Starting phenix.real_space_refine
on Thu Mar 13 06:22:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8id6_35358/03_2025/8id6_35358.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8id6_35358/03_2025/8id6_35358.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8id6_35358/03_2025/8id6_35358.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8id6_35358/03_2025/8id6_35358.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8id6_35358/03_2025/8id6_35358.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8id6_35358/03_2025/8id6_35358.cif"
  }
  resolution = 2.8
  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=   0.000 sd=   0.016
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      56      5.16       5
     C    5596      2.51       5
     N    1478      2.21       5
     O    1597      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8727
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2206
          Classifications: {'peptide': 290}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 12, 'TRANS': 277}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 101
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 67
    Chain: "A"
      Number of atoms: 1769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1769
          Classifications: {'peptide': 225}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 29
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 33
    Chain: "B"
      Number of atoms: 2569
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2569
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 28
    Chain: "Y"
      Number of atoms: 409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 409
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "S"
      Number of atoms: 1754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1754
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "R"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'OLA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.12, per 1000 atoms: 0.59
  Number of scatterers: 8727
  At special positions: 0
  Unit cell: (106.47, 128.778, 115.596, 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      56     16.00
     O    1597      8.00
     N    1478      7.00
     C    5596      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 160 " - pdb=" SG  CYS S 230 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.18
  Conformation dependent library (CDL) restraints added in 989.9 milliseconds
  

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2138

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 14 sheets defined
      37.0% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'R' and resid 37 through 69
      removed outlier: 3.983A  pdb=" N   THR R  45 " --> pdb=" O   ALA R  41 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU R  47 " --> pdb=" O   GLU R  43 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   VAL R  48 " --> pdb=" O   THR R  44 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 76 through 89
      removed outlier: 3.676A  pdb=" N   ASN R  80 " --> pdb=" O   CYS R  76 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 101
      removed outlier: 3.700A  pdb=" N   THR R 101 " --> pdb=" O   ALA R  97 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 109 through 114
    Processing helix  chain 'R' and resid 115 through 143
      removed outlier: 3.656A  pdb=" N   LEU R 120 " --> pdb=" O   TYR R 116 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   SER R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 152 through 169
      removed outlier: 3.738A  pdb=" N   ALA R 160 " --> pdb=" O   ALA R 156 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 176
      removed outlier: 3.742A  pdb=" N   VAL R 175 " --> pdb=" O   LEU R 171 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE R 176 " --> pdb=" O   PRO R 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 171 through 176'
    Processing helix  chain 'R' and resid 200 through 216
    Processing helix  chain 'R' and resid 216 through 244
      removed outlier: 3.563A  pdb=" N   SER R 244 " --> pdb=" O   ARG R 240 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 251 through 290
      removed outlier: 3.987A  pdb=" N   PHE R 273 " --> pdb=" O   LEU R 269 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   PHE R 274 " --> pdb=" O   MET R 270 " (cutoff:3.500A)
      Proline residue:  R 279  - end of helix
    Processing helix  chain 'R' and resid 301 through 312
      removed outlier: 3.605A  pdb=" N   TRP R 305 " --> pdb=" O   SER R 301 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 313 through 315
      No H-bonds generated for 'chain 'R' and resid 313 through 315'
    Processing helix  chain 'R' and resid 316 through 321
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.649A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.533A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 274
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.684A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.574A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 37
      removed outlier: 4.079A  pdb=" N   THR B  34 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   ASN B  35 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   ASN B  36 " --> pdb=" O   ILE B  33 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 8 through 24
      removed outlier: 3.889A  pdb=" N   ASN Y  24 " --> pdb=" O   LYS Y  20 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 29 through 44
    Processing helix  chain 'Y' and resid 45 through 48
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 74 through 76
      No H-bonds generated for 'chain 'S' and resid 74 through 76'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.759A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 221 through 225
      removed outlier: 3.974A  pdb=" N   VAL S 225 " --> pdb=" O   ALA S 222 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 177 through 181
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.223A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.715A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.824A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.786A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.141A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 152
      removed outlier: 3.996A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.070A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.514A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.725A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.093A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 142
    Processing sheet with id=AB4, first strand: chain 'S' and resid 147 through 149
      removed outlier: 3.614A  pdb=" N   GLY S 226 " --> pdb=" O   LEU S 246 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LEU S 175 " --> pdb=" O   TYR S 191 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   TYR S 191 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   TRP S 177 " --> pdb=" O   LEU S 189 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 147 through 149
      removed outlier: 3.614A  pdb=" N   GLY S 226 " --> pdb=" O   LEU S 246 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   THR S 239 " --> pdb=" O   GLN S 232 " (cutoff:3.500A)

    446 hydrogen bonds defined for protein.
    1236 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: 2.68

  Time building geometry restraints manager: 2.60 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1480
        1.32 -     1.45: 2392
        1.45 -     1.57: 4952
        1.57 -     1.70: 0
        1.70 -     1.82: 81
  Bond restraints: 8905
  Sorted by residual:
  bond pdb=" C   GLY R 151 "
       pdb=" N   ARG R 152 "
    ideal  model  delta    sigma   weight residual
    1.335  1.227  0.107 1.25e-02 6.40e+03 7.37e+01
  bond pdb=" C   ARG R 264 "
       pdb=" O   ARG R 264 "
    ideal  model  delta    sigma   weight residual
    1.237  1.198  0.038 1.16e-02 7.43e+03 1.09e+01
  bond pdb=" N   ARG R 152 "
       pdb=" CA  ARG R 152 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.20e-02 6.94e+03 6.64e+00
  bond pdb=" C   ARG A  21 "
       pdb=" O   ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.237  1.208  0.029 1.17e-02 7.31e+03 5.95e+00
  bond pdb=" CA  ARG R 264 "
       pdb=" C   ARG R 264 "
    ideal  model  delta    sigma   weight residual
    1.524  1.496  0.027 1.26e-02 6.30e+03 4.73e+00
  ... (remaining 8900 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 11746
        1.65 -     3.30: 269
        3.30 -     4.96: 47
        4.96 -     6.61: 18
        6.61 -     8.26: 7
  Bond angle restraints: 12087
  Sorted by residual:
  angle pdb=" N   SER S 194 "
        pdb=" CA  SER S 194 "
        pdb=" C   SER S 194 "
      ideal   model   delta    sigma   weight residual
     112.88  118.50   -5.62 1.29e+00 6.01e-01 1.89e+01
  angle pdb=" N   ASN S 195 "
        pdb=" CA  ASN S 195 "
        pdb=" C   ASN S 195 "
      ideal   model   delta    sigma   weight residual
     108.52  115.14   -6.62 1.63e+00 3.76e-01 1.65e+01
  angle pdb=" N   MET S 193 "
        pdb=" CA  MET S 193 "
        pdb=" C   MET S 193 "
      ideal   model   delta    sigma   weight residual
     110.80  119.06   -8.26 2.13e+00 2.20e-01 1.50e+01
  angle pdb=" CA  TYR R 247 "
        pdb=" CB  TYR R 247 "
        pdb=" CG  TYR R 247 "
      ideal   model   delta    sigma   weight residual
     113.90  120.14   -6.24 1.80e+00 3.09e-01 1.20e+01
  angle pdb=" N   ILE R  92 "
        pdb=" CA  ILE R  92 "
        pdb=" C   ILE R  92 "
      ideal   model   delta    sigma   weight residual
     108.88  115.75   -6.87 2.16e+00 2.14e-01 1.01e+01
  ... (remaining 12082 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.24: 4958
       17.24 -    34.48: 236
       34.48 -    51.72: 44
       51.72 -    68.96: 15
       68.96 -    86.21: 6
  Dihedral angle restraints: 5259
    sinusoidal: 1958
      harmonic: 3301
  Sorted by residual:
  dihedral pdb=" N   MET S 193 "
           pdb=" C   MET S 193 "
           pdb=" CA  MET S 193 "
           pdb=" CB  MET S 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.18   -9.38     0      2.50e+00 1.60e-01 1.41e+01
  dihedral pdb=" C   MET S 193 "
           pdb=" N   MET S 193 "
           pdb=" CA  MET S 193 "
           pdb=" CB  MET S 193 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.70    9.10     0      2.50e+00 1.60e-01 1.32e+01
  dihedral pdb=" CA  PHE S  32 "
           pdb=" C   PHE S  32 "
           pdb=" N   GLY S  33 "
           pdb=" CA  GLY S  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.64   17.36     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 5256 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 1308
       0.087 -    0.174: 99
       0.174 -    0.261: 5
       0.261 -    0.348: 1
       0.348 -    0.435: 1
  Chirality restraints: 1414
  Sorted by residual:
  chirality pdb=" CA  MET S 193 "
            pdb=" N   MET S 193 "
            pdb=" C   MET S 193 "
            pdb=" CB  MET S 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.44 2.00e-01 2.50e+01 4.73e+00
  chirality pdb=" CA  ARG S 192 "
            pdb=" N   ARG S 192 "
            pdb=" C   ARG S 192 "
            pdb=" CB  ARG S 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.04e+00
  chirality pdb=" CA  SER S 194 "
            pdb=" N   SER S 194 "
            pdb=" C   SER S 194 "
            pdb=" CB  SER S 194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 1411 not shown)

  Planarity restraints: 1515
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR Y  52 "   -0.067 5.00e-02 4.00e+02   9.92e-02 1.58e+01
        pdb=" N   PRO Y  53 "    0.172 5.00e-02 4.00e+02
        pdb=" CA  PRO Y  53 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO Y  53 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R 151 "   -0.019 2.00e-02 2.50e+03   3.84e-02 1.47e+01
        pdb=" C   GLY R 151 "    0.066 2.00e-02 2.50e+03
        pdb=" O   GLY R 151 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   ARG R 152 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER S 106 "    0.043 5.00e-02 4.00e+02   6.58e-02 6.93e+00
        pdb=" N   PRO S 107 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO S 107 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO S 107 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1512 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 319
        2.72 -     3.27: 8498
        3.27 -     3.81: 13918
        3.81 -     4.36: 17756
        4.36 -     4.90: 30337
  Nonbonded interactions: 70828
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG R 238 "
            pdb=" OD1 ASP R 259 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OD1 ASP B 247 "
            pdb=" OG1 THR B 249 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OE1 GLN A  52 "
            pdb=" ND2 ASN A 331 "
     model   vdw
     2.286 3.120
  ... (remaining 70823 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     22.620
  Find NCS groups from input model:        0.100
  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:             0.010
  Load rotamer database and sin/cos tables:13.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
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      :  0.004   0.107   8905  Z= 0.235
  Angle     :  0.668   8.258  12087  Z= 0.370
  Chirality :  0.048   0.435   1414
  Planarity :  0.006   0.099   1515
  Dihedral  : 11.398  86.206   3118
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.86 (0.25), residues: 1119
  helix:  1.10 (0.27), residues: 383
  sheet:  1.33 (0.29), residues: 283
  loop : -0.32 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 188 
 PHE   0.021   0.002   PHE A 189 
 TYR   0.017   0.002   TYR S 191 
 ARG   0.005   0.001   ARG S  72 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
REVERT: Y   21 MET cc_start: 0.6695 (mpp) cc_final: 0.6441 (ttp)
  outliers start: 0
  outliers final: 1
  residues processed: 137
  average time/residue: 1.4302
  time to fit residues: 207.2032
Evaluate side-chains
  94 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  270 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 84 optimal weight:   20.0000
   chunk 47 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 57 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0050
   chunk 53 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 101 optimal weight:    4.9990
   overall best weight:    1.5600

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

Flipped N/Q/H residues before XYZ refinement:
R 144 GLN
** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 322 ASN
A 195 HIS
B  44 GLN
B 259 GLN
B 340 ASN
S 187 GLN
S 195 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.179548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.113950 restraints weight = 9038.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.32
r_work: 0.2958 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2815 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8905  Z= 0.244
  Angle     :  0.595   6.879  12087  Z= 0.310
  Chirality :  0.044   0.159   1414
  Planarity :  0.005   0.072   1515
  Dihedral  :  5.285  50.825   1235
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  :  7.28 %
    Favored  : 90.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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 (0.25), residues: 1119
  helix:  1.64 (0.27), residues: 384
  sheet:  1.06 (0.29), residues: 294
  loop : -0.34 (0.27), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 207 
 HIS   0.006   0.002   HIS S 233 
 PHE   0.017   0.002   PHE B 199 
 TYR   0.019   0.002   TYR B 105 
 ARG   0.004   0.000   ARG S  72 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.874 
Fit side-chains
REVERT: R  178 ARG cc_start: 0.4985 (mmt180) cc_final: 0.4757 (mmm160)
REVERT: B  118 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7840 (p0)
REVERT: B  197 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7703 (mmp-170)
REVERT: Y   21 MET cc_start: 0.6942 (mpp) cc_final: 0.6306 (ttm)
  outliers start: 22
  outliers final: 7
  residues processed: 102
  average time/residue: 1.3992
  time to fit residues: 151.0800
Evaluate side-chains
  95 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  133 SER
Chi-restraints excluded: chain R residue  288 LEU
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  270 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 85 optimal weight:    7.9990
   chunk 63 optimal weight:    0.1980
   chunk 83 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 15 optimal weight:    0.0770
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 322 ASN
A 195 HIS
B 259 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.183251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.121288 restraints weight = 9579.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 2.34
r_work: 0.3051 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8905  Z= 0.147
  Angle     :  0.507   7.160  12087  Z= 0.266
  Chirality :  0.041   0.135   1414
  Planarity :  0.004   0.062   1515
  Dihedral  :  4.950  48.384   1235
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  9.02 %
    Favored  : 89.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.37 (0.25), residues: 1119
  helix:  1.97 (0.28), residues: 390
  sheet:  1.25 (0.29), residues: 280
  loop : -0.22 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 207 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.014   0.001   TYR S 191 
 ARG   0.004   0.000   ARG R 238 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  177 PHE cc_start: 0.6046 (m-80) cc_final: 0.5778 (m-80)
REVERT: R  316 LEU cc_start: 0.5957 (mt) cc_final: 0.5682 (mm)
REVERT: A  208 ARG cc_start: 0.7731 (mtm-85) cc_final: 0.7489 (ttp80)
REVERT: A  309 ASP cc_start: 0.7151 (t0) cc_final: 0.6917 (m-30)
REVERT: A  315 ASP cc_start: 0.7277 (p0) cc_final: 0.6940 (m-30)
REVERT: B  118 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7802 (p0)
REVERT: B  259 GLN cc_start: 0.8203 (mt0) cc_final: 0.7973 (mt0)
REVERT: Y   21 MET cc_start: 0.7365 (mpp) cc_final: 0.6533 (ttt)
REVERT: S  142 THR cc_start: 0.8540 (m) cc_final: 0.8271 (p)
  outliers start: 15
  outliers final: 5
  residues processed: 102
  average time/residue: 1.4754
  time to fit residues: 159.5994
Evaluate side-chains
  92 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  133 SER
Chi-restraints excluded: chain R residue  276 MET
Chi-restraints excluded: chain R residue  288 LEU
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  270 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 26 optimal weight:    0.0670
   chunk 108 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 14 optimal weight:   20.0000
   chunk 77 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 81 optimal weight:    7.9990
   chunk 2 optimal weight:    8.9990
   chunk 76 optimal weight:    0.8980
   chunk 97 optimal weight:   10.0000
   overall best weight:    1.9922

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

Flipped N/Q/H residues before XYZ refinement:
R  80 ASN
** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 322 ASN
** B 340 ASN ** 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 = 0.4131 r_free = 0.4131 target = 0.190648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.125685 restraints weight = 9277.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 2.42
r_work: 0.2961 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2815 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8905  Z= 0.275
  Angle     :  0.574   7.558  12087  Z= 0.299
  Chirality :  0.044   0.173   1414
  Planarity :  0.005   0.077   1515
  Dihedral  :  5.044  49.775   1235
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 10.00 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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 (0.25), residues: 1119
  helix:  1.86 (0.27), residues: 391
  sheet:  0.96 (0.29), residues: 287
  loop : -0.50 (0.27), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  82 
 HIS   0.007   0.001   HIS B  62 
 PHE   0.015   0.002   PHE B 151 
 TYR   0.014   0.002   TYR S 191 
 ARG   0.005   0.000   ARG S  72 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 1.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  177 PHE cc_start: 0.6334 (m-80) cc_final: 0.6098 (m-80)
REVERT: R  178 ARG cc_start: 0.4969 (mmt180) cc_final: 0.4742 (mmm160)
REVERT: R  214 LEU cc_start: 0.8398 (mp) cc_final: 0.7776 (tt)
REVERT: A  208 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7361 (ttp-110)
REVERT: A  315 ASP cc_start: 0.7585 (p0) cc_final: 0.7260 (m-30)
REVERT: B  118 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7745 (p0)
REVERT: B  259 GLN cc_start: 0.8071 (mt0) cc_final: 0.7865 (tt0)
REVERT: Y   21 MET cc_start: 0.7547 (mpp) cc_final: 0.6551 (ttt)
  outliers start: 21
  outliers final: 13
  residues processed: 96
  average time/residue: 1.7864
  time to fit residues: 182.1879
Evaluate side-chains
  93 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  113 LEU
Chi-restraints excluded: chain R residue  133 SER
Chi-restraints excluded: chain R residue  322 ASN
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain S residue  156 VAL
Chi-restraints excluded: chain S residue  205 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   chunk 104 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 11 optimal weight:    8.9990
   chunk 107 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.194302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.137025 restraints weight = 9266.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.28
r_work: 0.3021 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8905  Z= 0.208
  Angle     :  0.524   6.319  12087  Z= 0.275
  Chirality :  0.042   0.146   1414
  Planarity :  0.004   0.072   1515
  Dihedral  :  4.887  47.670   1235
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 10.43 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.20 (0.25), residues: 1119
  helix:  2.15 (0.27), residues: 387
  sheet:  0.88 (0.29), residues: 292
  loop : -0.46 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B  62 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.015   0.001   TYR S 191 
 ARG   0.003   0.000   ARG S  72 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 1.001 
Fit side-chains
   revert: symmetry clash
REVERT: R  177 PHE cc_start: 0.6313 (m-80) cc_final: 0.6096 (m-80)
REVERT: R  178 ARG cc_start: 0.5134 (mmt180) cc_final: 0.4929 (mmm160)
REVERT: R  214 LEU cc_start: 0.8428 (mp) cc_final: 0.7812 (tt)
REVERT: R  316 LEU cc_start: 0.6211 (mt) cc_final: 0.5933 (mm)
REVERT: A  208 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7522 (ttp80)
REVERT: A  315 ASP cc_start: 0.7597 (p0) cc_final: 0.7319 (m-30)
REVERT: B  118 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7733 (p0)
REVERT: B  259 GLN cc_start: 0.8038 (mt0) cc_final: 0.7822 (tt0)
REVERT: Y   21 MET cc_start: 0.7589 (mpp) cc_final: 0.6612 (ttt)
  outliers start: 22
  outliers final: 11
  residues processed: 96
  average time/residue: 1.4382
  time to fit residues: 146.4089
Evaluate side-chains
  92 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  113 LEU
Chi-restraints excluded: chain R residue  133 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  156 VAL
Chi-restraints excluded: chain S residue  205 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   chunk 26 optimal weight:    0.3980
   chunk 10 optimal weight:    4.9990
   chunk 29 optimal weight:    0.2980
   chunk 60 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.6784

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

Flipped N/Q/H residues before XYZ refinement:
** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 322 ASN
** B 340 ASN ** 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 = 0.4199 r_free = 0.4199 target = 0.196831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.134302 restraints weight = 9277.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 2.45
r_work: 0.2988 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8905  Z= 0.144
  Angle     :  0.493   7.332  12087  Z= 0.254
  Chirality :  0.041   0.156   1414
  Planarity :  0.004   0.063   1515
  Dihedral  :  4.573  43.396   1235
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 11.52 %
    Favored  : 86.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.46 (0.25), residues: 1119
  helix:  2.47 (0.28), residues: 386
  sheet:  0.99 (0.29), residues: 286
  loop : -0.37 (0.28), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 207 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.014   0.001   TYR S 191 
 ARG   0.002   0.000   ARG R 238 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  214 LEU cc_start: 0.8399 (mp) cc_final: 0.7802 (tt)
REVERT: R  316 LEU cc_start: 0.5971 (mt) cc_final: 0.5706 (mm)
REVERT: A   29 LYS cc_start: 0.7681 (mptt) cc_final: 0.7168 (tmmt)
REVERT: A  315 ASP cc_start: 0.7674 (p0) cc_final: 0.7374 (m-30)
REVERT: B  118 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7718 (p0)
REVERT: B  259 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7675 (tt0)
REVERT: Y   21 MET cc_start: 0.7539 (mpp) cc_final: 0.6596 (ttt)
  outliers start: 17
  outliers final: 10
  residues processed: 95
  average time/residue: 1.4596
  time to fit residues: 147.1560
Evaluate side-chains
  95 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  113 LEU
Chi-restraints excluded: chain R residue  133 SER
Chi-restraints excluded: chain R residue  322 ASN
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  156 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 111 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9990
   chunk 84 optimal weight:   20.0000
   chunk 32 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 85 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 322 ASN
B 259 GLN
** B 340 ASN ** 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 = 0.4165 r_free = 0.4165 target = 0.193147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.127883 restraints weight = 9282.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 2.08
r_work: 0.2940 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2796 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8905  Z= 0.293
  Angle     :  0.571   7.281  12087  Z= 0.298
  Chirality :  0.044   0.168   1414
  Planarity :  0.005   0.075   1515
  Dihedral  :  4.830  42.847   1235
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 11.52 %
    Favored  : 86.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.18 (0.25), residues: 1119
  helix:  2.24 (0.27), residues: 389
  sheet:  0.84 (0.29), residues: 285
  loop : -0.57 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  82 
 HIS   0.008   0.001   HIS B  62 
 PHE   0.015   0.002   PHE B 278 
 TYR   0.013   0.002   TYR S 191 
 ARG   0.006   0.000   ARG R 238 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
REVERT: R  178 ARG cc_start: 0.5068 (mmt180) cc_final: 0.4850 (mmm160)
REVERT: R  214 LEU cc_start: 0.8464 (mp) cc_final: 0.7870 (tt)
REVERT: A   29 LYS cc_start: 0.7894 (mptt) cc_final: 0.7389 (tmmt)
REVERT: A  205 ARG cc_start: 0.7432 (mmt180) cc_final: 0.7037 (mmp-170)
REVERT: B  118 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7660 (p0)
REVERT: Y   21 MET cc_start: 0.7500 (mpp) cc_final: 0.6548 (ttt)
  outliers start: 21
  outliers final: 13
  residues processed: 98
  average time/residue: 1.9801
  time to fit residues: 204.7136
Evaluate side-chains
  94 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 1.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  133 SER
Chi-restraints excluded: chain R residue  276 MET
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  156 VAL
Chi-restraints excluded: chain S residue  205 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 106 optimal weight:    0.3980
   chunk 103 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 95 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 63 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 15 optimal weight:   40.0000
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 322 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 184 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.195914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.131207 restraints weight = 9346.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 2.12
r_work: 0.2998 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8905  Z= 0.154
  Angle     :  0.506   7.729  12087  Z= 0.262
  Chirality :  0.041   0.144   1414
  Planarity :  0.004   0.066   1515
  Dihedral  :  4.542  43.585   1235
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 12.39 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.42 (0.25), residues: 1119
  helix:  2.49 (0.27), residues: 389
  sheet:  0.88 (0.29), residues: 291
  loop : -0.44 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.012   0.001   TYR S 191 
 ARG   0.005   0.000   ARG R 238 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
REVERT: R  214 LEU cc_start: 0.8410 (mp) cc_final: 0.7826 (tt)
REVERT: R  270 MET cc_start: 0.8194 (mtp) cc_final: 0.7949 (mtm)
REVERT: R  316 LEU cc_start: 0.6225 (mt) cc_final: 0.5952 (mm)
REVERT: A   29 LYS cc_start: 0.7682 (mptt) cc_final: 0.7193 (tmmt)
REVERT: A  205 ARG cc_start: 0.7416 (mmt-90) cc_final: 0.7007 (mmp-170)
REVERT: B  118 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7659 (p0)
REVERT: Y   21 MET cc_start: 0.7282 (mpp) cc_final: 0.6306 (ttt)
  outliers start: 19
  outliers final: 11
  residues processed: 95
  average time/residue: 1.4395
  time to fit residues: 144.7088
Evaluate side-chains
  94 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  118 MET
Chi-restraints excluded: chain R residue  133 SER
Chi-restraints excluded: chain R residue  322 ASN
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain S residue  156 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 103 optimal weight:    0.1980
   chunk 0 optimal weight:   20.0000
   chunk 35 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 97 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 98 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0370
   overall best weight:    0.6260

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

Flipped N/Q/H residues before XYZ refinement:
** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 184 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.196736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.133854 restraints weight = 9326.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 2.29
r_work: 0.3018 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8905  Z= 0.143
  Angle     :  0.500  10.598  12087  Z= 0.257
  Chirality :  0.041   0.136   1414
  Planarity :  0.004   0.063   1515
  Dihedral  :  4.429  44.268   1235
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 12.39 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.50 (0.25), residues: 1119
  helix:  2.62 (0.27), residues: 387
  sheet:  0.87 (0.29), residues: 286
  loop : -0.38 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 297 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.013   0.001   TYR S 191 
 ARG   0.006   0.000   ARG R 238 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
REVERT: R  214 LEU cc_start: 0.8459 (mp) cc_final: 0.7880 (tt)
REVERT: R  270 MET cc_start: 0.8241 (mtp) cc_final: 0.7996 (mtm)
REVERT: R  316 LEU cc_start: 0.6188 (mt) cc_final: 0.5931 (mm)
REVERT: A   29 LYS cc_start: 0.7723 (mptt) cc_final: 0.7220 (tmmt)
REVERT: A  205 ARG cc_start: 0.7415 (mmt-90) cc_final: 0.7009 (mmp-170)
REVERT: B  118 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7698 (p0)
REVERT: Y   21 MET cc_start: 0.7283 (mpp) cc_final: 0.6301 (ttt)
  outliers start: 16
  outliers final: 11
  residues processed: 95
  average time/residue: 1.4733
  time to fit residues: 148.2093
Evaluate side-chains
  93 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  118 MET
Chi-restraints excluded: chain R residue  133 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain S residue  156 VAL
Chi-restraints excluded: chain S residue  205 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 100 optimal weight:    8.9990
   chunk 44 optimal weight:    8.9990
   chunk 72 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0050
   chunk 108 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   overall best weight:    1.3398

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

Flipped N/Q/H residues before XYZ refinement:
** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 322 ASN
B 155 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 184 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.194926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.134429 restraints weight = 9307.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.21
r_work: 0.3069 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8905  Z= 0.206
  Angle     :  0.532   9.317  12087  Z= 0.275
  Chirality :  0.042   0.146   1414
  Planarity :  0.004   0.068   1515
  Dihedral  :  4.539  44.602   1235
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.72 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.40 (0.25), residues: 1119
  helix:  2.55 (0.27), residues: 387
  sheet:  0.90 (0.29), residues: 289
  loop : -0.51 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.014   0.001   TYR S 191 
 ARG   0.006   0.000   ARG R 238 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
REVERT: R  214 LEU cc_start: 0.8481 (mp) cc_final: 0.7905 (tt)
REVERT: R  316 LEU cc_start: 0.6215 (mt) cc_final: 0.5937 (mm)
REVERT: A   29 LYS cc_start: 0.7845 (mptt) cc_final: 0.7377 (tmmt)
REVERT: A  205 ARG cc_start: 0.7468 (mmt-90) cc_final: 0.7064 (mmp-170)
REVERT: B  118 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7697 (p0)
REVERT: Y   21 MET cc_start: 0.7211 (mpp) cc_final: 0.6235 (ttt)
  outliers start: 14
  outliers final: 12
  residues processed: 91
  average time/residue: 1.4104
  time to fit residues: 136.3393
Evaluate side-chains
  94 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  133 SER
Chi-restraints excluded: chain R residue  322 ASN
Chi-restraints excluded: chain A residue   24 ARG
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain S residue  156 VAL
Chi-restraints excluded: chain S residue  205 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   chunk 51 optimal weight:    9.9990
   chunk 74 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 102 optimal weight:    9.9990
   chunk 96 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 322 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 184 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.195031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.131539 restraints weight = 9294.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.45
r_work: 0.2964 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2820 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.143   8905  Z= 0.270
  Angle     :  0.946  59.196  12087  Z= 0.554
  Chirality :  0.043   0.374   1414
  Planarity :  0.004   0.068   1515
  Dihedral  :  4.522  44.625   1235
  Min Nonbonded Distance : 1.804

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 12.93 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  1.40 (0.25), residues: 1119
  helix:  2.56 (0.27), residues: 387
  sheet:  0.88 (0.29), residues: 289
  loop : -0.51 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.013   0.001   PHE B 234 
 TYR   0.014   0.001   TYR S 191 
 ARG   0.005   0.000   ARG B 134 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9061.32 seconds
wall clock time: 158 minutes 39.45 seconds (9519.45 seconds total)