Starting phenix.real_space_refine
on Sun May 11 02:41:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kgk_37224/05_2025/8kgk_37224.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kgk_37224/05_2025/8kgk_37224.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kgk_37224/05_2025/8kgk_37224.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kgk_37224/05_2025/8kgk_37224.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kgk_37224/05_2025/8kgk_37224.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kgk_37224/05_2025/8kgk_37224.cif"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.098
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      53      5.16       5
     C    4738      2.51       5
     N    1298      2.21       5
     O    1387      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7476
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 1888
          Classifications: {'peptide': 256}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 10, 'TRANS': 245}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 132
          Unresolved non-hydrogen dihedrals: 90
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 46
    Chain: "B"
      Number of atoms: 1804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1804
          Classifications: {'peptide': 229}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 6, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 109
          Unresolved non-hydrogen angles: 128
          Unresolved non-hydrogen dihedrals: 90
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 64
    Chain: "C"
      Number of atoms: 2503
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 339, 2497
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 133
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 78
      Conformer: "B"
        Number of residues, atoms: 339, 2497
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 133
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 78
          bond proxies already assigned to first conformer: 2537
    Chain: "D"
      Number of atoms: 353
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 353
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 80
          Unresolved non-hydrogen angles: 95
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "E"
      Number of atoms: 928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 928
          Classifications: {'peptide': 126}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 23
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ACYS C 233 " occ=0.50
      ... (10 atoms not shown)
      pdb=" SG BCYS C 233 " occ=0.50
  Time building chain proxies: 5.42, per 1000 atoms: 0.72
  Number of scatterers: 7476
  At special positions: 0
  Unit cell: (71.28, 95.04, 128.52, 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      53     16.00
     O    1387      8.00
     N    1298      7.00
     C    4738      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 115 " - pdb=" SG  CYS A 195 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  99 " - pdb=" SG  CYS E 107 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.73
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1890

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      43.1% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 70
      removed outlier: 3.533A  pdb=" N   THR A  70 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 75
      removed outlier: 3.677A  pdb=" N   ARG A  74 " --> pdb=" O   PRO A  71 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   LYS A  75 " --> pdb=" O   ALA A  72 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 71 through 75'
    Processing helix  chain 'A' and resid 76 through 102
      removed outlier: 4.638A  pdb=" N   MET A  94 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
      Proline residue:  A  95  - end of helix
    Processing helix  chain 'A' and resid 112 through 145
    Processing helix  chain 'A' and resid 146 through 154
      removed outlier: 3.696A  pdb=" N   GLU A 151 " --> pdb=" O   PRO A 147 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL A 152 " --> pdb=" O   MET A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 185
      Proline residue:  A 177  - end of helix
    Processing helix  chain 'A' and resid 202 through 217
    Processing helix  chain 'A' and resid 217 through 238
    Processing helix  chain 'A' and resid 284 through 314
      Proline residue:  A 302  - end of helix
      removed outlier: 3.525A  pdb=" N   ALA A 314 " --> pdb=" O   VAL A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 341
      removed outlier: 3.519A  pdb=" N   SER A 324 " --> pdb=" O   GLY A 320 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   CYS A 333 " --> pdb=" O   ILE A 329 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   PHE A 334 " --> pdb=" O   GLY A 330 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   THR A 335 " --> pdb=" O   TYR A 331 " (cutoff:3.500A)
      Proline residue:  A 338  - end of helix
    Processing helix  chain 'A' and resid 347 through 355
    Processing helix  chain 'B' and resid 13 through 39
      removed outlier: 3.703A  pdb=" N   GLN B  35 " --> pdb=" O   GLN B  31 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   VAL B  36 " --> pdb=" O   LYS B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 61
    Processing helix  chain 'B' and resid 233 through 238
      removed outlier: 3.535A  pdb=" N   GLN B 236 " --> pdb=" O   LYS B 233 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   CYS B 237 " --> pdb=" O   TRP B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 268
    Processing helix  chain 'B' and resid 269 through 273
      removed outlier: 3.733A  pdb=" N   ARG B 273 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 294
    Processing helix  chain 'B' and resid 297 through 302
      removed outlier: 3.785A  pdb=" N   TYR B 301 " --> pdb=" O   LYS B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 306
      removed outlier: 3.915A  pdb=" N   ALA B 306 " --> pdb=" O   PRO B 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 303 through 306'
    Processing helix  chain 'B' and resid 321 through 343
      removed outlier: 3.681A  pdb=" N   ILE B 338 " --> pdb=" O   GLU B 334 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   SER B 342 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   GLY B 343 " --> pdb=" O   SER B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 381
    Processing helix  chain 'C' and resid 3 through 26
    Processing helix  chain 'C' and resid 29 through 35
      removed outlier: 3.860A  pdb=" N   ILE C  33 " --> pdb=" O   THR C  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 9 through 24
      removed outlier: 3.656A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.587A  pdb=" N   THR E  91 " --> pdb=" O   PRO E  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 209 through 214
      removed outlier: 6.039A  pdb=" N   HIS B  41 " --> pdb=" O   HIS B 220 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   PHE B 222 " --> pdb=" O   HIS B  41 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   LEU B  43 " --> pdb=" O   PHE B 222 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ALA B 243 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51
      removed outlier: 4.154A  pdb=" N   ARG C  46 " --> pdb=" O   ASN C 340 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ASN C 340 " --> pdb=" O   ARG C  46 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 62
      removed outlier: 3.811A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   SER C  72 " --> pdb=" O   ILE C  80 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE C  80 " --> pdb=" O   SER C  72 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.955A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   GLY C 116 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   ILE C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151
      removed outlier: 4.219A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 7.116A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 7.279A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 232
      removed outlier: 6.543A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLN C 259 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278
      removed outlier: 6.444A  pdb=" N   GLY C 288 " --> pdb=" O   THR C 274 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   VAL C 276 " --> pdb=" O   LEU C 286 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   LEU C 286 " --> pdb=" O   VAL C 276 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   PHE C 278 " --> pdb=" O   LEU C 284 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   LEU C 284 " --> pdb=" O   PHE C 278 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   CYS C 294 " --> pdb=" O   VAL C 307 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   VAL C 307 " --> pdb=" O   CYS C 294 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   VAL C 296 " --> pdb=" O   ALA C 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60
      removed outlier: 3.940A  pdb=" N   SER E  59 " --> pdb=" O   ASP E  50 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   ASP E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   MET E  34 " --> pdb=" O   ASP E  50 " (cutoff:3.500A)

    408 hydrogen bonds defined for protein.
    1185 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: 2.16

  Time building geometry restraints manager: 2.03 seconds

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

  Histogram of bond lengths:
        1.12 -     1.26: 1222
        1.26 -     1.40: 1961
        1.40 -     1.54: 4350
        1.54 -     1.68: 24
        1.68 -     1.82: 73
  Bond restraints: 7630
  Sorted by residual:
  bond pdb=" N   CYS A 115 "
       pdb=" CA  CYS A 115 "
    ideal  model  delta    sigma   weight residual
    1.459  1.318  0.141 1.21e-02 6.83e+03 1.36e+02
  bond pdb=" C   LEU A 117 "
       pdb=" O   LEU A 117 "
    ideal  model  delta    sigma   weight residual
    1.237  1.122  0.114 1.19e-02 7.06e+03 9.20e+01
  bond pdb=" C   ALA A 114 "
       pdb=" O   ALA A 114 "
    ideal  model  delta    sigma   weight residual
    1.237  1.131  0.106 1.17e-02 7.31e+03 8.22e+01
  bond pdb=" C   GLU A 112 "
       pdb=" O   GLU A 112 "
    ideal  model  delta    sigma   weight residual
    1.237  1.135  0.102 1.17e-02 7.31e+03 7.62e+01
  bond pdb=" C   VAL A 113 "
       pdb=" O   VAL A 113 "
    ideal  model  delta    sigma   weight residual
    1.237  1.162  0.075 1.17e-02 7.31e+03 4.09e+01
  ... (remaining 7625 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 10178
        2.05 -     4.10: 175
        4.10 -     6.16: 28
        6.16 -     8.21: 11
        8.21 -    10.26: 4
  Bond angle restraints: 10396
  Sorted by residual:
  angle pdb=" O   CYS A 115 "
        pdb=" C   CYS A 115 "
        pdb=" N   ARG A 116 "
      ideal   model   delta    sigma   weight residual
     122.12  114.14    7.98 1.06e+00 8.90e-01 5.66e+01
  angle pdb=" N   GLU A 112 "
        pdb=" CA  GLU A 112 "
        pdb=" C   GLU A 112 "
      ideal   model   delta    sigma   weight residual
     111.28  103.25    8.03 1.09e+00 8.42e-01 5.43e+01
  angle pdb=" CA  CYS A 115 "
        pdb=" C   CYS A 115 "
        pdb=" N   ARG A 116 "
      ideal   model   delta    sigma   weight residual
     117.30  125.55   -8.25 1.16e+00 7.43e-01 5.05e+01
  angle pdb=" N   CYS A 115 "
        pdb=" CA  CYS A 115 "
        pdb=" CB  CYS A 115 "
      ideal   model   delta    sigma   weight residual
     110.12  120.38  -10.26 1.47e+00 4.63e-01 4.87e+01
  angle pdb=" C   PRO A 192 "
        pdb=" N   PRO A 193 "
        pdb=" CA  PRO A 193 "
      ideal   model   delta    sigma   weight residual
     119.84  111.81    8.03 1.25e+00 6.40e-01 4.13e+01
  ... (remaining 10391 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.42: 4076
       17.42 -    34.83: 331
       34.83 -    52.25: 62
       52.25 -    69.66: 10
       69.66 -    87.08: 6
  Dihedral angle restraints: 4485
    sinusoidal: 1561
      harmonic: 2924
  Sorted by residual:
  dihedral pdb=" CB  CYS A 115 "
           pdb=" SG  CYS A 115 "
           pdb=" SG  CYS A 195 "
           pdb=" CB  CYS A 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -166.54   80.54     1      1.00e+01 1.00e-02 8.02e+01
  dihedral pdb=" N   CYS A 115 "
           pdb=" C   CYS A 115 "
           pdb=" CA  CYS A 115 "
           pdb=" CB  CYS A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.80  -12.00     0      2.50e+00 1.60e-01 2.30e+01
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  96 "
           pdb=" CB  CYS E  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   59.67   33.33     1      1.00e+01 1.00e-02 1.58e+01
  ... (remaining 4482 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.150: 1196
       0.150 -    0.301: 7
       0.301 -    0.451: 3
       0.451 -    0.601: 0
       0.601 -    0.751: 1
  Chirality restraints: 1207
  Sorted by residual:
  chirality pdb=" CA  CYS A 115 "
            pdb=" N   CYS A 115 "
            pdb=" C   CYS A 115 "
            pdb=" CB  CYS A 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.76    0.75 2.00e-01 2.50e+01 1.41e+01
  chirality pdb=" CA  PHE A 125 "
            pdb=" N   PHE A 125 "
            pdb=" C   PHE A 125 "
            pdb=" CB  PHE A 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" CA  LEU A 121 "
            pdb=" N   LEU A 121 "
            pdb=" C   LEU A 121 "
            pdb=" CB  LEU A 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.50e+00
  ... (remaining 1204 not shown)

  Planarity restraints: 1336
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 122 "    0.023 2.00e-02 2.50e+03   4.56e-02 2.08e+01
        pdb=" C   SER A 122 "   -0.079 2.00e-02 2.50e+03
        pdb=" O   SER A 122 "    0.030 2.00e-02 2.50e+03
        pdb=" N   VAL A 123 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 192 "    0.047 5.00e-02 4.00e+02   7.06e-02 7.97e+00
        pdb=" N   PRO A 193 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A 193 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 193 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 113 "    0.014 2.00e-02 2.50e+03   2.77e-02 7.67e+00
        pdb=" C   VAL A 113 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   VAL A 113 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ALA A 114 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1333 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 162
        2.68 -     3.23: 7282
        3.23 -     3.79: 12160
        3.79 -     4.34: 15905
        4.34 -     4.90: 26492
  Nonbonded interactions: 62001
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C  86 "
            pdb=" OD1 ASN C  88 "
     model   vdw
     2.122 3.040
  nonbonded pdb=" NH1 ARG C 283 "
            pdb=" OD1 ASP C 298 "
     model   vdw
     2.146 3.120
  nonbonded pdb=" OG  SER C 279 "
            pdb=" OD1 ASP D  48 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG  SER C  74 "
            pdb=" OD1 ASP C  76 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   PHE E  29 "
            pdb=" NH2 ARG E  72 "
     model   vdw
     2.240 3.120
  ... (remaining 61996 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.490
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.260
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
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      :  0.005   0.141   7633  Z= 0.396
  Angle     :  0.689  10.262  10402  Z= 0.416
  Chirality :  0.051   0.751   1207
  Planarity :  0.005   0.071   1336
  Dihedral  : 13.366  87.077   2586
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.63 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  0.67 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.27), residues: 991
  helix:  2.09 (0.26), residues: 398
  sheet: -0.39 (0.36), residues: 206
  loop : -0.36 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP C  82 
 HIS   0.005   0.001   HIS C  91 
 PHE   0.016   0.001   PHE A 120 
 TYR   0.019   0.001   TYR A 303 
 ARG   0.007   0.001   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13549 (  408)
  hydrogen bonds       : angle       5.82895 ( 1185)
  SS BOND              : bond        0.00562 (    3)
  SS BOND              : angle       1.55650 (    6)
  covalent geometry    : bond        0.00541 ( 7630)
  covalent geometry    : angle       0.68830 (10396)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 204
  time to evaluate  : 0.856 
Fit side-chains
REVERT: C  179 THR cc_start: 0.8973 (m) cc_final: 0.8696 (t)
REVERT: C  217 MET cc_start: 0.7308 (ttp) cc_final: 0.6900 (ttm)
REVERT: C  297 TRP cc_start: 0.7994 (m100) cc_final: 0.7268 (m100)
  outliers start: 3
  outliers final: 0
  residues processed: 207
  average time/residue: 0.1909
  time to fit residues: 53.0109
Evaluate side-chains
  176 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:   30.0000
   chunk 73 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 49 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 46 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 337 ASN
B  23 ASN
** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 HIS
C 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.153756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.117350 restraints weight = 10253.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 3.10
r_work: 0.3360 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3380
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3380
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7633  Z= 0.235
  Angle     :  0.626   7.315  10402  Z= 0.332
  Chirality :  0.045   0.243   1207
  Planarity :  0.005   0.048   1336
  Dihedral  :  4.578  32.262   1086
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 11.19 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.27), residues: 991
  helix:  2.18 (0.25), residues: 402
  sheet: -0.54 (0.35), residues: 210
  loop : -0.36 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C  82 
 HIS   0.007   0.002   HIS C 142 
 PHE   0.017   0.002   PHE D  61 
 TYR   0.017   0.002   TYR E  95 
 ARG   0.004   0.001   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04106 (  408)
  hydrogen bonds       : angle       4.75622 ( 1185)
  SS BOND              : bond        0.00249 (    3)
  SS BOND              : angle       1.17495 (    6)
  covalent geometry    : bond        0.00535 ( 7630)
  covalent geometry    : angle       0.62507 (10396)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 183
  time to evaluate  : 0.807 
Fit side-chains
REVERT: A  355 GLN cc_start: 0.6129 (mp10) cc_final: 0.5910 (mp10)
REVERT: C  179 THR cc_start: 0.8970 (m) cc_final: 0.8518 (p)
REVERT: C  215 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7458 (tm-30)
REVERT: C  217 MET cc_start: 0.7613 (ttp) cc_final: 0.7307 (ttp)
REVERT: C  293 ASN cc_start: 0.7941 (m-40) cc_final: 0.7662 (m-40)
REVERT: C  334 SER cc_start: 0.8956 (m) cc_final: 0.8704 (m)
REVERT: E  117 TYR cc_start: 0.7987 (m-80) cc_final: 0.7763 (m-80)
  outliers start: 17
  outliers final: 11
  residues processed: 190
  average time/residue: 0.2128
  time to fit residues: 55.0621
Evaluate side-chains
  178 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 167
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain B residue  283 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 93 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9980
   chunk 92 optimal weight:    8.9990
   chunk 54 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 81 optimal weight:   50.0000
   chunk 55 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 307 HIS
A 337 ASN
** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 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 = 0.3953 r_free = 0.3953 target = 0.156305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.118156 restraints weight = 14170.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 3.72
r_work: 0.3363 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3382
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3382 r_free = 0.3382    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3382 r_free = 0.3382    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3382
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7633  Z= 0.142
  Angle     :  0.558   8.430  10402  Z= 0.291
  Chirality :  0.042   0.158   1207
  Planarity :  0.004   0.045   1336
  Dihedral  :  4.410  31.429   1086
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.09 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.27), residues: 991
  helix:  2.52 (0.26), residues: 398
  sheet: -0.60 (0.35), residues: 211
  loop : -0.40 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C  82 
 HIS   0.007   0.001   HIS B 220 
 PHE   0.011   0.001   PHE C 241 
 TYR   0.014   0.001   TYR B 381 
 ARG   0.005   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03468 (  408)
  hydrogen bonds       : angle       4.44650 ( 1185)
  SS BOND              : bond        0.00407 (    3)
  SS BOND              : angle       1.16162 (    6)
  covalent geometry    : bond        0.00325 ( 7630)
  covalent geometry    : angle       0.55774 (10396)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 183
  time to evaluate  : 1.032 
Fit side-chains
REVERT: A  173 MET cc_start: 0.8644 (mmm) cc_final: 0.8178 (mmm)
REVERT: B  378 LEU cc_start: 0.7920 (mt) cc_final: 0.7677 (mt)
REVERT: C  101 MET cc_start: 0.9265 (mtt) cc_final: 0.9017 (mtt)
REVERT: C  179 THR cc_start: 0.8969 (m) cc_final: 0.8523 (p)
REVERT: C  217 MET cc_start: 0.7575 (ttp) cc_final: 0.7223 (ttm)
REVERT: C  293 ASN cc_start: 0.7883 (m-40) cc_final: 0.7623 (m-40)
REVERT: C  334 SER cc_start: 0.8993 (m) cc_final: 0.8763 (m)
REVERT: E  117 TYR cc_start: 0.7841 (m-80) cc_final: 0.7552 (m-80)
  outliers start: 16
  outliers final: 12
  residues processed: 190
  average time/residue: 0.2191
  time to fit residues: 55.8371
Evaluate side-chains
  184 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 172
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain B residue  220 HIS
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  283 LYS
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 80 optimal weight:   30.0000
   chunk 4 optimal weight:    0.8980
   chunk 5 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   chunk 92 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 337 ASN
B  23 ASN
** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  74 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.156702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.116112 restraints weight = 17283.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 4.20
r_work: 0.3331 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3349
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3349
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7633  Z= 0.139
  Angle     :  0.544   7.910  10402  Z= 0.284
  Chirality :  0.042   0.258   1207
  Planarity :  0.004   0.044   1336
  Dihedral  :  4.362  30.868   1086
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.71 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.27), residues: 991
  helix:  2.61 (0.25), residues: 398
  sheet: -0.66 (0.34), residues: 221
  loop : -0.40 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C  82 
 HIS   0.007   0.001   HIS B 220 
 PHE   0.012   0.001   PHE D  61 
 TYR   0.019   0.002   TYR B 381 
 ARG   0.006   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03322 (  408)
  hydrogen bonds       : angle       4.33741 ( 1185)
  SS BOND              : bond        0.00520 (    3)
  SS BOND              : angle       0.97592 (    6)
  covalent geometry    : bond        0.00319 ( 7630)
  covalent geometry    : angle       0.54404 (10396)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 0.780 
Fit side-chains
REVERT: A  173 MET cc_start: 0.8640 (mmm) cc_final: 0.8095 (mmm)
REVERT: A  337 ASN cc_start: 0.8660 (m-40) cc_final: 0.8432 (m110)
REVERT: C  179 THR cc_start: 0.8971 (m) cc_final: 0.8528 (p)
REVERT: C  217 MET cc_start: 0.7549 (ttp) cc_final: 0.7258 (ttm)
REVERT: C  293 ASN cc_start: 0.7869 (m-40) cc_final: 0.7633 (m-40)
REVERT: C  334 SER cc_start: 0.8977 (m) cc_final: 0.8722 (m)
REVERT: E   83 MET cc_start: 0.2868 (mtp) cc_final: 0.1868 (mtp)
REVERT: E   90 ASP cc_start: 0.7262 (m-30) cc_final: 0.7004 (m-30)
REVERT: E  117 TYR cc_start: 0.7903 (m-80) cc_final: 0.7669 (m-80)
  outliers start: 20
  outliers final: 17
  residues processed: 193
  average time/residue: 0.1875
  time to fit residues: 48.8447
Evaluate side-chains
  191 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 174
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain B residue  220 HIS
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  283 LYS
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain C residue   82 TRP
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 85 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 84 optimal weight:    0.2980
   chunk 44 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 77 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
B  23 ASN
** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  44 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.154757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.113292 restraints weight = 20106.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 4.50
r_work: 0.3291 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3306
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3306 r_free = 0.3306    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3306 r_free = 0.3306    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3306
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7633  Z= 0.176
  Angle     :  0.566   8.090  10402  Z= 0.297
  Chirality :  0.043   0.260   1207
  Planarity :  0.004   0.044   1336
  Dihedral  :  4.424  31.863   1086
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 16.58 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.27), residues: 991
  helix:  2.42 (0.26), residues: 404
  sheet: -0.73 (0.33), residues: 225
  loop : -0.36 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP C  82 
 HIS   0.007   0.001   HIS B 220 
 PHE   0.013   0.001   PHE D  61 
 TYR   0.017   0.002   TYR B 381 
 ARG   0.005   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03420 (  408)
  hydrogen bonds       : angle       4.35617 ( 1185)
  SS BOND              : bond        0.00573 (    3)
  SS BOND              : angle       1.01787 (    6)
  covalent geometry    : bond        0.00404 ( 7630)
  covalent geometry    : angle       0.56608 (10396)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 174
  time to evaluate  : 0.795 
Fit side-chains
REVERT: A  231 MET cc_start: 0.8149 (ttm) cc_final: 0.7793 (ttm)
REVERT: A  337 ASN cc_start: 0.8711 (m-40) cc_final: 0.8480 (m110)
REVERT: C  217 MET cc_start: 0.7521 (ttp) cc_final: 0.7190 (ttm)
REVERT: C  334 SER cc_start: 0.8890 (m) cc_final: 0.8673 (m)
REVERT: E   83 MET cc_start: 0.3223 (mtp) cc_final: 0.1687 (mtp)
REVERT: E   90 ASP cc_start: 0.7389 (m-30) cc_final: 0.7132 (m-30)
REVERT: E  117 TYR cc_start: 0.8007 (m-80) cc_final: 0.7552 (m-80)
  outliers start: 27
  outliers final: 20
  residues processed: 187
  average time/residue: 0.1964
  time to fit residues: 49.0246
Evaluate side-chains
  190 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 170
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain B residue   23 ASN
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  220 HIS
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  283 LYS
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain C residue   82 TRP
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain C residue  298 ASP
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 41 optimal weight:   20.0000
   chunk 66 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 63 optimal weight:    0.2980
   chunk 79 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  23 ASN
** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 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 = 0.3962 r_free = 0.3962 target = 0.157005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.114931 restraints weight = 24709.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 5.01
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3492
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3492 r_free = 0.3492    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3492 r_free = 0.3492    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3492
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7633  Z= 0.125
  Angle     :  0.551   8.421  10402  Z= 0.285
  Chirality :  0.042   0.250   1207
  Planarity :  0.004   0.044   1336
  Dihedral  :  4.327  29.553   1086
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 19.00 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.27), residues: 991
  helix:  2.56 (0.26), residues: 403
  sheet: -0.78 (0.33), residues: 227
  loop : -0.34 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C  82 
 HIS   0.007   0.001   HIS B 220 
 PHE   0.012   0.001   PHE A 340 
 TYR   0.020   0.002   TYR B 381 
 ARG   0.006   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03156 (  408)
  hydrogen bonds       : angle       4.26828 ( 1185)
  SS BOND              : bond        0.00466 (    3)
  SS BOND              : angle       0.87716 (    6)
  covalent geometry    : bond        0.00288 ( 7630)
  covalent geometry    : angle       0.55087 (10396)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 178
  time to evaluate  : 0.774 
Fit side-chains
REVERT: A  173 MET cc_start: 0.8535 (mmm) cc_final: 0.8058 (mmm)
REVERT: A  231 MET cc_start: 0.7811 (ttm) cc_final: 0.7514 (ttm)
REVERT: A  337 ASN cc_start: 0.8595 (m-40) cc_final: 0.8288 (m110)
REVERT: B  252 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7432 (p0)
REVERT: C  156 GLN cc_start: 0.7605 (tt0) cc_final: 0.7325 (tt0)
REVERT: C  334 SER cc_start: 0.8871 (m) cc_final: 0.8614 (m)
REVERT: E   83 MET cc_start: 0.2507 (mtp) cc_final: 0.1729 (mtp)
REVERT: E   90 ASP cc_start: 0.7296 (m-30) cc_final: 0.6916 (m-30)
REVERT: E   95 TYR cc_start: 0.7252 (m-80) cc_final: 0.6409 (m-80)
REVERT: E  117 TYR cc_start: 0.7640 (m-80) cc_final: 0.7398 (m-80)
  outliers start: 21
  outliers final: 14
  residues processed: 190
  average time/residue: 0.2060
  time to fit residues: 52.0566
Evaluate side-chains
  186 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 171
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain B residue  220 HIS
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain C residue   82 TRP
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain E residue   49 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 73 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 67 optimal weight:    7.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
B  23 ASN
** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 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 = 0.3942 r_free = 0.3942 target = 0.155028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.113451 restraints weight = 21128.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 4.65
r_work: 0.3294 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3309
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3309
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7633  Z= 0.163
  Angle     :  0.571   7.949  10402  Z= 0.298
  Chirality :  0.043   0.274   1207
  Planarity :  0.004   0.043   1336
  Dihedral  :  4.394  30.670   1086
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 19.27 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.27), residues: 991
  helix:  2.46 (0.26), residues: 404
  sheet: -0.75 (0.34), residues: 224
  loop : -0.34 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP C  82 
 HIS   0.007   0.001   HIS B 220 
 PHE   0.014   0.001   PHE A 306 
 TYR   0.020   0.002   TYR B 381 
 ARG   0.006   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03321 (  408)
  hydrogen bonds       : angle       4.32522 ( 1185)
  SS BOND              : bond        0.00667 (    3)
  SS BOND              : angle       1.09912 (    6)
  covalent geometry    : bond        0.00378 ( 7630)
  covalent geometry    : angle       0.57092 (10396)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 176
  time to evaluate  : 0.903 
Fit side-chains
REVERT: A  173 MET cc_start: 0.8690 (mmm) cc_final: 0.8246 (mmm)
REVERT: A  231 MET cc_start: 0.8151 (ttm) cc_final: 0.7812 (ttm)
REVERT: A  337 ASN cc_start: 0.8677 (m-40) cc_final: 0.8439 (m110)
REVERT: B  252 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7485 (p0)
REVERT: C  101 MET cc_start: 0.9334 (mtt) cc_final: 0.9126 (mtt)
REVERT: C  334 SER cc_start: 0.8896 (m) cc_final: 0.8670 (m)
REVERT: E   83 MET cc_start: 0.3335 (mtp) cc_final: 0.1995 (mtp)
REVERT: E   90 ASP cc_start: 0.7285 (m-30) cc_final: 0.6979 (m-30)
REVERT: E  117 TYR cc_start: 0.8036 (m-80) cc_final: 0.7548 (m-80)
  outliers start: 25
  outliers final: 21
  residues processed: 189
  average time/residue: 0.1925
  time to fit residues: 48.9499
Evaluate side-chains
  195 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 173
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain B residue   23 ASN
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  220 HIS
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  283 LYS
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain C residue   82 TRP
Chi-restraints excluded: chain C residue  220 GLN
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 95 optimal weight:    0.5980
   chunk 30 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  23 ASN
** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 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 = 0.3964 r_free = 0.3964 target = 0.157071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.117220 restraints weight = 19872.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 4.43
r_work: 0.3338 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3357
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3357
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7633  Z= 0.122
  Angle     :  0.570  14.484  10402  Z= 0.290
  Chirality :  0.043   0.306   1207
  Planarity :  0.004   0.043   1336
  Dihedral  :  4.313  28.823   1086
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.68 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.27), residues: 991
  helix:  2.47 (0.26), residues: 400
  sheet: -0.65 (0.34), residues: 221
  loop : -0.38 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C  82 
 HIS   0.007   0.001   HIS B 220 
 PHE   0.012   0.001   PHE A 306 
 TYR   0.016   0.001   TYR B 381 
 ARG   0.006   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03151 (  408)
  hydrogen bonds       : angle       4.25214 ( 1185)
  SS BOND              : bond        0.00547 (    3)
  SS BOND              : angle       1.12996 (    6)
  covalent geometry    : bond        0.00284 ( 7630)
  covalent geometry    : angle       0.56963 (10396)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 173
  time to evaluate  : 0.875 
Fit side-chains
REVERT: A  173 MET cc_start: 0.8684 (mmm) cc_final: 0.8271 (mmm)
REVERT: A  231 MET cc_start: 0.8109 (ttm) cc_final: 0.7772 (ttm)
REVERT: A  337 ASN cc_start: 0.8674 (m-40) cc_final: 0.8432 (m110)
REVERT: B   23 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8184 (t160)
REVERT: B  252 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7268 (p0)
REVERT: C  156 GLN cc_start: 0.7665 (tt0) cc_final: 0.7382 (tt0)
REVERT: C  229 ILE cc_start: 0.8703 (mt) cc_final: 0.8425 (mm)
REVERT: C  297 TRP cc_start: 0.8342 (m100) cc_final: 0.7719 (m100)
REVERT: C  334 SER cc_start: 0.8973 (m) cc_final: 0.8725 (m)
REVERT: E   83 MET cc_start: 0.3317 (mtp) cc_final: 0.1958 (mtp)
REVERT: E   95 TYR cc_start: 0.7317 (m-80) cc_final: 0.6631 (m-80)
REVERT: E  117 TYR cc_start: 0.7991 (m-80) cc_final: 0.7711 (m-80)
  outliers start: 20
  outliers final: 16
  residues processed: 184
  average time/residue: 0.1863
  time to fit residues: 46.4718
Evaluate side-chains
  186 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 168
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain B residue   23 ASN
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  220 HIS
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain C residue   75 GLN
Chi-restraints excluded: chain C residue   82 TRP
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0870
   chunk 77 optimal weight:   10.0000
   chunk 93 optimal weight:    0.0270
   overall best weight:    0.7818

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

Flipped N/Q/H residues before XYZ refinement:
** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 ASN ** 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 = 0.3973 r_free = 0.3973 target = 0.158037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.117047 restraints weight = 19073.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 4.44
r_work: 0.3336 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3353
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3353 r_free = 0.3353    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3353 r_free = 0.3353    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3353
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7633  Z= 0.124
  Angle     :  0.572  12.287  10402  Z= 0.291
  Chirality :  0.042   0.250   1207
  Planarity :  0.004   0.043   1336
  Dihedral  :  4.266  28.231   1086
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 20.22 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.27), residues: 991
  helix:  2.47 (0.26), residues: 400
  sheet: -0.69 (0.34), residues: 224
  loop : -0.34 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP C  82 
 HIS   0.006   0.001   HIS B 220 
 PHE   0.011   0.001   PHE C 241 
 TYR   0.017   0.001   TYR B 381 
 ARG   0.007   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03123 (  408)
  hydrogen bonds       : angle       4.24267 ( 1185)
  SS BOND              : bond        0.00673 (    3)
  SS BOND              : angle       1.11595 (    6)
  covalent geometry    : bond        0.00289 ( 7630)
  covalent geometry    : angle       0.57129 (10396)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 172
  time to evaluate  : 0.880 
Fit side-chains
REVERT: A  173 MET cc_start: 0.8659 (mmm) cc_final: 0.8233 (mmm)
REVERT: A  231 MET cc_start: 0.8132 (ttm) cc_final: 0.7757 (ttm)
REVERT: A  337 ASN cc_start: 0.8705 (m-40) cc_final: 0.8466 (m110)
REVERT: B  252 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7226 (p0)
REVERT: C  156 GLN cc_start: 0.7694 (tt0) cc_final: 0.7413 (tt0)
REVERT: C  229 ILE cc_start: 0.8668 (mt) cc_final: 0.8382 (mm)
REVERT: C  297 TRP cc_start: 0.8325 (m100) cc_final: 0.7746 (m100)
REVERT: C  334 SER cc_start: 0.8950 (m) cc_final: 0.8696 (m)
REVERT: E   83 MET cc_start: 0.3352 (mtp) cc_final: 0.1948 (mtp)
REVERT: E   95 TYR cc_start: 0.7343 (m-80) cc_final: 0.6621 (m-80)
REVERT: E  117 TYR cc_start: 0.7984 (m-80) cc_final: 0.7519 (m-80)
  outliers start: 19
  outliers final: 18
  residues processed: 180
  average time/residue: 0.1926
  time to fit residues: 47.0689
Evaluate side-chains
  191 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 172
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  220 HIS
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain C residue   75 GLN
Chi-restraints excluded: chain C residue   82 TRP
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 48 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
B  23 ASN
** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  44 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.155257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.114920 restraints weight = 15113.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 3.97
r_work: 0.3330 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3334
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3334 r_free = 0.3334    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3334 r_free = 0.3334    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3334
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7633  Z= 0.183
  Angle     :  0.596  11.386  10402  Z= 0.311
  Chirality :  0.043   0.252   1207
  Planarity :  0.004   0.042   1336
  Dihedral  :  4.490  31.156   1086
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.95 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.27), residues: 991
  helix:  2.36 (0.26), residues: 406
  sheet: -0.87 (0.34), residues: 229
  loop : -0.37 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP C  82 
 HIS   0.008   0.001   HIS B 220 
 PHE   0.012   0.002   PHE D  61 
 TYR   0.024   0.002   TYR B 381 
 ARG   0.007   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03385 (  408)
  hydrogen bonds       : angle       4.37263 ( 1185)
  SS BOND              : bond        0.00831 (    3)
  SS BOND              : angle       2.57479 (    6)
  covalent geometry    : bond        0.00426 ( 7630)
  covalent geometry    : angle       0.59282 (10396)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 174
  time to evaluate  : 0.862 
Fit side-chains
REVERT: A  173 MET cc_start: 0.8698 (mmm) cc_final: 0.8163 (mmm)
REVERT: A  231 MET cc_start: 0.8155 (ttm) cc_final: 0.7768 (ttm)
REVERT: A  337 ASN cc_start: 0.8689 (m-40) cc_final: 0.8431 (m110)
REVERT: B  252 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7160 (p0)
REVERT: C  334 SER cc_start: 0.8917 (m) cc_final: 0.8690 (m)
REVERT: E   83 MET cc_start: 0.3150 (mtp) cc_final: 0.1736 (mtp)
REVERT: E   90 ASP cc_start: 0.7408 (m-30) cc_final: 0.7060 (m-30)
REVERT: E  117 TYR cc_start: 0.8039 (m-80) cc_final: 0.7760 (m-80)
  outliers start: 20
  outliers final: 17
  residues processed: 184
  average time/residue: 0.1944
  time to fit residues: 48.2060
Evaluate side-chains
  189 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 171
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  220 HIS
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain C residue   82 TRP
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 76 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B  23 ASN
** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 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 = 0.3965 r_free = 0.3965 target = 0.156983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.117007 restraints weight = 20568.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 4.52
r_work: 0.3331 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3347
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3347
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   7633  Z= 0.130
  Angle     :  0.578  11.731  10402  Z= 0.298
  Chirality :  0.042   0.238   1207
  Planarity :  0.004   0.043   1336
  Dihedral  :  4.364  29.019   1086
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 20.75 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.27), residues: 991
  helix:  2.46 (0.26), residues: 400
  sheet: -0.84 (0.34), residues: 227
  loop : -0.40 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C  82 
 HIS   0.007   0.001   HIS B 220 
 PHE   0.011   0.001   PHE C 241 
 TYR   0.016   0.001   TYR B 381 
 ARG   0.007   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03154 (  408)
  hydrogen bonds       : angle       4.26631 ( 1185)
  SS BOND              : bond        0.00742 (    3)
  SS BOND              : angle       3.26630 (    6)
  covalent geometry    : bond        0.00312 ( 7630)
  covalent geometry    : angle       0.57251 (10396)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4507.42 seconds
wall clock time: 78 minutes 32.63 seconds (4712.63 seconds total)