Starting phenix.real_space_refine
on Wed Mar 12 05:29:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kgk_37224/03_2025/8kgk_37224.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kgk_37224/03_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_37224/03_2025/8kgk_37224.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kgk_37224/03_2025/8kgk_37224.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kgk_37224/03_2025/8kgk_37224.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kgk_37224/03_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-5624/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: 5.90, per 1000 atoms: 0.79
  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: 1.80
  Conformation dependent library (CDL) restraints added in 1.5 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: 0.80
  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: 2.22

  Time building geometry restraints manager: 2.15 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:             0.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     23.120
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.040
-------------------------------------------------------------------------------
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   7630  Z= 0.352
  Angle     :  0.688  10.262  10396  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 

*********************** 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  : 0.949 
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: 0.1989
  time to fit residues: 54.8644
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  : 0.830 
-------------------------------------------------------------------------------
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:    0.9990
   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:    6.9990
   overall best weight:    1.9786

-------------------------------------------------------------------------------
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 = 0.3939 r_free = 0.3939 target = 0.155214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.119163 restraints weight = 10259.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 3.08
r_work: 0.3389 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3402
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3402 r_free = 0.3402    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3402 r_free = 0.3402    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3402
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   7630  Z= 0.316
  Angle     :  0.607   7.941  10396  Z= 0.320
  Chirality :  0.044   0.274   1207
  Planarity :  0.005   0.047   1336
  Dihedral  :  4.459  30.885   1086
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.32 %
    Favored  : 86.79 %
  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:  2.26 (0.25), residues: 404
  sheet: -0.46 (0.36), residues: 206
  loop : -0.37 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C  82 
 HIS   0.006   0.002   HIS B 220 
 PHE   0.014   0.002   PHE D  61 
 TYR   0.015   0.002   TYR E  95 
 ARG   0.004   0.001   ARG B  38 

*********************** 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
  197 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 183
  time to evaluate  : 1.250 
Fit side-chains
REVERT: A  355 GLN cc_start: 0.6022 (mp10) cc_final: 0.5765 (mp10)
REVERT: C  179 THR cc_start: 0.8967 (m) cc_final: 0.8518 (p)
REVERT: C  215 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7428 (tm-30)
REVERT: C  217 MET cc_start: 0.7646 (ttp) cc_final: 0.7398 (ttp)
REVERT: C  293 ASN cc_start: 0.7878 (m-40) cc_final: 0.7605 (m-40)
REVERT: C  334 SER cc_start: 0.9044 (m) cc_final: 0.8787 (m)
REVERT: D   48 ASP cc_start: 0.8097 (t0) cc_final: 0.7884 (m-30)
REVERT: E  117 TYR cc_start: 0.7931 (m-80) cc_final: 0.7727 (m-80)
REVERT: E  120 GLN cc_start: 0.8186 (mp10) cc_final: 0.7986 (mp10)
  outliers start: 14
  outliers final: 10
  residues processed: 189
  average time/residue: 0.3007
  time to fit residues: 76.3633
Evaluate side-chains
  181 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 171
  time to evaluate  : 2.194 
-------------------------------------------------------------------------------
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  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:    3.9990
   chunk 93 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 92 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 81 optimal weight:   50.0000
   chunk 55 optimal weight:    0.0470
   chunk 19 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.7082

-------------------------------------------------------------------------------
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 = 0.3978 r_free = 0.3978 target = 0.158613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.120264 restraints weight = 14943.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 3.84
r_work: 0.3385 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3405
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3405 r_free = 0.3405    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3405 r_free = 0.3405    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3405
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7630  Z= 0.182
  Angle     :  0.538   8.408  10396  Z= 0.281
  Chirality :  0.041   0.164   1207
  Planarity :  0.004   0.045   1336
  Dihedral  :  4.291  29.461   1086
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 14.96 %
    Favored  : 83.56 %
  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:  1.15 (0.27), residues: 991
  helix:  2.48 (0.26), residues: 404
  sheet: -0.37 (0.36), residues: 206
  loop : -0.43 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C  82 
 HIS   0.007   0.001   HIS B 220 
 PHE   0.011   0.001   PHE C 241 
 TYR   0.013   0.001   TYR B 381 
 ARG   0.005   0.000   ARG B  38 

*********************** 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
  197 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 186
  time to evaluate  : 0.957 
Fit side-chains
REVERT: A  168 VAL cc_start: 0.8734 (t) cc_final: 0.8533 (m)
REVERT: A  173 MET cc_start: 0.8621 (mmm) cc_final: 0.8223 (mmm)
REVERT: C  101 MET cc_start: 0.9177 (mtt) cc_final: 0.8947 (mtt)
REVERT: C  179 THR cc_start: 0.8976 (m) cc_final: 0.8523 (p)
REVERT: C  217 MET cc_start: 0.7580 (ttp) cc_final: 0.7202 (ttm)
REVERT: C  334 SER cc_start: 0.8944 (m) cc_final: 0.8692 (m)
REVERT: E   83 MET cc_start: 0.2697 (mtp) cc_final: 0.1969 (mtp)
REVERT: E  117 TYR cc_start: 0.7853 (m-80) cc_final: 0.7533 (m-80)
REVERT: E  120 GLN cc_start: 0.8186 (mp10) cc_final: 0.7985 (mp10)
  outliers start: 11
  outliers final: 5
  residues processed: 190
  average time/residue: 0.2388
  time to fit residues: 62.5128
Evaluate side-chains
  177 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 172
  time to evaluate  : 1.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain B residue  220 HIS
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain E residue   49 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 80 optimal weight:   30.0000
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 54 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 92 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   overall best weight:    2.3386

-------------------------------------------------------------------------------
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**
C 176 GLN
C 230 ASN
D  44 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.152575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.112173 restraints weight = 15744.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 3.98
r_work: 0.3281 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3301
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3301 r_free = 0.3301    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3301 r_free = 0.3301    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3301
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7630  Z= 0.349
  Angle     :  0.605   7.335  10396  Z= 0.320
  Chirality :  0.044   0.164   1207
  Planarity :  0.004   0.045   1336
  Dihedral  :  4.587  34.655   1086
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 14.96 %
    Favored  : 81.40 %
  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:  2.33 (0.25), residues: 398
  sheet: -0.68 (0.33), residues: 245
  loop : -0.36 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP C  82 
 HIS   0.008   0.002   HIS B 220 
 PHE   0.021   0.002   PHE D  61 
 TYR   0.023   0.002   TYR B 381 
 ARG   0.006   0.000   ARG B  38 

*********************** 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
  201 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 174
  time to evaluate  : 0.757 
Fit side-chains
REVERT: A  231 MET cc_start: 0.8049 (ttm) cc_final: 0.7576 (ttm)
REVERT: A  337 ASN cc_start: 0.8654 (m-40) cc_final: 0.8417 (m110)
REVERT: A  343 CYS cc_start: 0.8489 (m) cc_final: 0.8274 (m)
REVERT: B  378 LEU cc_start: 0.8023 (mt) cc_final: 0.7751 (mt)
REVERT: C  217 MET cc_start: 0.7621 (ttp) cc_final: 0.7391 (ttm)
REVERT: D   48 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7815 (m-30)
REVERT: E  117 TYR cc_start: 0.8042 (m-80) cc_final: 0.7768 (m-80)
  outliers start: 27
  outliers final: 19
  residues processed: 187
  average time/residue: 0.1885
  time to fit residues: 47.7021
Evaluate side-chains
  187 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 167
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
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  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   75 GLN
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain E residue   35 ASN
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:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0980
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 77 optimal weight:    9.9990
   chunk 62 optimal weight:    0.3980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3968 r_free = 0.3968 target = 0.157543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.116023 restraints weight = 20222.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 4.57
r_work: 0.3324 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3345
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3345 r_free = 0.3345    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3345 r_free = 0.3345    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3345
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7630  Z= 0.178
  Angle     :  0.544   8.389  10396  Z= 0.284
  Chirality :  0.041   0.172   1207
  Planarity :  0.004   0.044   1336
  Dihedral  :  4.376  30.358   1086
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.98 %
    Favored  : 80.05 %
  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:  1.06 (0.27), residues: 991
  helix:  2.57 (0.26), residues: 398
  sheet: -0.64 (0.34), residues: 221
  loop : -0.45 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP C  82 
 HIS   0.007   0.001   HIS B 220 
 PHE   0.024   0.001   PHE A 232 
 TYR   0.015   0.002   TYR B 381 
 ARG   0.005   0.000   ARG B  38 

*********************** 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
  199 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 177
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A  231 MET cc_start: 0.8085 (ttm) cc_final: 0.7675 (ttm)
REVERT: A  337 ASN cc_start: 0.8712 (m-40) cc_final: 0.8471 (m110)
REVERT: B  252 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7240 (p0)
REVERT: C  217 MET cc_start: 0.7487 (ttp) cc_final: 0.7152 (ttm)
REVERT: C  334 SER cc_start: 0.9026 (m) cc_final: 0.8807 (m)
REVERT: D   48 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7796 (m-30)
REVERT: E   83 MET cc_start: 0.2925 (mtp) cc_final: 0.1825 (mtp)
REVERT: E   90 ASP cc_start: 0.7295 (m-30) cc_final: 0.7070 (m-30)
REVERT: E  117 TYR cc_start: 0.7909 (m-80) cc_final: 0.7689 (m-80)
  outliers start: 22
  outliers final: 14
  residues processed: 185
  average time/residue: 0.2045
  time to fit residues: 50.4242
Evaluate side-chains
  184 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 168
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
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  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  255 LEU
Chi-restraints excluded: chain D residue   48 ASP
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:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 75 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
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 = 0.3921 r_free = 0.3921 target = 0.153089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.111158 restraints weight = 21179.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 4.62
r_work: 0.3260 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3277
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3277 r_free = 0.3277    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3277 r_free = 0.3277    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3277
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7630  Z= 0.328
  Angle     :  0.602   8.156  10396  Z= 0.315
  Chirality :  0.044   0.326   1207
  Planarity :  0.004   0.044   1336
  Dihedral  :  4.564  33.209   1086
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 18.33 %
    Favored  : 77.90 %
  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:  2.39 (0.26), residues: 399
  sheet: -0.84 (0.33), residues: 226
  loop : -0.36 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP C  82 
 HIS   0.008   0.001   HIS B 220 
 PHE   0.018   0.002   PHE A 232 
 TYR   0.025   0.002   TYR B 381 
 ARG   0.006   0.000   ARG B  38 

*********************** 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
  201 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 173
  time to evaluate  : 0.855 
Fit side-chains
REVERT: A  173 MET cc_start: 0.8670 (mmm) cc_final: 0.8234 (mmm)
REVERT: A  231 MET cc_start: 0.8100 (ttm) cc_final: 0.7705 (ttm)
REVERT: A  337 ASN cc_start: 0.8717 (m-40) cc_final: 0.8484 (m110)
REVERT: C  217 MET cc_start: 0.7581 (ttp) cc_final: 0.7209 (ttm)
REVERT: D   48 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7857 (m-30)
REVERT: E   83 MET cc_start: 0.3557 (mtp) cc_final: 0.1923 (mtp)
REVERT: E   90 ASP cc_start: 0.7322 (m-30) cc_final: 0.7070 (m-30)
REVERT: E  117 TYR cc_start: 0.8081 (m-80) cc_final: 0.7592 (m-80)
  outliers start: 28
  outliers final: 21
  residues processed: 187
  average time/residue: 0.1975
  time to fit residues: 49.7457
Evaluate side-chains
  188 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 166
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
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   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   75 GLN
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   48 ASP
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain E residue   35 ASN
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue  125 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 83 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 47 optimal weight:    4.9990
   chunk 37 optimal weight:    0.6980
   chunk 73 optimal weight:    0.0470
   chunk 3 optimal weight:    0.9990
   chunk 51 optimal weight:    8.9990
   chunk 67 optimal weight:    7.9990
   overall best weight:    1.7484

-------------------------------------------------------------------------------
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 = 0.3927 r_free = 0.3927 target = 0.154273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.112326 restraints weight = 20388.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 4.58
r_work: 0.3270 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3289
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3289
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7630  Z= 0.282
  Angle     :  0.598   9.993  10396  Z= 0.310
  Chirality :  0.043   0.247   1207
  Planarity :  0.004   0.044   1336
  Dihedral  :  4.564  32.734   1086
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 18.33 %
    Favored  : 77.76 %
  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:  0.83 (0.27), residues: 991
  helix:  2.32 (0.26), residues: 399
  sheet: -0.89 (0.33), residues: 226
  loop : -0.40 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP C  82 
 HIS   0.008   0.001   HIS B 220 
 PHE   0.017   0.002   PHE A 232 
 TYR   0.022   0.002   TYR B 381 
 ARG   0.007   0.000   ARG B  38 

*********************** 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
  199 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 170
  time to evaluate  : 0.845 
Fit side-chains
REVERT: A  142 TYR cc_start: 0.7349 (m-80) cc_final: 0.7117 (t80)
REVERT: A  173 MET cc_start: 0.8623 (mmm) cc_final: 0.8160 (mmm)
REVERT: A  231 MET cc_start: 0.8227 (ttm) cc_final: 0.7778 (ttm)
REVERT: A  337 ASN cc_start: 0.8710 (m-40) cc_final: 0.8440 (m110)
REVERT: C  101 MET cc_start: 0.9349 (mtt) cc_final: 0.9137 (mtt)
REVERT: C  217 MET cc_start: 0.7566 (ttp) cc_final: 0.7223 (ttm)
REVERT: D   48 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7840 (m-30)
REVERT: E   83 MET cc_start: 0.3571 (mtp) cc_final: 0.1867 (mtp)
REVERT: E   90 ASP cc_start: 0.7404 (m-30) cc_final: 0.7142 (m-30)
REVERT: E  117 TYR cc_start: 0.8052 (m-80) cc_final: 0.7544 (m-80)
  outliers start: 29
  outliers final: 24
  residues processed: 188
  average time/residue: 0.1840
  time to fit residues: 46.7546
Evaluate side-chains
  192 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 167
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
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   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  321 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain C residue   75 GLN
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 D residue   48 ASP
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain E residue   35 ASN
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue   61 THR
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:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 95 optimal weight:    0.0070
   chunk 30 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.6798

-------------------------------------------------------------------------------
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 = 0.3963 r_free = 0.3963 target = 0.156971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.115473 restraints weight = 19830.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 4.51
r_work: 0.3314 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3339
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3339 r_free = 0.3339    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 = 0.3339 r_free = 0.3339    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3339
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   7630  Z= 0.197
  Angle     :  0.562   9.781  10396  Z= 0.291
  Chirality :  0.042   0.257   1207
  Planarity :  0.004   0.044   1336
  Dihedral  :  4.406  29.879   1086
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 19.54 %
    Favored  : 76.95 %
  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:  2.50 (0.26), residues: 398
  sheet: -0.69 (0.35), residues: 218
  loop : -0.46 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP C  82 
 HIS   0.007   0.001   HIS B 220 
 PHE   0.016   0.001   PHE A 232 
 TYR   0.017   0.001   TYR B 381 
 ARG   0.006   0.000   ARG B  38 

*********************** 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
  201 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 175
  time to evaluate  : 0.861 
Fit side-chains
REVERT: A  173 MET cc_start: 0.8620 (mmm) cc_final: 0.8162 (mmm)
REVERT: A  231 MET cc_start: 0.8179 (ttm) cc_final: 0.7759 (ttm)
REVERT: A  337 ASN cc_start: 0.8718 (m-40) cc_final: 0.8472 (m110)
REVERT: C  156 GLN cc_start: 0.7651 (tt0) cc_final: 0.7373 (tt0)
REVERT: D   48 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7829 (m-30)
REVERT: E   83 MET cc_start: 0.3212 (mtp) cc_final: 0.1912 (mtp)
REVERT: E   90 ASP cc_start: 0.7379 (m-30) cc_final: 0.7011 (m-30)
REVERT: E   95 TYR cc_start: 0.7384 (m-80) cc_final: 0.6498 (m-80)
REVERT: E  117 TYR cc_start: 0.7986 (m-80) cc_final: 0.7510 (m-80)
  outliers start: 26
  outliers final: 22
  residues processed: 189
  average time/residue: 0.1947
  time to fit residues: 49.4131
Evaluate side-chains
  193 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 170
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
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  283 LYS
Chi-restraints excluded: chain B residue  321 ASP
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain C residue   75 GLN
Chi-restraints excluded: chain C residue   82 TRP
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain D residue   48 ASP
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:    8.9990
   chunk 47 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 49 optimal weight:    8.9990
   chunk 77 optimal weight:    5.9990
   chunk 93 optimal weight:   10.0000
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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**
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 = 0.3908 r_free = 0.3908 target = 0.152368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.112136 restraints weight = 18168.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 4.23
r_work: 0.3268 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3291
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3291 r_free = 0.3291    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3291 r_free = 0.3291    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3291
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7630  Z= 0.354
  Angle     :  0.631  12.824  10396  Z= 0.331
  Chirality :  0.044   0.272   1207
  Planarity :  0.004   0.043   1336
  Dihedral  :  4.639  33.302   1086
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 19.14 %
    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:  0.89 (0.27), residues: 991
  helix:  2.27 (0.26), residues: 401
  sheet: -0.66 (0.34), residues: 237
  loop : -0.40 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP C  82 
 HIS   0.008   0.001   HIS B 220 
 PHE   0.015   0.002   PHE A 232 
 TYR   0.028   0.002   TYR B 381 
 ARG   0.007   0.001   ARG B  38 

*********************** 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
  200 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 173
  time to evaluate  : 0.877 
Fit side-chains
REVERT: A  231 MET cc_start: 0.8198 (ttm) cc_final: 0.7710 (ttm)
REVERT: A  337 ASN cc_start: 0.8717 (m-40) cc_final: 0.8473 (m110)
REVERT: A  341 TYR cc_start: 0.8811 (m-80) cc_final: 0.7700 (m-80)
REVERT: A  343 CYS cc_start: 0.8650 (m) cc_final: 0.8432 (m)
REVERT: D   48 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7885 (m-30)
REVERT: E   83 MET cc_start: 0.3685 (mtp) cc_final: 0.1831 (mtp)
REVERT: E   90 ASP cc_start: 0.7482 (m-30) cc_final: 0.7215 (m-30)
REVERT: E  117 TYR cc_start: 0.8116 (m-80) cc_final: 0.7741 (m-80)
  outliers start: 27
  outliers final: 22
  residues processed: 191
  average time/residue: 0.1836
  time to fit residues: 47.4264
Evaluate side-chains
  190 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 167
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
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  283 LYS
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain C residue   75 GLN
Chi-restraints excluded: chain C residue   82 TRP
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue   61 THR
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:    0.7980
   chunk 90 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 67 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0030
   chunk 48 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.9594

-------------------------------------------------------------------------------
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 = 0.3955 r_free = 0.3955 target = 0.156811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.116521 restraints weight = 15327.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 4.01
r_work: 0.3329 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3346
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3346 r_free = 0.3346    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3346 r_free = 0.3346    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3346
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   7630  Z= 0.221
  Angle     :  0.587  13.533  10396  Z= 0.304
  Chirality :  0.043   0.305   1207
  Planarity :  0.004   0.044   1336
  Dihedral  :  4.504  30.287   1086
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 20.08 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.27), residues: 991
  helix:  2.50 (0.26), residues: 398
  sheet: -0.71 (0.34), residues: 222
  loop : -0.43 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP C  82 
 HIS   0.007   0.001   HIS B 220 
 PHE   0.015   0.001   PHE A 232 
 TYR   0.019   0.002   TYR B 381 
 ARG   0.007   0.000   ARG B  38 

********************** 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
  203 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 177
  time to evaluate  : 0.833 
Fit side-chains
REVERT: A  173 MET cc_start: 0.8637 (mmm) cc_final: 0.8359 (mmm)
REVERT: A  231 MET cc_start: 0.8186 (ttm) cc_final: 0.7721 (ttm)
REVERT: A  337 ASN cc_start: 0.8718 (m-40) cc_final: 0.8473 (m110)
REVERT: B   23 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8050 (t160)
REVERT: C  156 GLN cc_start: 0.7692 (tt0) cc_final: 0.7397 (tt0)
REVERT: C  334 SER cc_start: 0.8881 (m) cc_final: 0.8628 (m)
REVERT: D   44 HIS cc_start: 0.7250 (m170) cc_final: 0.7037 (m-70)
REVERT: D   48 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7779 (m-30)
REVERT: E   83 MET cc_start: 0.3418 (mtp) cc_final: 0.2087 (mtp)
REVERT: E   90 ASP cc_start: 0.7415 (m-30) cc_final: 0.7102 (m-30)
REVERT: E  117 TYR cc_start: 0.8005 (m-80) cc_final: 0.7532 (m-80)
  outliers start: 26
  outliers final: 21
  residues processed: 192
  average time/residue: 0.1881
  time to fit residues: 48.4809
Evaluate side-chains
  197 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 174
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
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   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  338 ILE
Chi-restraints excluded: chain C residue   75 GLN
Chi-restraints excluded: chain C residue   82 TRP
Chi-restraints excluded: chain C residue  179 THR
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain E residue   49 SER
Chi-restraints excluded: chain E residue   61 THR
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:    0.9990
   chunk 76 optimal weight:    9.9990
   chunk 3 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.3944 r_free = 0.3944 target = 0.155181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.113938 restraints weight = 20108.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 4.59
r_work: 0.3292 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3308
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3308 r_free = 0.3308    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3308 r_free = 0.3308    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3308
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   7630  Z= 0.245
  Angle     :  0.600  12.994  10396  Z= 0.312
  Chirality :  0.043   0.303   1207
  Planarity :  0.004   0.044   1336
  Dihedral  :  4.453  30.177   1086
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 20.22 %
    Favored  : 76.82 %
  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:  2.43 (0.26), residues: 398
  sheet: -0.78 (0.34), residues: 225
  loop : -0.40 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.087   0.003   TRP C 211 
 HIS   0.007   0.001   HIS B 220 
 PHE   0.027   0.001   PHE A 232 
 TYR   0.022   0.002   TYR B 381 
 ARG   0.007   0.000   ARG B  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4843.41 seconds
wall clock time: 86 minutes 5.73 seconds (5165.73 seconds total)