Starting phenix.real_space_refine
on Wed Mar  4 02:47:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ntm_12591/03_2026/7ntm_12591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ntm_12591/03_2026/7ntm_12591.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ntm_12591/03_2026/7ntm_12591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ntm_12591/03_2026/7ntm_12591.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ntm_12591/03_2026/7ntm_12591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ntm_12591/03_2026/7ntm_12591.cif"
  }
  resolution = 2.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.022
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: 5
    Type Number    sf(0)   Gaussians
     Zn      8      6.06       5
     S      56      5.16       5
     C    6556      2.51       5
     N    1760      2.21       5
     O    1956      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10336
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 347, 2582
          Classifications: {'peptide': 347}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333}
    Chain: "B"
      Number of atoms: 2582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 347, 2582
          Classifications: {'peptide': 347}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333}
    Chain: "D"
      Number of atoms: 2582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 347, 2582
          Classifications: {'peptide': 347}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333}
    Chain: "C"
      Number of atoms: 2582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 347, 2582
          Classifications: {'peptide': 347}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    340  SG  CYS A  43      38.557  22.324  26.956  1.00 61.37           S
  ATOM   1159  SG  CYS A 153      39.151  27.004  28.663  1.00 52.86           S
  ATOM    766  SG  CYS A 100      35.384  34.553  48.913  1.00 63.83           S
  ATOM    793  SG  CYS A 103      35.197  35.182  45.606  1.00 58.40           S
  ATOM    851  SG  CYS A 111      33.407  32.254  46.328  1.00 56.85           S
  ATOM   2922  SG  CYS B  43      75.521  22.601  58.159  1.00 59.45           S
  ATOM   3741  SG  CYS B 153      75.027  26.886  56.389  1.00 52.44           S
  ATOM   3348  SG  CYS B 100      78.374  35.166  36.250  1.00 64.62           S
  ATOM   3375  SG  CYS B 103      79.375  34.932  39.507  1.00 56.68           S
  ATOM   3433  SG  CYS B 111      80.669  32.247  38.640  1.00 56.55           S
  ATOM   5504  SG  CYS D  43      75.607  62.548  27.015  1.00 59.46           S
  ATOM   6323  SG  CYS D 153      75.027  58.119  28.612  1.00 51.08           S
  ATOM   5911  SG  CYS D  97      81.654  50.042  47.764  1.00 61.19           S
  ATOM   5930  SG  CYS D 100      78.101  50.395  48.840  1.00 65.41           S
  ATOM   5957  SG  CYS D 103      79.309  49.924  45.663  1.00 57.83           S
  ATOM   6015  SG  CYS D 111      80.737  52.740  46.512  1.00 55.09           S
  ATOM   8086  SG  CYS C  43      38.698  62.436  58.188  1.00 59.60           S
  ATOM   8905  SG  CYS C 153      39.118  58.117  56.393  1.00 51.26           S
  ATOM   8512  SG  CYS C 100      35.947  50.617  36.389  1.00 74.89           S
  ATOM   8539  SG  CYS C 103      34.816  49.669  39.226  1.00 55.83           S
  ATOM   8597  SG  CYS C 111      33.383  52.792  38.450  1.00 55.10           S

  Time building chain proxies: 2.58, per 1000 atoms: 0.25
  Number of scatterers: 10336
  At special positions: 0
  Unit cell: (114.761, 85.6152, 85.6152, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      8     29.99
     S      56     16.00
     O    1956      8.00
     N    1760      7.00
     C    6556      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 277 " - pdb=" SG  CYS B 277 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 277 " - pdb=" SG  CYS C 277 " distance=2.59

  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: 1.01
  Conformation dependent library (CDL) restraints added in 442.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A  43 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A 153 "
        pdb="ZN    ZN A 401 " - pdb=" NE2 HIS A  66 "
      pdb="  ZN A 402 "
        pdb="ZN    ZN A 402 " - pdb=" SG  CYS A 111 "
        pdb="ZN    ZN A 402 " - pdb=" SG  CYS A 100 "
        pdb="ZN    ZN A 402 " - pdb=" SG  CYS A 103 "
      pdb="  ZN B 401 "
        pdb="ZN    ZN B 401 " - pdb=" NE2 HIS B  66 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS B 153 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS B  43 "
      pdb="  ZN B 402 "
        pdb="ZN    ZN B 402 " - pdb=" SG  CYS B 103 "
        pdb="ZN    ZN B 402 " - pdb=" SG  CYS B 100 "
        pdb="ZN    ZN B 402 " - pdb=" SG  CYS B 111 "
      pdb="  ZN C 401 "
        pdb="ZN    ZN C 401 " - pdb=" NE2 HIS C  66 "
        pdb="ZN    ZN C 401 " - pdb=" SG  CYS C  43 "
        pdb="ZN    ZN C 401 " - pdb=" SG  CYS C 153 "
      pdb="  ZN C 402 "
        pdb="ZN    ZN C 402 " - pdb=" SG  CYS C 103 "
        pdb="ZN    ZN C 402 " - pdb=" SG  CYS C 100 "
        pdb="ZN    ZN C 402 " - pdb=" SG  CYS C 111 "
      pdb="  ZN D 401 "
        pdb="ZN    ZN D 401 " - pdb=" NE2 HIS D  66 "
        pdb="ZN    ZN D 401 " - pdb=" SG  CYS D  43 "
        pdb="ZN    ZN D 401 " - pdb=" SG  CYS D 153 "
      pdb="  ZN D 402 "
        pdb="ZN    ZN D 402 " - pdb=" SG  CYS D  97 "
        pdb="ZN    ZN D 402 " - pdb=" SG  CYS D 103 "
        pdb="ZN    ZN D 402 " - pdb=" SG  CYS D 111 "
        pdb="ZN    ZN D 402 " - pdb=" SG  CYS D 100 "
      Number of angles added : 6


  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2424

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 15 sheets defined
      33.1% alpha, 25.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 52
      removed outlier: 3.993A  pdb=" N   LEU A  47 " --> pdb=" O   CYS A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 106
    Processing helix  chain 'A' and resid 107 through 111
    Processing helix  chain 'A' and resid 149 through 152
    Processing helix  chain 'A' and resid 153 through 166
    Processing helix  chain 'A' and resid 180 through 193
      removed outlier: 3.970A  pdb=" N   LEU A 185 " --> pdb=" O   GLY A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 212
    Processing helix  chain 'A' and resid 226 through 235
      removed outlier: 3.580A  pdb=" N   ALA A 230 " --> pdb=" O   ASP A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 258
    Processing helix  chain 'A' and resid 279 through 287
      removed outlier: 3.700A  pdb=" N   GLN A 283 " --> pdb=" O   ASP A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 311
    Processing helix  chain 'A' and resid 324 through 335
    Processing helix  chain 'B' and resid 44 through 52
    Processing helix  chain 'B' and resid 101 through 106
    Processing helix  chain 'B' and resid 107 through 111
      removed outlier: 3.613A  pdb=" N   CYS B 111 " --> pdb=" O   GLU B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 152
    Processing helix  chain 'B' and resid 153 through 164
    Processing helix  chain 'B' and resid 180 through 193
      removed outlier: 3.913A  pdb=" N   LEU B 185 " --> pdb=" O   GLY B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 212
    Processing helix  chain 'B' and resid 226 through 235
      removed outlier: 3.600A  pdb=" N   ALA B 230 " --> pdb=" O   ASP B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 256
    Processing helix  chain 'B' and resid 279 through 287
      removed outlier: 3.852A  pdb=" N   GLN B 283 " --> pdb=" O   ASP B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 311
    Processing helix  chain 'B' and resid 324 through 335
      removed outlier: 4.090A  pdb=" N   GLU B 330 " --> pdb=" O   PRO B 326 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 52
    Processing helix  chain 'D' and resid 107 through 111
      removed outlier: 3.553A  pdb=" N   CYS D 111 " --> pdb=" O   GLU D 108 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 149 through 152
    Processing helix  chain 'D' and resid 153 through 164
    Processing helix  chain 'D' and resid 180 through 193
      removed outlier: 4.061A  pdb=" N   LEU D 185 " --> pdb=" O   GLY D 181 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA D 186 " --> pdb=" O   LEU D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 205 through 213
    Processing helix  chain 'D' and resid 226 through 235
      removed outlier: 3.549A  pdb=" N   ALA D 230 " --> pdb=" O   ASP D 226 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 258
    Processing helix  chain 'D' and resid 279 through 287
      removed outlier: 3.699A  pdb=" N   GLN D 283 " --> pdb=" O   ASP D 279 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 297 through 311
    Processing helix  chain 'D' and resid 324 through 335
      removed outlier: 4.102A  pdb=" N   GLU D 330 " --> pdb=" O   PRO D 326 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 52
      removed outlier: 4.126A  pdb=" N   LEU C  47 " --> pdb=" O   CYS C  43 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 100 through 105
      removed outlier: 3.721A  pdb=" N   LEU C 105 " --> pdb=" O   GLU C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 111
      removed outlier: 3.828A  pdb=" N   CYS C 111 " --> pdb=" O   GLU C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 149 through 152
    Processing helix  chain 'C' and resid 153 through 164
    Processing helix  chain 'C' and resid 180 through 193
      removed outlier: 4.044A  pdb=" N   LEU C 185 " --> pdb=" O   GLY C 181 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 214
    Processing helix  chain 'C' and resid 226 through 235
      removed outlier: 3.636A  pdb=" N   ALA C 230 " --> pdb=" O   ASP C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 248 through 258
      removed outlier: 3.570A  pdb=" N   ILE C 252 " --> pdb=" O   SER C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 279 through 287
      removed outlier: 3.828A  pdb=" N   GLN C 283 " --> pdb=" O   ASP C 279 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 311
    Processing helix  chain 'C' and resid 324 through 335
      removed outlier: 4.081A  pdb=" N   GLU C 330 " --> pdb=" O   PRO C 326 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 24
      removed outlier: 3.637A  pdb=" N   LEU A  62 " --> pdb=" O   PHE A  11 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 132
      removed outlier: 6.542A  pdb=" N   LEU A  33 " --> pdb=" O   MET A  75 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   MET A  75 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   ILE A  35 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   VAL A  73 " --> pdb=" O   ILE A  35 " (cutoff:3.500A)
      removed outlier: 5.424A  pdb=" N   VAL A  37 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   VAL A  71 " --> pdb=" O   VAL A  37 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   GLU A  67 " --> pdb=" O   GLY A  41 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   TYR A  87 " --> pdb=" O   ILE A 139 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 132
      removed outlier: 5.921A  pdb=" N   LYS A 318 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   ASP A 344 " --> pdb=" O   LYS A 318 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   VAL A 320 " --> pdb=" O   ASP A 344 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 220
      removed outlier: 6.814A  pdb=" N   VAL A 197 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 8.084A  pdb=" N   ILE A 219 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   GLY A 199 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   TRP A 172 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   HIS A 240 " --> pdb=" O   THR A 264 " (cutoff:3.500A)
      removed outlier: 7.985A  pdb=" N   VAL A 266 " --> pdb=" O   HIS A 240 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   VAL A 242 " --> pdb=" O   VAL A 266 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   HIS B 240 " --> pdb=" O   THR B 264 " (cutoff:3.500A)
      removed outlier: 8.142A  pdb=" N   VAL B 266 " --> pdb=" O   HIS B 240 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   VAL B 242 " --> pdb=" O   VAL B 266 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   TRP B 172 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   VAL B 197 " --> pdb=" O   VAL B 217 " (cutoff:3.500A)
      removed outlier: 8.172A  pdb=" N   ILE B 219 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   GLY B 199 " --> pdb=" O   ILE B 219 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 24
      removed outlier: 3.525A  pdb=" N   LYS B  21 " --> pdb=" O   GLY B   8 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY B   8 " --> pdb=" O   LYS B  21 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE B  11 " --> pdb=" O   LEU B  62 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LEU B  62 " --> pdb=" O   PHE B  11 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 132
      removed outlier: 6.381A  pdb=" N   ASN B  36 " --> pdb=" O   VAL B  72 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   VAL B  72 " --> pdb=" O   ASN B  36 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   LYS B  38 " --> pdb=" O   GLY B  70 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   GLY B  70 " --> pdb=" O   LYS B  38 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   SER B  40 " --> pdb=" O   GLY B  68 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   GLY B  68 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   TYR B  87 " --> pdb=" O   ILE B 139 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 132
      removed outlier: 4.774A  pdb=" N   TYR B 341 " --> pdb=" O   VAL B  42 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   LYS B 318 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   ASP B 344 " --> pdb=" O   LYS B 318 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   VAL B 320 " --> pdb=" O   ASP B 344 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 96
      removed outlier: 5.445A  pdb=" N   ASP B 115 " --> pdb=" O   ASN B  94 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 24
      removed outlier: 3.506A  pdb=" N   LYS D  21 " --> pdb=" O   GLY D   8 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY D   8 " --> pdb=" O   LYS D  21 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LEU D  62 " --> pdb=" O   PHE D  11 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 128 through 132
      removed outlier: 6.428A  pdb=" N   ASN D  36 " --> pdb=" O   VAL D  72 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   VAL D  72 " --> pdb=" O   ASN D  36 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   LYS D  38 " --> pdb=" O   GLY D  70 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   GLY D  70 " --> pdb=" O   LYS D  38 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   SER D  40 " --> pdb=" O   GLY D  68 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   GLY D  68 " --> pdb=" O   SER D  40 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   TYR D  87 " --> pdb=" O   ILE D 139 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 128 through 132
      removed outlier: 4.791A  pdb=" N   TYR D 341 " --> pdb=" O   VAL D  42 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   VAL D 320 " --> pdb=" O   ASP D 344 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 217 through 219
      removed outlier: 6.794A  pdb=" N   VAL D 197 " --> pdb=" O   VAL D 217 " (cutoff:3.500A)
      removed outlier: 8.202A  pdb=" N   ILE D 219 " --> pdb=" O   VAL D 197 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   GLY D 199 " --> pdb=" O   ILE D 219 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   TRP D 172 " --> pdb=" O   ALA D 239 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   HIS D 240 " --> pdb=" O   ASN D 262 " (cutoff:3.500A)
      removed outlier: 7.728A  pdb=" N   HIS C 240 " --> pdb=" O   ASN C 262 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   TRP C 172 " --> pdb=" O   ALA C 239 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   VAL C 197 " --> pdb=" O   VAL C 217 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ILE C 219 " --> pdb=" O   VAL C 197 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   GLY C 199 " --> pdb=" O   ILE C 219 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 5 through 10
      removed outlier: 3.530A  pdb=" N   GLY C   8 " --> pdb=" O   LYS C  21 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS C  21 " --> pdb=" O   GLY C   8 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 132
      removed outlier: 6.440A  pdb=" N   ASN C  36 " --> pdb=" O   VAL C  72 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   VAL C  72 " --> pdb=" O   ASN C  36 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   LYS C  38 " --> pdb=" O   GLY C  70 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   GLY C  70 " --> pdb=" O   LYS C  38 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   SER C  40 " --> pdb=" O   GLY C  68 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   GLY C  68 " --> pdb=" O   SER C  40 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   TYR C  87 " --> pdb=" O   ILE C 139 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 128 through 132
      removed outlier: 4.817A  pdb=" N   TYR C 341 " --> pdb=" O   VAL C  42 " (cutoff:3.500A)
      removed outlier: 5.943A  pdb=" N   LYS C 318 " --> pdb=" O   VAL C 342 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   ASP C 344 " --> pdb=" O   LYS C 318 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   VAL C 320 " --> pdb=" O   ASP C 344 " (cutoff:3.500A)

    418 hydrogen bonds defined for protein.
    1191 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.59

  Time building geometry restraints manager: 1.40 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1984
        1.33 -     1.45: 2457
        1.45 -     1.57: 6023
        1.57 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 10544
  Sorted by residual:
  bond pdb=" C   TYR C 102 "
       pdb=" N   CYS C 103 "
    ideal  model  delta    sigma   weight residual
    1.334  1.552 -0.218 1.41e-02 5.03e+03 2.40e+02
  bond pdb=" C   CYS C 103 "
       pdb=" N   GLU C 104 "
    ideal  model  delta    sigma   weight residual
    1.335  1.507 -0.172 1.35e-02 5.49e+03 1.62e+02
  bond pdb=" C   ALA C  99 "
       pdb=" N   CYS C 100 "
    ideal  model  delta    sigma   weight residual
    1.328  1.250  0.078 8.50e-03 1.38e+04 8.41e+01
  bond pdb=" C   MET C  98 "
       pdb=" N   ALA C  99 "
    ideal  model  delta    sigma   weight residual
    1.336  1.482 -0.146 1.68e-02 3.54e+03 7.56e+01
  bond pdb=" C   CYS D  97 "
       pdb=" N   MET D  98 "
    ideal  model  delta    sigma   weight residual
    1.333  1.229  0.104 1.39e-02 5.18e+03 5.55e+01
  ... (remaining 10539 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.83: 14222
        4.83 -     9.66: 53
        9.66 -    14.50: 10
       14.50 -    19.33: 3
       19.33 -    24.16: 4
  Bond angle restraints: 14292
  Sorted by residual:
  angle pdb=" O   CYS D  97 "
        pdb=" C   CYS D  97 "
        pdb=" N   MET D  98 "
      ideal   model   delta    sigma   weight residual
     122.36  146.52  -24.16 1.42e+00 4.96e-01 2.89e+02
  angle pdb=" CA  CYS D  97 "
        pdb=" C   CYS D  97 "
        pdb=" N   MET D  98 "
      ideal   model   delta    sigma   weight residual
     118.14   94.95   23.19 1.56e+00 4.11e-01 2.21e+02
  angle pdb=" C   CYS D  97 "
        pdb=" N   MET D  98 "
        pdb=" CA  MET D  98 "
      ideal   model   delta    sigma   weight residual
     122.40  101.89   20.51 1.45e+00 4.76e-01 2.00e+02
  angle pdb=" C   TYR C 102 "
        pdb=" CA  TYR C 102 "
        pdb=" CB  TYR C 102 "
      ideal   model   delta    sigma   weight residual
     110.85  132.40  -21.55 1.70e+00 3.46e-01 1.61e+02
  angle pdb=" O   MET C  98 "
        pdb=" C   MET C  98 "
        pdb=" N   ALA C  99 "
      ideal   model   delta    sigma   weight residual
     122.59  139.43  -16.84 1.33e+00 5.65e-01 1.60e+02
  ... (remaining 14287 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.02: 5310
       16.02 -    32.03: 594
       32.03 -    48.05: 227
       48.05 -    64.06: 45
       64.06 -    80.08: 6
  Dihedral angle restraints: 6182
    sinusoidal: 2318
      harmonic: 3864
  Sorted by residual:
  dihedral pdb=" C   TYR C 102 "
           pdb=" N   TYR C 102 "
           pdb=" CA  TYR C 102 "
           pdb=" CB  TYR C 102 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -153.14   30.54     0      2.50e+00 1.60e-01 1.49e+02
  dihedral pdb=" N   TYR C 102 "
           pdb=" C   TYR C 102 "
           pdb=" CA  TYR C 102 "
           pdb=" CB  TYR C 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  145.00  -22.20     0      2.50e+00 1.60e-01 7.89e+01
  dihedral pdb=" CB  CYS D 277 "
           pdb=" SG  CYS D 277 "
           pdb=" SG  CYS C 277 "
           pdb=" CB  CYS C 277 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -35.08  -50.92     1      1.00e+01 1.00e-02 3.55e+01
  ... (remaining 6179 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.223: 1574
       0.223 -    0.446: 15
       0.446 -    0.670: 2
       0.670 -    0.893: 0
       0.893 -    1.116: 1
  Chirality restraints: 1592
  Sorted by residual:
  chirality pdb=" CA  TYR C 102 "
            pdb=" N   TYR C 102 "
            pdb=" C   TYR C 102 "
            pdb=" CB  TYR C 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.39    1.12 2.00e-01 2.50e+01 3.11e+01
  chirality pdb=" CA  ALA D  99 "
            pdb=" N   ALA D  99 "
            pdb=" C   ALA D  99 "
            pdb=" CB  ALA D  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    3.06   -0.58 2.00e-01 2.50e+01 8.27e+00
  chirality pdb=" CA  ALA C  99 "
            pdb=" N   ALA C  99 "
            pdb=" C   ALA C  99 "
            pdb=" CB  ALA C  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.99    0.50 2.00e-01 2.50e+01 6.20e+00
  ... (remaining 1589 not shown)

  Planarity restraints: 1844
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C  99 "   -0.036 2.00e-02 2.50e+03   6.88e-02 4.73e+01
        pdb=" C   ALA C  99 "    0.119 2.00e-02 2.50e+03
        pdb=" O   ALA C  99 "   -0.040 2.00e-02 2.50e+03
        pdb=" N   CYS C 100 "   -0.043 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D 210 "   -0.021 2.00e-02 2.50e+03   4.31e-02 1.85e+01
        pdb=" C   PHE D 210 "    0.074 2.00e-02 2.50e+03
        pdb=" O   PHE D 210 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ARG D 211 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET C  98 "   -0.015 2.00e-02 2.50e+03   3.76e-02 1.41e+01
        pdb=" C   MET C  98 "    0.065 2.00e-02 2.50e+03
        pdb=" O   MET C  98 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ALA C  99 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 1841 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 57
        2.55 -     3.14: 7304
        3.14 -     3.72: 15370
        3.72 -     4.31: 23133
        4.31 -     4.90: 37616
  Nonbonded interactions: 83480
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU D 108 "
            pdb=" NE2 GLN D 135 "
     model   vdw
     1.962 3.120
  nonbonded pdb=" OE1 GLU B 108 "
            pdb=" NE2 GLN B 135 "
     model   vdw
     1.974 3.120
  nonbonded pdb=" O   LEU B 232 "
            pdb=" O   ASP B 236 "
     model   vdw
     1.986 3.040
  nonbonded pdb=" O   SER C 176 "
            pdb=" CG2 VAL C 245 "
     model   vdw
     2.033 3.460
  nonbonded pdb=" O   SER D 176 "
            pdb=" CG2 VAL D 245 "
     model   vdw
     2.039 3.460
  ... (remaining 83475 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.810
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     12.010
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  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:6.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9375
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      :  0.021   0.921  10571  Z= 1.145
  Angle     :  1.653  34.408  14302  Z= 1.218
  Chirality :  0.105   1.116   1592
  Planarity :  0.003   0.069   1844
  Dihedral  : 15.613  80.079   3752
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 17.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 16.14 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.58 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.56 (0.17), residues: 1380
  helix: -2.61 (0.17), residues: 464
  sheet: -1.10 (0.28), residues: 268
  loop : -2.69 (0.18), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 340 
 TYR   0.009   0.001   TYR A 329 
 PHE   0.010   0.001   PHE D  11 
 TRP   0.007   0.001   TRP B 172 
 HIS   0.003   0.001   HIS D  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.01286 (10544)
  covalent geometry    : angle       1.60913 (14292)
  SS BOND              : bond        0.39369 (    2)
  SS BOND              : angle      18.11518 (    4)
  hydrogen bonds       : bond        0.18446 (  402)
  hydrogen bonds       : angle       7.36218 ( 1191)
  metal coordination   : bond        0.32544 (   25)
  metal coordination   : angle      11.30170 (    6)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 40
  time to evaluate  : 0.380 
Fit side-chains
REVERT: B   27 LYS cc_start: 0.9596 (OUTLIER) cc_final: 0.9024 (mttt)
  outliers start: 19
  outliers final: 5
  residues processed: 58
  average time/residue: 0.6716
  time to fit residues: 41.7484
Evaluate side-chains
  32 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 26
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 GLU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain B residue   27 LYS
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain C residue  182 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  94 ASN
A 244 ASN
B 126 GLN
D 126 GLN
C  78 ASN
C 138 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2071 r_free = 0.2071 target = 0.026467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 21)----------------|
| r_work = 0.1910 r_free = 0.1910 target = 0.022995 restraints weight = 28046.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.1909 rms_B_bonded: 0.94
r_work: 0.1855 rms_B_bonded: 1.25 restraints_weight: 0.5000
r_work: 0.1782 rms_B_bonded: 2.18 restraints_weight: 0.2500
r_work (final): 0.1782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9429
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10571  Z= 0.108
  Angle     :  0.503  10.750  14302  Z= 0.263
  Chirality :  0.044   0.131   1592
  Planarity :  0.003   0.039   1844
  Dihedral  :  5.712  61.261   1491
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 16.23 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.65 (0.20), residues: 1380
  helix: -0.56 (0.24), residues: 464
  sheet: -0.23 (0.31), residues: 264
  loop : -1.85 (0.19), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 257 
 TYR   0.034   0.001   TYR A 258 
 PHE   0.014   0.002   PHE D  11 
 TRP   0.005   0.000   TRP A  92 
 HIS   0.003   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (10544)
  covalent geometry    : angle       0.48260 (14292)
  SS BOND              : bond        0.00295 (    2)
  SS BOND              : angle       1.83587 (    4)
  hydrogen bonds       : bond        0.04027 (  402)
  hydrogen bonds       : angle       5.01097 ( 1191)
  metal coordination   : bond        0.00646 (   25)
  metal coordination   : angle       6.70054 (    6)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 25
  time to evaluate  : 0.404 
Fit side-chains
REVERT: B  182 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8606 (mp)
REVERT: C  182 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8730 (mp)
  outliers start: 28
  outliers final: 6
  residues processed: 53
  average time/residue: 0.5030
  time to fit residues: 29.4053
Evaluate side-chains
  33 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  317 ILE
Chi-restraints excluded: chain B residue    1 SER
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain D residue    1 SER
Chi-restraints excluded: chain D residue   96 SER
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  213 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 80 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   chunk 45 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9990
   chunk 124 optimal weight:    5.9990
   chunk 134 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 110 optimal weight:    0.0070
   chunk 131 optimal weight:    9.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    2.2006

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

Flipped N/Q/H residues before XYZ refinement:
A  66 HIS
A 107 ASN
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 107 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.1945 r_free = 0.1945 target = 0.023581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.1774 r_free = 0.1774 target = 0.020108 restraints weight = 29642.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.1772 rms_B_bonded: 0.93
r_work: 0.1712 rms_B_bonded: 1.24 restraints_weight: 0.5000
r_work: 0.1637 rms_B_bonded: 2.14 restraints_weight: 0.2500
r_work (final): 0.1637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9507
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.353  10571  Z= 0.190
  Angle     :  0.507   9.604  14302  Z= 0.265
  Chirality :  0.045   0.140   1592
  Planarity :  0.003   0.041   1844
  Dihedral  :  4.863  55.041   1482
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.86 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.21), residues: 1380
  helix:  0.22 (0.25), residues: 440
  sheet:  0.14 (0.30), residues: 292
  loop : -1.39 (0.21), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 211 
 TYR   0.023   0.001   TYR A 258 
 PHE   0.016   0.002   PHE D  11 
 TRP   0.005   0.001   TRP A  92 
 HIS   0.003   0.001   HIS B 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (10544)
  covalent geometry    : angle       0.49118 (14292)
  SS BOND              : bond        0.00501 (    2)
  SS BOND              : angle       1.63457 (    4)
  hydrogen bonds       : bond        0.05029 (  402)
  hydrogen bonds       : angle       5.10591 ( 1191)
  metal coordination   : bond        0.07092 (   25)
  metal coordination   : angle       6.10938 (    6)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 25
  time to evaluate  : 0.278 
Fit side-chains
  outliers start: 15
  outliers final: 4
  residues processed: 40
  average time/residue: 0.5517
  time to fit residues: 24.1823
Evaluate side-chains
  29 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 SER
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain D residue   96 SER
Chi-restraints excluded: chain C residue  213 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 127 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 43 optimal weight:    0.3980
   chunk 31 optimal weight:    4.9990
   chunk 134 optimal weight:    7.9990
   chunk 117 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 70 optimal weight:    7.9990
   overall best weight:    2.6186

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

Flipped N/Q/H residues before XYZ refinement:
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.1921 r_free = 0.1921 target = 0.023048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.1748 r_free = 0.1748 target = 0.019602 restraints weight = 30091.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.1746 rms_B_bonded: 0.92
r_work: 0.1687 rms_B_bonded: 1.23 restraints_weight: 0.5000
r_work: 0.1612 rms_B_bonded: 2.12 restraints_weight: 0.2500
r_work (final): 0.1612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9520
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10571  Z= 0.171
  Angle     :  0.506   8.616  14302  Z= 0.264
  Chirality :  0.045   0.137   1592
  Planarity :  0.003   0.041   1844
  Dihedral  :  4.490  52.024   1476
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.95 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.21), residues: 1380
  helix:  0.44 (0.25), residues: 440
  sheet:  0.30 (0.30), residues: 292
  loop : -1.25 (0.21), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 211 
 TYR   0.018   0.001   TYR A 258 
 PHE   0.015   0.002   PHE D  11 
 TRP   0.006   0.001   TRP A  92 
 HIS   0.003   0.001   HIS B 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (10544)
  covalent geometry    : angle       0.49168 (14292)
  SS BOND              : bond        0.00551 (    2)
  SS BOND              : angle       1.61440 (    4)
  hydrogen bonds       : bond        0.05029 (  402)
  hydrogen bonds       : angle       5.11341 ( 1191)
  metal coordination   : bond        0.00590 (   25)
  metal coordination   : angle       5.61486 (    6)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 25
  time to evaluate  : 0.376 
Fit side-chains
  outliers start: 15
  outliers final: 6
  residues processed: 40
  average time/residue: 0.5218
  time to fit residues: 23.0075
Evaluate side-chains
  31 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 25
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 SER
Chi-restraints excluded: chain A residue   97 CYS
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue    1 SER
Chi-restraints excluded: chain D residue    1 SER
Chi-restraints excluded: chain C residue  213 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 82 optimal weight:    0.3980
   chunk 119 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 132 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 113 optimal weight:    8.9990
   chunk 126 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 133 optimal weight:    0.9980
   overall best weight:    2.6786

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

Flipped N/Q/H residues before XYZ refinement:
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.1911 r_free = 0.1911 target = 0.022845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.1738 r_free = 0.1738 target = 0.019410 restraints weight = 29977.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.1736 rms_B_bonded: 0.92
r_work: 0.1676 rms_B_bonded: 1.22 restraints_weight: 0.5000
r_work: 0.1601 rms_B_bonded: 2.10 restraints_weight: 0.2500
r_work (final): 0.1601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9524
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10571  Z= 0.173
  Angle     :  0.502   8.125  14302  Z= 0.262
  Chirality :  0.045   0.138   1592
  Planarity :  0.003   0.041   1844
  Dihedral  :  4.475  49.734   1476
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.32 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.22), residues: 1380
  helix:  0.34 (0.25), residues: 464
  sheet:  0.33 (0.30), residues: 292
  loop : -1.15 (0.22), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 260 
 TYR   0.017   0.001   TYR A 258 
 PHE   0.015   0.002   PHE B 221 
 TRP   0.006   0.001   TRP A  92 
 HIS   0.003   0.001   HIS B 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (10544)
  covalent geometry    : angle       0.48857 (14292)
  SS BOND              : bond        0.00573 (    2)
  SS BOND              : angle       1.58911 (    4)
  hydrogen bonds       : bond        0.05036 (  402)
  hydrogen bonds       : angle       5.10394 ( 1191)
  metal coordination   : bond        0.00509 (   25)
  metal coordination   : angle       5.46389 (    6)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 25
  time to evaluate  : 0.339 
Fit side-chains
  outliers start: 15
  outliers final: 6
  residues processed: 40
  average time/residue: 0.5130
  time to fit residues: 22.5877
Evaluate side-chains
  31 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 25
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 SER
Chi-restraints excluded: chain A residue   97 CYS
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue    1 SER
Chi-restraints excluded: chain D residue    1 SER
Chi-restraints excluded: chain C residue  213 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 128 optimal weight:    7.9990
   chunk 72 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 117 optimal weight:    0.6980
   chunk 64 optimal weight:    6.9990
   chunk 55 optimal weight:    6.9990
   chunk 120 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.1885 r_free = 0.1885 target = 0.022280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.1708 r_free = 0.1708 target = 0.018833 restraints weight = 30471.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.1706 rms_B_bonded: 0.92
r_work: 0.1644 rms_B_bonded: 1.22 restraints_weight: 0.5000
r_work: 0.1569 rms_B_bonded: 2.09 restraints_weight: 0.2500
r_work (final): 0.1569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9540
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  10571  Z= 0.219
  Angle     :  0.529   8.139  14302  Z= 0.276
  Chirality :  0.047   0.139   1592
  Planarity :  0.003   0.040   1844
  Dihedral  :  4.600  49.545   1476
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 17.16 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.22), residues: 1380
  helix:  0.30 (0.25), residues: 464
  sheet:  0.34 (0.30), residues: 292
  loop : -1.18 (0.22), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 260 
 TYR   0.015   0.001   TYR A 258 
 PHE   0.017   0.002   PHE C 221 
 TRP   0.007   0.001   TRP A  92 
 HIS   0.003   0.001   HIS D 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 (10544)
  covalent geometry    : angle       0.51592 (14292)
  SS BOND              : bond        0.00692 (    2)
  SS BOND              : angle       1.84294 (    4)
  hydrogen bonds       : bond        0.05598 (  402)
  hydrogen bonds       : angle       5.22454 ( 1191)
  metal coordination   : bond        0.00549 (   25)
  metal coordination   : angle       5.44364 (    6)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 24
  time to evaluate  : 0.404 
Fit side-chains
  outliers start: 14
  outliers final: 5
  residues processed: 38
  average time/residue: 0.5472
  time to fit residues: 22.9458
Evaluate side-chains
  29 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 CYS
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue    1 SER
Chi-restraints excluded: chain D residue    1 SER
Chi-restraints excluded: chain C residue  213 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 83 optimal weight:    0.7980
   chunk 124 optimal weight:    4.9990
   chunk 101 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 133 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.1934 r_free = 0.1934 target = 0.023342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.1764 r_free = 0.1764 target = 0.019903 restraints weight = 29536.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.1762 rms_B_bonded: 0.91
r_work: 0.1702 rms_B_bonded: 1.22 restraints_weight: 0.5000
r_work: 0.1628 rms_B_bonded: 2.11 restraints_weight: 0.2500
r_work (final): 0.1628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9511
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10571  Z= 0.124
  Angle     :  0.468   8.188  14302  Z= 0.243
  Chirality :  0.044   0.135   1592
  Planarity :  0.003   0.041   1844
  Dihedral  :  4.321  45.207   1476
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 17.54 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.22), residues: 1380
  helix:  0.55 (0.25), residues: 464
  sheet:  0.39 (0.30), residues: 292
  loop : -1.00 (0.23), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 260 
 TYR   0.017   0.001   TYR A 258 
 PHE   0.014   0.002   PHE D  11 
 TRP   0.005   0.001   TRP B  92 
 HIS   0.003   0.001   HIS B 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (10544)
  covalent geometry    : angle       0.45387 (14292)
  SS BOND              : bond        0.00360 (    2)
  SS BOND              : angle       1.41352 (    4)
  hydrogen bonds       : bond        0.04301 (  402)
  hydrogen bonds       : angle       4.91675 ( 1191)
  metal coordination   : bond        0.00461 (   25)
  metal coordination   : angle       5.46332 (    6)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 25
  time to evaluate  : 0.410 
Fit side-chains
  outliers start: 12
  outliers final: 8
  residues processed: 37
  average time/residue: 0.4852
  time to fit residues: 19.8114
Evaluate side-chains
  33 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 SER
Chi-restraints excluded: chain A residue   97 CYS
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue    1 SER
Chi-restraints excluded: chain D residue    1 SER
Chi-restraints excluded: chain C residue  120 THR
Chi-restraints excluded: chain C residue  213 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 116 optimal weight:    0.9990
   chunk 127 optimal weight:    4.9990
   chunk 113 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 88 optimal weight:    8.9990
   chunk 133 optimal weight:    0.6980
   chunk 92 optimal weight:    9.9990
   chunk 58 optimal weight:    4.9990
   chunk 63 optimal weight:    8.9990
   chunk 125 optimal weight:    1.9990
   chunk 84 optimal weight:    6.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.1907 r_free = 0.1907 target = 0.022776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.1734 r_free = 0.1734 target = 0.019335 restraints weight = 29895.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.1732 rms_B_bonded: 0.91
r_work: 0.1672 rms_B_bonded: 1.22 restraints_weight: 0.5000
r_work: 0.1596 rms_B_bonded: 2.09 restraints_weight: 0.2500
r_work (final): 0.1596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9525
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  10571  Z= 0.165
  Angle     :  0.493   8.455  14302  Z= 0.256
  Chirality :  0.045   0.138   1592
  Planarity :  0.003   0.040   1844
  Dihedral  :  4.381  43.793   1476
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 17.91 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.22), residues: 1380
  helix:  0.52 (0.25), residues: 464
  sheet:  0.41 (0.30), residues: 292
  loop : -0.99 (0.23), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 260 
 TYR   0.015   0.001   TYR A 258 
 PHE   0.015   0.002   PHE B 221 
 TRP   0.006   0.001   TRP B  92 
 HIS   0.003   0.001   HIS B 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (10544)
  covalent geometry    : angle       0.47907 (14292)
  SS BOND              : bond        0.00524 (    2)
  SS BOND              : angle       1.56253 (    4)
  hydrogen bonds       : bond        0.04894 (  402)
  hydrogen bonds       : angle       5.04078 ( 1191)
  metal coordination   : bond        0.00477 (   25)
  metal coordination   : angle       5.60355 (    6)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.451 
Fit side-chains
  outliers start: 8
  outliers final: 7
  residues processed: 33
  average time/residue: 0.5539
  time to fit residues: 20.1166
Evaluate side-chains
  32 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 SER
Chi-restraints excluded: chain A residue   97 CYS
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue    1 SER
Chi-restraints excluded: chain C residue  120 THR
Chi-restraints excluded: chain C residue  213 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 127 optimal weight:    3.9990
   chunk 134 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 74 optimal weight:    8.9990
   chunk 117 optimal weight:    2.9990
   chunk 129 optimal weight:    7.9990
   chunk 120 optimal weight:    0.7980
   chunk 91 optimal weight:    4.9990
   chunk 105 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    1.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.1957 r_free = 0.1957 target = 0.023859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.1790 r_free = 0.1790 target = 0.020413 restraints weight = 29387.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.1788 rms_B_bonded: 0.92
r_work: 0.1729 rms_B_bonded: 1.22 restraints_weight: 0.5000
r_work: 0.1655 rms_B_bonded: 2.12 restraints_weight: 0.2500
r_work (final): 0.1655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9496
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10571  Z= 0.106
  Angle     :  0.452   8.535  14302  Z= 0.233
  Chirality :  0.044   0.135   1592
  Planarity :  0.003   0.041   1844
  Dihedral  :  4.121  38.844   1476
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 18.28 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.22), residues: 1380
  helix:  0.72 (0.25), residues: 464
  sheet:  0.44 (0.30), residues: 292
  loop : -0.82 (0.23), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 260 
 TYR   0.017   0.001   TYR A 258 
 PHE   0.013   0.001   PHE A  11 
 TRP   0.004   0.001   TRP B  92 
 HIS   0.003   0.000   HIS B 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (10544)
  covalent geometry    : angle       0.43716 (14292)
  SS BOND              : bond        0.00282 (    2)
  SS BOND              : angle       1.27734 (    4)
  hydrogen bonds       : bond        0.03928 (  402)
  hydrogen bonds       : angle       4.78583 ( 1191)
  metal coordination   : bond        0.00436 (   25)
  metal coordination   : angle       5.60273 (    6)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.487 
Fit side-chains
  outliers start: 7
  outliers final: 5
  residues processed: 32
  average time/residue: 0.5804
  time to fit residues: 20.4244
Evaluate side-chains
  30 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 CYS
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue    1 SER
Chi-restraints excluded: chain C residue  120 THR
Chi-restraints excluded: chain C residue  213 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 100 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 102 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 115 optimal weight:   10.0000
   chunk 48 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.9388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.1934 r_free = 0.1934 target = 0.023358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.1765 r_free = 0.1765 target = 0.019916 restraints weight = 29427.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.1763 rms_B_bonded: 0.91
r_work: 0.1703 rms_B_bonded: 1.22 restraints_weight: 0.5000
r_work: 0.1629 rms_B_bonded: 2.10 restraints_weight: 0.2500
r_work (final): 0.1629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9508
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10571  Z= 0.134
  Angle     :  0.474   9.171  14302  Z= 0.244
  Chirality :  0.044   0.138   1592
  Planarity :  0.003   0.040   1844
  Dihedral  :  4.168  38.572   1476
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 18.56 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.22), residues: 1380
  helix:  0.70 (0.25), residues: 464
  sheet:  0.45 (0.30), residues: 292
  loop : -0.81 (0.23), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 260 
 TYR   0.015   0.001   TYR A 258 
 PHE   0.015   0.002   PHE D  11 
 TRP   0.005   0.001   TRP B  92 
 HIS   0.003   0.001   HIS D 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (10544)
  covalent geometry    : angle       0.45742 (14292)
  SS BOND              : bond        0.00396 (    2)
  SS BOND              : angle       1.41948 (    4)
  hydrogen bonds       : bond        0.04404 (  402)
  hydrogen bonds       : angle       4.88536 ( 1191)
  metal coordination   : bond        0.00441 (   25)
  metal coordination   : angle       6.02477 (    6)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 25
  time to evaluate  : 0.347 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 31
  average time/residue: 0.5307
  time to fit residues: 18.0947
Evaluate side-chains
  30 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 SER
Chi-restraints excluded: chain A residue   97 CYS
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain C residue  120 THR
Chi-restraints excluded: chain C residue  213 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 97 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   chunk 46 optimal weight:    9.9990
   chunk 32 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 121 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    1.7586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.1941 r_free = 0.1941 target = 0.023504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.1772 r_free = 0.1772 target = 0.020050 restraints weight = 29687.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.1770 rms_B_bonded: 0.92
r_work: 0.1710 rms_B_bonded: 1.23 restraints_weight: 0.5000
r_work: 0.1635 rms_B_bonded: 2.11 restraints_weight: 0.2500
r_work (final): 0.1635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9505
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10571  Z= 0.125
  Angle     :  0.468   8.976  14302  Z= 0.241
  Chirality :  0.044   0.138   1592
  Planarity :  0.003   0.040   1844
  Dihedral  :  4.137  37.685   1476
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 18.38 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.22), residues: 1380
  helix:  0.72 (0.25), residues: 464
  sheet:  0.45 (0.30), residues: 292
  loop : -0.78 (0.23), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 260 
 TYR   0.016   0.001   TYR A 258 
 PHE   0.014   0.002   PHE D  11 
 TRP   0.005   0.001   TRP A  92 
 HIS   0.003   0.001   HIS B 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10544)
  covalent geometry    : angle       0.45208 (14292)
  SS BOND              : bond        0.00364 (    2)
  SS BOND              : angle       1.37462 (    4)
  hydrogen bonds       : bond        0.04261 (  402)
  hydrogen bonds       : angle       4.85670 ( 1191)
  metal coordination   : bond        0.00440 (   25)
  metal coordination   : angle       5.88390 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2072.43 seconds
wall clock time: 36 minutes 18.49 seconds (2178.49 seconds total)