight:    6.9990
   chunk 93 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 14 optimal weight:    9.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
R  99 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.163609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.119761 restraints weight = 11608.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.123634 restraints weight = 6300.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.126272 restraints weight = 4092.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.4951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9067  Z= 0.286
  Angle     :  0.561   7.009  12244  Z= 0.295
  Chirality :  0.042   0.131   1434
  Planarity :  0.004   0.039   1579
  Dihedral  :  4.454  30.601   1254
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 15.90 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  0.62 (0.23), residues: 1149
  helix:  0.60 (0.21), residues: 548
  sheet:  1.48 (0.32), residues: 222
  loop : -0.39 (0.29), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP T  86 
 HIS   0.006   0.001   HIS O   3 
 PHE   0.019   0.002   PHE A 165 
 TYR   0.017   0.002   TYR X  61 
 ARG   0.004   0.000   ARG N  77 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 242
  time to evaluate  : 0.992 
Fit side-chains
REVERT: A  101 LYS cc_start: 0.6097 (tttm) cc_final: 0.5775 (tppt)
REVERT: A  126 LYS cc_start: 0.7454 (tptt) cc_final: 0.6821 (pttt)
REVERT: A  215 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7710 (mtm180)
REVERT: N   15 GLU cc_start: 0.8026 (tp30) cc_final: 0.7716 (tm-30)
REVERT: N   50 TYR cc_start: 0.9212 (p90) cc_final: 0.8825 (p90)
REVERT: N   70 ASP cc_start: 0.7878 (p0) cc_final: 0.7577 (p0)
REVERT: O   45 VAL cc_start: 0.9014 (t) cc_final: 0.8770 (m)
REVERT: R   35 ASP cc_start: 0.7399 (t0) cc_final: 0.6872 (t0)
REVERT: R  111 GLU cc_start: 0.8291 (mp0) cc_final: 0.7774 (mp0)
REVERT: R  176 GLN cc_start: 0.7911 (mp10) cc_final: 0.7349 (mp10)
REVERT: S   53 LYS cc_start: 0.8131 (ttmt) cc_final: 0.7826 (ttmm)
REVERT: S   65 LYS cc_start: 0.7882 (mmtp) cc_final: 0.7635 (mttm)
REVERT: S  135 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6488 (tm-30)
REVERT: T   52 MET cc_start: 0.8382 (mmm) cc_final: 0.8035 (mmm)
REVERT: T   81 GLU cc_start: 0.7612 (pm20) cc_final: 0.7340 (pm20)
REVERT: X  105 GLU cc_start: 0.8017 (tt0) cc_final: 0.7775 (tt0)
  outliers start: 51
  outliers final: 35
  residues processed: 269
  average time/residue: 0.2291
  time to fit residues: 83.9989
Evaluate side-chains
  271 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 236
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   19 ASP
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  208 SER
Chi-restraints excluded: chain N residue   32 SER
Chi-restraints excluded: chain N residue   46 THR
Chi-restraints excluded: chain O residue   59 ARG
Chi-restraints excluded: chain O residue   69 LEU
Chi-restraints excluded: chain R residue   28 ILE
Chi-restraints excluded: chain R residue   49 ASP
Chi-restraints excluded: chain R residue   72 SER
Chi-restraints excluded: chain R residue  131 THR
Chi-restraints excluded: chain R residue  150 SER
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  252 ASN
Chi-restraints excluded: chain S residue   77 GLU
Chi-restraints excluded: chain S residue  109 THR
Chi-restraints excluded: chain S residue  131 THR
Chi-restraints excluded: chain T residue   67 MET
Chi-restraints excluded: chain T residue   92 LEU
Chi-restraints excluded: chain T residue  100 LEU
Chi-restraints excluded: chain T residue  112 SER
Chi-restraints excluded: chain T residue  131 THR
Chi-restraints excluded: chain T residue  132 VAL
Chi-restraints excluded: chain T residue  133 THR
Chi-restraints excluded: chain T residue  147 LEU
Chi-restraints excluded: chain X residue  113 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 95 optimal weight:    0.0370
   chunk 36 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 97 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 108 optimal weight:    0.5980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
** R 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.164807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.122566 restraints weight = 11518.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.126502 restraints weight = 6101.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.129183 restraints weight = 3891.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.5261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9067  Z= 0.156
  Angle     :  0.498   7.905  12244  Z= 0.261
  Chirality :  0.040   0.125   1434
  Planarity :  0.003   0.040   1579
  Dihedral  :  4.165  30.665   1254
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.80 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.23), residues: 1149
  helix:  1.22 (0.21), residues: 548
  sheet:  1.59 (0.32), residues: 222
  loop : -0.36 (0.29), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP R  86 
 HIS   0.004   0.001   HIS R 264 
 PHE   0.019   0.001   PHE A 165 
 TYR   0.016   0.001   TYR X  61 
 ARG   0.005   0.000   ARG A  30 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 254
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.8172 (tppt) cc_final: 0.7924 (tppt)
REVERT: A   80 ARG cc_start: 0.7763 (tmt170) cc_final: 0.7352 (tmm160)
REVERT: A  101 LYS cc_start: 0.5995 (tttm) cc_final: 0.5724 (tppt)
REVERT: A  126 LYS cc_start: 0.7383 (tptt) cc_final: 0.6779 (pttt)
REVERT: A  215 ARG cc_start: 0.7899 (mtp180) cc_final: 0.7609 (mtm180)
REVERT: N   50 TYR cc_start: 0.9179 (p90) cc_final: 0.8776 (p90)
REVERT: N   70 ASP cc_start: 0.7892 (p0) cc_final: 0.7606 (p0)
REVERT: O   51 ARG cc_start: 0.8211 (ttm110) cc_final: 0.7939 (ttm110)
REVERT: R   35 ASP cc_start: 0.7318 (t0) cc_final: 0.6717 (t0)
REVERT: R  111 GLU cc_start: 0.8214 (mp0) cc_final: 0.7761 (mp0)
REVERT: R  176 GLN cc_start: 0.7963 (mp10) cc_final: 0.7352 (mp10)
REVERT: R  294 LYS cc_start: 0.7769 (mptt) cc_final: 0.7529 (mptt)
REVERT: S   65 LYS cc_start: 0.7808 (mmtp) cc_final: 0.7572 (mttm)
REVERT: S  119 ARG cc_start: 0.8409 (ttp80) cc_final: 0.8009 (ttp80)
REVERT: T   52 MET cc_start: 0.8255 (mmm) cc_final: 0.7693 (mmm)
REVERT: X   37 GLU cc_start: 0.7849 (tp30) cc_final: 0.7550 (tp30)
  outliers start: 28
  outliers final: 19
  residues processed: 265
  average time/residue: 0.2208
  time to fit residues: 79.0049
Evaluate side-chains
  261 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 242
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   19 ASP
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain N residue   46 THR
Chi-restraints excluded: chain O residue   59 ARG
Chi-restraints excluded: chain R residue   49 ASP
Chi-restraints excluded: chain R residue  131 THR
Chi-restraints excluded: chain R residue  150 SER
Chi-restraints excluded: chain R residue  252 ASN
Chi-restraints excluded: chain R residue  298 THR
Chi-restraints excluded: chain S residue  109 THR
Chi-restraints excluded: chain S residue  131 THR
Chi-restraints excluded: chain T residue   92 LEU
Chi-restraints excluded: chain T residue  112 SER
Chi-restraints excluded: chain T residue  147 LEU
Chi-restraints excluded: chain T residue  150 SER
Chi-restraints excluded: chain X residue  113 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 86 optimal weight:    0.7980
   chunk 91 optimal weight:    0.4980
   chunk 102 optimal weight:    0.9990
   chunk 87 optimal weight:    0.4980
   chunk 107 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
R 268 HIS
T  46 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.165998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.123181 restraints weight = 11574.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.127104 restraints weight = 6134.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.129841 restraints weight = 3930.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.5442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9067  Z= 0.177
  Angle     :  0.512   9.705  12244  Z= 0.265
  Chirality :  0.040   0.150   1434
  Planarity :  0.003   0.039   1579
  Dihedral  :  4.083  32.816   1254
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 19.33 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.23), residues: 1149
  helix:  1.52 (0.21), residues: 546
  sheet:  1.66 (0.32), residues: 222
  loop : -0.38 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R  86 
 HIS   0.005   0.001   HIS R 264 
 PHE   0.019   0.001   PHE A 165 
 TYR   0.013   0.001   TYR X  61 
 ARG   0.006   0.000   ARG A  30 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 240
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.8341 (tppt) cc_final: 0.8125 (tppt)
REVERT: A  101 LYS cc_start: 0.5928 (tttm) cc_final: 0.5694 (tppt)
REVERT: A  126 LYS cc_start: 0.7430 (tptt) cc_final: 0.6835 (pttt)
REVERT: A  215 ARG cc_start: 0.7934 (mtp180) cc_final: 0.7734 (mtm180)
REVERT: N   50 TYR cc_start: 0.9172 (p90) cc_final: 0.8781 (p90)
REVERT: N   70 ASP cc_start: 0.7881 (p0) cc_final: 0.7569 (p0)
REVERT: R   35 ASP cc_start: 0.7410 (t0) cc_final: 0.6796 (t0)
REVERT: R  176 GLN cc_start: 0.7946 (mp10) cc_final: 0.7369 (mp10)
REVERT: S   65 LYS cc_start: 0.7828 (mmtp) cc_final: 0.7596 (mttm)
REVERT: S  119 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8015 (ttp80)
REVERT: T   52 MET cc_start: 0.8340 (mmm) cc_final: 0.7873 (mmm)
REVERT: X   37 GLU cc_start: 0.7797 (tp30) cc_final: 0.7506 (tp30)
  outliers start: 39
  outliers final: 29
  residues processed: 259
  average time/residue: 0.2299
  time to fit residues: 80.2622
Evaluate side-chains
  253 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 224
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   19 ASP
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain N residue   46 THR
Chi-restraints excluded: chain O residue   59 ARG
Chi-restraints excluded: chain O residue   69 LEU
Chi-restraints excluded: chain R residue   49 ASP
Chi-restraints excluded: chain R residue   72 SER
Chi-restraints excluded: chain R residue   96 GLU
Chi-restraints excluded: chain R residue  131 THR
Chi-restraints excluded: chain R residue  150 SER
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  252 ASN
Chi-restraints excluded: chain R residue  278 ILE
Chi-restraints excluded: chain R residue  298 THR
Chi-restraints excluded: chain S residue  131 THR
Chi-restraints excluded: chain T residue   67 MET
Chi-restraints excluded: chain T residue   92 LEU
Chi-restraints excluded: chain T residue  112 SER
Chi-restraints excluded: chain T residue  147 LEU
Chi-restraints excluded: chain T residue  150 SER
Chi-restraints excluded: chain T residue  155 LEU
Chi-restraints excluded: chain X residue   74 ILE
Chi-restraints excluded: chain X residue  113 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 109 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 12 optimal weight:    9.9990
   chunk 26 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** R 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.164423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.121696 restraints weight = 11703.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.125647 restraints weight = 6196.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.128404 restraints weight = 3953.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.5580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9067  Z= 0.187
  Angle     :  0.509   8.316  12244  Z= 0.265
  Chirality :  0.040   0.145   1434
  Planarity :  0.003   0.040   1579
  Dihedral  :  4.176  36.566   1254
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 19.87 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.24), residues: 1149
  helix:  1.69 (0.21), residues: 550
  sheet:  1.75 (0.32), residues: 221
  loop : -0.39 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R  86 
 HIS   0.004   0.001   HIS R 264 
 PHE   0.019   0.001   PHE A 165 
 TYR   0.014   0.001   TYR A 200 
 ARG   0.006   0.000   ARG A  30 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 237
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.8368 (tppt) cc_final: 0.8065 (tppt)
REVERT: A   78 MET cc_start: 0.7479 (mmm) cc_final: 0.7032 (mmm)
REVERT: A   88 MET cc_start: 0.6577 (mmm) cc_final: 0.6307 (mmm)
REVERT: A  101 LYS cc_start: 0.5997 (tttm) cc_final: 0.5729 (tppt)
REVERT: A  126 LYS cc_start: 0.7417 (tptt) cc_final: 0.6828 (pttt)
REVERT: N   50 TYR cc_start: 0.9163 (p90) cc_final: 0.8801 (p90)
REVERT: N   70 ASP cc_start: 0.7863 (p0) cc_final: 0.7557 (p0)
REVERT: O   51 ARG cc_start: 0.8213 (ttm110) cc_final: 0.7245 (ttt-90)
REVERT: R   35 ASP cc_start: 0.7414 (t0) cc_final: 0.6803 (t0)
REVERT: R  111 GLU cc_start: 0.8330 (mp0) cc_final: 0.7820 (mp0)
REVERT: R  176 GLN cc_start: 0.7749 (mp10) cc_final: 0.7230 (mp10)
REVERT: S   58 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7830 (mt-10)
REVERT: S   65 LYS cc_start: 0.7856 (mmtp) cc_final: 0.7632 (mttm)
REVERT: S  119 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8022 (ttp80)
REVERT: T   52 MET cc_start: 0.8321 (mmm) cc_final: 0.7737 (mmm)
  outliers start: 38
  outliers final: 31
  residues processed: 251
  average time/residue: 0.2321
  time to fit residues: 78.3805
Evaluate side-chains
  267 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 236
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ASP
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   70 CYS
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  204 GLN
Chi-restraints excluded: chain A residue  208 SER
Chi-restraints excluded: chain N residue   46 THR
Chi-restraints excluded: chain N residue  103 SER
Chi-restraints excluded: chain O residue   59 ARG
Chi-restraints excluded: chain O residue   69 LEU
Chi-restraints excluded: chain R residue   49 ASP
Chi-restraints excluded: chain R residue   72 SER
Chi-restraints excluded: chain R residue  131 THR
Chi-restraints excluded: chain R residue  150 SER
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  278 ILE
Chi-restraints excluded: chain R residue  298 THR
Chi-restraints excluded: chain S residue  131 THR
Chi-restraints excluded: chain T residue   67 MET
Chi-restraints excluded: chain T residue   92 LEU
Chi-restraints excluded: chain T residue  147 LEU
Chi-restraints excluded: chain T residue  150 SER
Chi-restraints excluded: chain T residue  155 LEU
Chi-restraints excluded: chain X residue   74 ILE
Chi-restraints excluded: chain X residue  113 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 19 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9980
   chunk 69 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 94 optimal weight:    0.8980
   chunk 3 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
R 268 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.163770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.120098 restraints weight = 11642.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.124094 restraints weight = 6157.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.126880 restraints weight = 3947.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.5698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9067  Z= 0.229
  Angle     :  0.532   8.313  12244  Z= 0.277
  Chirality :  0.041   0.139   1434
  Planarity :  0.003   0.040   1579
  Dihedral  :  4.354  42.282   1254
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 18.90 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.24), residues: 1149
  helix:  1.73 (0.21), residues: 546
  sheet:  1.71 (0.32), residues: 223
  loop : -0.49 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 229 
 HIS   0.005   0.001   HIS R 264 
 PHE   0.019   0.001   PHE A 165 
 TYR   0.012   0.001   TYR A 200 
 ARG   0.003   0.000   ARG A  80 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 246
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.8380 (tppt) cc_final: 0.8140 (tppt)
REVERT: A   78 MET cc_start: 0.7453 (mmm) cc_final: 0.7019 (mmm)
REVERT: A   88 MET cc_start: 0.6621 (mmm) cc_final: 0.6218 (mmm)
REVERT: A  101 LYS cc_start: 0.6014 (tttm) cc_final: 0.5778 (tppt)
REVERT: A  126 LYS cc_start: 0.7407 (tptt) cc_final: 0.6810 (pttt)
REVERT: A  131 LYS cc_start: 0.7647 (mttt) cc_final: 0.7173 (mmtm)
REVERT: A  215 ARG cc_start: 0.7859 (mtm180) cc_final: 0.7562 (mtm180)
REVERT: N   50 TYR cc_start: 0.9180 (p90) cc_final: 0.8837 (p90)
REVERT: N   70 ASP cc_start: 0.7807 (p0) cc_final: 0.7525 (p0)
REVERT: O   51 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7301 (ttt-90)
REVERT: R   35 ASP cc_start: 0.7444 (t0) cc_final: 0.6873 (t0)
REVERT: R  111 GLU cc_start: 0.8367 (mp0) cc_final: 0.7849 (mp0)
REVERT: R  176 GLN cc_start: 0.7766 (mp10) cc_final: 0.7148 (mp10)
REVERT: S   65 LYS cc_start: 0.7888 (mmtp) cc_final: 0.7668 (mttm)
REVERT: S  119 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8038 (ttp80)
REVERT: S  135 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6574 (tm-30)
REVERT: T   95 MET cc_start: 0.7891 (tpp) cc_final: 0.7250 (ttt)
REVERT: X   27 LYS cc_start: 0.7949 (tppp) cc_final: 0.7739 (tppt)
  outliers start: 39
  outliers final: 31
  residues processed: 265
  average time/residue: 0.2287
  time to fit residues: 81.4908
Evaluate side-chains
  261 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 230
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   70 CYS
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain N residue   32 SER
Chi-restraints excluded: chain N residue   46 THR
Chi-restraints excluded: chain N residue  103 SER
Chi-restraints excluded: chain O residue   59 ARG
Chi-restraints excluded: chain O residue   69 LEU
Chi-restraints excluded: chain R residue   49 ASP
Chi-restraints excluded: chain R residue   72 SER
Chi-restraints excluded: chain R residue  131 THR
Chi-restraints excluded: chain R residue  150 SER
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  278 ILE
Chi-restraints excluded: chain R residue  298 THR
Chi-restraints excluded: chain S residue  131 THR
Chi-restraints excluded: chain T residue   25 SER
Chi-restraints excluded: chain T residue   67 MET
Chi-restraints excluded: chain T residue   92 LEU
Chi-restraints excluded: chain T residue  100 LEU
Chi-restraints excluded: chain T residue  131 THR
Chi-restraints excluded: chain T residue  147 LEU
Chi-restraints excluded: chain T residue  150 SER
Chi-restraints excluded: chain T residue  155 LEU
Chi-restraints excluded: chain X residue   74 ILE
Chi-restraints excluded: chain X residue  113 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 94 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 8 optimal weight:    8.9990
   chunk 106 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 103 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
O  34 GLN
** R 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.161791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.118627 restraints weight = 11673.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.122485 restraints weight = 6209.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.125134 restraints weight = 3996.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.5824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9067  Z= 0.283
  Angle     :  0.570   9.010  12244  Z= 0.297
  Chirality :  0.042   0.143   1434
  Planarity :  0.004   0.039   1579
  Dihedral  :  4.710  54.257   1254
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 19.23 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.24), residues: 1149
  helix:  1.56 (0.21), residues: 546
  sheet:  1.72 (0.33), residues: 220
  loop : -0.62 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP T  86 
 HIS   0.005   0.001   HIS R 264 
 PHE   0.018   0.002   PHE R 295 
 TYR   0.017   0.002   TYR X  61 
 ARG   0.004   0.000   ARG T 158 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 236
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.7467 (mmm) cc_final: 0.7035 (mmm)
REVERT: A   88 MET cc_start: 0.6595 (mmm) cc_final: 0.6081 (mmm)
REVERT: A  101 LYS cc_start: 0.5968 (tttm) cc_final: 0.5705 (tppt)
REVERT: A  126 LYS cc_start: 0.7410 (tptt) cc_final: 0.6820 (pttt)
REVERT: A  131 LYS cc_start: 0.7754 (mttt) cc_final: 0.7271 (mmtm)
REVERT: A  215 ARG cc_start: 0.7890 (mtm180) cc_final: 0.7453 (mtm180)
REVERT: N   50 TYR cc_start: 0.9210 (p90) cc_final: 0.8895 (p90)
REVERT: N   70 ASP cc_start: 0.7803 (p0) cc_final: 0.7499 (p0)
REVERT: O   51 ARG cc_start: 0.8171 (ttm110) cc_final: 0.7147 (ttt-90)
REVERT: R   35 ASP cc_start: 0.7528 (t0) cc_final: 0.6947 (t0)
REVERT: R  111 GLU cc_start: 0.8424 (mp0) cc_final: 0.7877 (mp0)
REVERT: S   65 LYS cc_start: 0.7838 (mmtp) cc_final: 0.7602 (mttm)
REVERT: S   98 VAL cc_start: 0.8086 (t) cc_final: 0.7854 (t)
REVERT: S  119 ARG cc_start: 0.8430 (ttp80) cc_final: 0.7991 (ttp80)
REVERT: S  135 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6573 (tm-30)
REVERT: T   52 MET cc_start: 0.8429 (mmm) cc_final: 0.7900 (mmm)
REVERT: T   81 GLU cc_start: 0.7546 (pm20) cc_final: 0.7204 (pm20)
REVERT: T   95 MET cc_start: 0.7955 (tpp) cc_final: 0.7400 (ttt)
REVERT: X   27 LYS cc_start: 0.7989 (tppp) cc_final: 0.7699 (tppt)
  outliers start: 43
  outliers final: 35
  residues processed: 257
  average time/residue: 0.2318
  time to fit residues: 79.8319
Evaluate side-chains
  272 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 237
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  204 GLN
Chi-restraints excluded: chain N residue   32 SER
Chi-restraints excluded: chain N residue   46 THR
Chi-restraints excluded: chain N residue  103 SER
Chi-restraints excluded: chain O residue   59 ARG
Chi-restraints excluded: chain O residue   69 LEU
Chi-restraints excluded: chain O residue   97 GLU
Chi-restraints excluded: chain R residue   28 ILE
Chi-restraints excluded: chain R residue   49 ASP
Chi-restraints excluded: chain R residue   72 SER
Chi-restraints excluded: chain R residue  131 THR
Chi-restraints excluded: chain R residue  150 SER
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  278 ILE
Chi-restraints excluded: chain R residue  298 THR
Chi-restraints excluded: chain S residue  131 THR
Chi-restraints excluded: chain T residue   25 SER
Chi-restraints excluded: chain T residue   92 LEU
Chi-restraints excluded: chain T residue  100 LEU
Chi-restraints excluded: chain T residue  131 THR
Chi-restraints excluded: chain T residue  133 THR
Chi-restraints excluded: chain T residue  147 LEU
Chi-restraints excluded: chain T residue  150 SER
Chi-restraints excluded: chain T residue  155 LEU
Chi-restraints excluded: chain X residue   74 ILE
Chi-restraints excluded: chain X residue  113 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0670
   chunk 8 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 67 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 47 optimal weight:    0.3980
   chunk 19 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
O  34 GLN
R 252 ASN
** R 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.166899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.123640 restraints weight = 11662.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.127698 restraints weight = 6120.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.130467 restraints weight = 3907.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.6004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9067  Z= 0.161
  Angle     :  0.532  10.910  12244  Z= 0.276
  Chirality :  0.040   0.140   1434
  Planarity :  0.003   0.039   1579
  Dihedral  :  4.415  50.511   1254
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.73 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.24), residues: 1149
  helix:  1.92 (0.21), residues: 550
  sheet:  1.78 (0.33), residues: 221
  loop : -0.52 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP R  86 
 HIS   0.006   0.001   HIS R 264 
 PHE   0.019   0.001   PHE A 165 
 TYR   0.016   0.001   TYR X  61 
 ARG   0.004   0.000   ARG T 158 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 242
  time to evaluate  : 0.924 
Fit side-chains
REVERT: A   78 MET cc_start: 0.7403 (mmm) cc_final: 0.6972 (mmt)
REVERT: A   82 ASP cc_start: 0.6080 (t0) cc_final: 0.5654 (t0)
REVERT: A   88 MET cc_start: 0.6536 (mmm) cc_final: 0.6184 (mmm)
REVERT: A  101 LYS cc_start: 0.5910 (tttm) cc_final: 0.5680 (tppt)
REVERT: A  126 LYS cc_start: 0.7402 (tptt) cc_final: 0.6726 (pttp)
REVERT: A  131 LYS cc_start: 0.7805 (mttt) cc_final: 0.7257 (mmtm)
REVERT: A  215 ARG cc_start: 0.7835 (mtm180) cc_final: 0.7428 (mtm180)
REVERT: N   50 TYR cc_start: 0.9160 (p90) cc_final: 0.8822 (p90)
REVERT: N   70 ASP cc_start: 0.7720 (p0) cc_final: 0.7416 (p0)
REVERT: O   51 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7276 (ttt-90)
REVERT: R   35 ASP cc_start: 0.7465 (t0) cc_final: 0.6962 (t0)
REVERT: R  111 GLU cc_start: 0.8308 (mp0) cc_final: 0.7918 (mp0)
REVERT: R  277 GLU cc_start: 0.7926 (tt0) cc_final: 0.7116 (mp0)
REVERT: S   65 LYS cc_start: 0.7801 (mmtp) cc_final: 0.7587 (mttm)
REVERT: S  119 ARG cc_start: 0.8416 (ttp80) cc_final: 0.7917 (ttt-90)
REVERT: T   52 MET cc_start: 0.8321 (mmm) cc_final: 0.7599 (mmm)
REVERT: T   81 GLU cc_start: 0.7525 (pm20) cc_final: 0.7140 (pm20)
REVERT: X   27 LYS cc_start: 0.7921 (tppp) cc_final: 0.7655 (tppt)
  outliers start: 29
  outliers final: 27
  residues processed: 256
  average time/residue: 0.2246
  time to fit residues: 77.8151
Evaluate side-chains
  265 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 238
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  204 GLN
Chi-restraints excluded: chain N residue    5 VAL
Chi-restraints excluded: chain N residue   32 SER
Chi-restraints excluded: chain N residue   46 THR
Chi-restraints excluded: chain O residue   59 ARG
Chi-restraints excluded: chain O residue   69 LEU
Chi-restraints excluded: chain R residue   49 ASP
Chi-restraints excluded: chain R residue   72 SER
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  131 THR
Chi-restraints excluded: chain R residue  150 SER
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  252 ASN
Chi-restraints excluded: chain R residue  278 ILE
Chi-restraints excluded: chain R residue  298 THR
Chi-restraints excluded: chain S residue  131 THR
Chi-restraints excluded: chain T residue   92 LEU
Chi-restraints excluded: chain T residue  147 LEU
Chi-restraints excluded: chain T residue  150 SER
Chi-restraints excluded: chain T residue  155 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 102 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 110 optimal weight:    9.9990
   chunk 111 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 108 optimal weight:    0.5980
   chunk 1 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9990
   chunk 101 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
R 252 ASN
** R 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.165339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.121890 restraints weight = 11688.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.125943 restraints weight = 6179.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.128680 restraints weight = 3959.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.6027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.107   9067  Z= 0.242
  Angle     :  0.893  59.191  12244  Z= 0.539
  Chirality :  0.043   0.603   1434
  Planarity :  0.004   0.068   1579
  Dihedral  :  4.454  50.500   1254
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.57 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 21.05 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.24), residues: 1149
  helix:  1.95 (0.21), residues: 550
  sheet:  1.74 (0.33), residues: 222
  loop : -0.51 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  57 
 HIS   0.005   0.001   HIS R 264 
 PHE   0.019   0.001   PHE A 165 
 TYR   0.015   0.001   TYR X  61 
 ARG   0.004   0.000   ARG T 158 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3318.94 seconds
wall clock time: 60 minutes 0.73 seconds (3600.73 seconds total)