Starting phenix.real_space_refine
on Sat Jun  7 12:14:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iz4_35833/06_2025/8iz4_35833.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iz4_35833/06_2025/8iz4_35833.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iz4_35833/06_2025/8iz4_35833.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iz4_35833/06_2025/8iz4_35833.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iz4_35833/06_2025/8iz4_35833.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iz4_35833/06_2025/8iz4_35833.cif"
  }
  resolution = 2.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.011
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
     P       1      5.49       5
     S      64      5.16       5
     C    5655      2.51       5
     N    1486      2.21       5
     O    1651      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8857
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1747
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1747
          Classifications: {'peptide': 223}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 2, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 42
          Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "B"
      Number of atoms: 2622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 342, 2622
          Classifications: {'peptide': 342}
          Link IDs: {'PTRANS': 5, 'TRANS': 336}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "E"
      Number of atoms: 1779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1779
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2210
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 4, 'TRANS': 276}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 81
          Unresolved non-hydrogen dihedrals: 73
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "R"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 63
          Unusual residues: {'CLR': 1, 'TJR': 1}
          Inner-chain residues flagged as termini: ['pdbres="SER R 602 "']
          Classifications: {'peptide': 1, 'undetermined': 2}
          Modifications used: {'COO': 1}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 5.84, per 1000 atoms: 0.66
  Number of scatterers: 8857
  At special positions: 0
  Unit cell: (110.21, 127.33, 110.21, 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)
     S      64     16.00
     P       1     15.00
     O    1651      8.00
     N    1486      7.00
     C    5655      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 127 " - pdb=" SG  CYS R 204 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.56
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2122

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 13 sheets defined
      39.0% alpha, 23.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.545A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.020A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.706A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 24
      removed outlier: 3.576A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.537A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 52 through 81
    Processing helix  chain 'R' and resid 87 through 116
      Proline residue:  R 108  - end of helix
    Processing helix  chain 'R' and resid 123 through 157
      removed outlier: 3.564A  pdb=" N   TYR R 135 " --> pdb=" O   GLY R 131 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 168 through 197
      removed outlier: 4.077A  pdb=" N   GLY R 197 " --> pdb=" O   THR R 193 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 213 through 252
    Processing helix  chain 'R' and resid 259 through 295
      Proline residue:  R 281  - end of helix
      removed outlier: 3.967A  pdb=" N   PHE R 287 " --> pdb=" O   HIS R 283 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   ILE R 288 " --> pdb=" O   ALA R 284 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 298 through 331
      removed outlier: 3.591A  pdb=" N   GLU R 303 " --> pdb=" O   CYS R 299 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   VAL R 314 " --> pdb=" O   GLU R 310 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ASN R 319 " --> pdb=" O   LEU R 315 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   SER R 320 " --> pdb=" O   SER R 316 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   CYS R 321 " --> pdb=" O   SER R 317 " (cutoff:3.500A)
      Proline residue:  R 324  - end of helix
    Processing helix  chain 'R' and resid 331 through 340
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.738A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.576A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.543A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 5.972A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.268A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.688A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.791A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.519A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.752A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (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 11 through 12
      removed outlier: 6.852A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12
      removed outlier: 4.288A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.596A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)

    488 hydrogen bonds defined for protein.
    1365 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: 2.59

  Time building geometry restraints manager: 2.93 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1423
        1.31 -     1.43: 2505
        1.43 -     1.56: 5015
        1.56 -     1.68: 1
        1.68 -     1.81: 93
  Bond restraints: 9037
  Sorted by residual:
  bond pdb=" CAK TJR R 601 "
       pdb=" OAJ TJR R 601 "
    ideal  model  delta    sigma   weight residual
    1.344  1.398 -0.054 2.00e-02 2.50e+03 7.32e+00
  bond pdb=" CAI TJR R 601 "
       pdb=" OAJ TJR R 601 "
    ideal  model  delta    sigma   weight residual
    1.446  1.398  0.048 2.00e-02 2.50e+03 5.69e+00
  bond pdb=" OAD TJR R 601 "
       pdb=" PAC TJR R 601 "
    ideal  model  delta    sigma   weight residual
    1.542  1.510  0.032 2.00e-02 2.50e+03 2.56e+00
  bond pdb=" OAF TJR R 601 "
       pdb=" PAC TJR R 601 "
    ideal  model  delta    sigma   weight residual
    1.679  1.647  0.032 2.00e-02 2.50e+03 2.53e+00
  bond pdb=" CAK TJR R 601 "
       pdb=" OAE TJR R 601 "
    ideal  model  delta    sigma   weight residual
    1.213  1.184  0.029 2.00e-02 2.50e+03 2.07e+00
  ... (remaining 9032 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 12159
        1.63 -     3.25: 75
        3.25 -     4.88: 8
        4.88 -     6.51: 3
        6.51 -     8.14: 1
  Bond angle restraints: 12246
  Sorted by residual:
  angle pdb=" CAI TJR R 601 "
        pdb=" OAJ TJR R 601 "
        pdb=" CAK TJR R 601 "
      ideal   model   delta    sigma   weight residual
     121.91  113.77    8.14 3.00e+00 1.11e-01 7.36e+00
  angle pdb=" C   ARG E 191 "
        pdb=" N   MET E 192 "
        pdb=" CA  MET E 192 "
      ideal   model   delta    sigma   weight residual
     121.54  125.59   -4.05 1.91e+00 2.74e-01 4.50e+00
  angle pdb=" OAD TJR R 601 "
        pdb=" PAC TJR R 601 "
        pdb=" OAF TJR R 601 "
      ideal   model   delta    sigma   weight residual
     104.39  109.76   -5.37 3.00e+00 1.11e-01 3.20e+00
  angle pdb=" CAG TJR R 601 "
        pdb=" CAH TJR R 601 "
        pdb=" OBC TJR R 601 "
      ideal   model   delta    sigma   weight residual
     112.70  107.86    4.84 3.00e+00 1.11e-01 2.61e+00
  angle pdb=" C   ASP B 333 "
        pdb=" N   SER B 334 "
        pdb=" CA  SER B 334 "
      ideal   model   delta    sigma   weight residual
     123.93  126.33   -2.40 1.54e+00 4.22e-01 2.43e+00
  ... (remaining 12241 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.96: 5180
       16.96 -    33.91: 163
       33.91 -    50.87: 37
       50.87 -    67.83: 12
       67.83 -    84.78: 2
  Dihedral angle restraints: 5394
    sinusoidal: 2102
      harmonic: 3292
  Sorted by residual:
  dihedral pdb=" CA  GLN B  75 "
           pdb=" C   GLN B  75 "
           pdb=" N   ASP B  76 "
           pdb=" CA  ASP B  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.76   21.24     0      5.00e+00 4.00e-02 1.80e+01
  dihedral pdb=" CA  ARG E 191 "
           pdb=" C   ARG E 191 "
           pdb=" N   MET E 192 "
           pdb=" CA  MET E 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.24   18.76     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  PHE E  32 "
           pdb=" C   PHE E  32 "
           pdb=" N   GLY E  33 "
           pdb=" CA  GLY E  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.01   17.99     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 5391 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 841
       0.026 -    0.051: 337
       0.051 -    0.076: 146
       0.076 -    0.102: 51
       0.102 -    0.127: 33
  Chirality restraints: 1408
  Sorted by residual:
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  THR B 164 "
            pdb=" N   THR B 164 "
            pdb=" C   THR B 164 "
            pdb=" CB  THR B 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 3.99e-01
  chirality pdb=" CA  ILE B 338 "
            pdb=" N   ILE B 338 "
            pdb=" C   ILE B 338 "
            pdb=" CB  ILE B 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 1405 not shown)

  Planarity restraints: 1534
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.028 5.00e-02 4.00e+02   4.31e-02 2.97e+00
        pdb=" N   PRO B 236 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE R 255 "   -0.019 5.00e-02 4.00e+02   2.86e-02 1.31e+00
        pdb=" N   PRO R 256 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO R 256 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO R 256 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "    0.017 5.00e-02 4.00e+02   2.62e-02 1.10e+00
        pdb=" N   PRO B 194 "   -0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1531 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1763
        2.78 -     3.31: 8318
        3.31 -     3.84: 14728
        3.84 -     4.37: 18077
        4.37 -     4.90: 31569
  Nonbonded interactions: 74455
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR E 175 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OD1 ASP A 341 "
            pdb=" OH  TYR R 261 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASP B 154 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   LYS C  20 "
            pdb=" ND2 ASN C  24 "
     model   vdw
     2.286 3.120
  ... (remaining 74450 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.470
  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:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.840
  Find NCS groups from input model:        0.080
  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:13.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
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      :  0.002   0.090   9041  Z= 0.136
  Angle     :  0.389   8.137  12252  Z= 0.202
  Chirality :  0.038   0.127   1408
  Planarity :  0.003   0.043   1534
  Dihedral  :  9.423  84.784   3263
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  3.04 %
    Favored  : 95.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.24), residues: 1118
  helix:  1.65 (0.25), residues: 413
  sheet:  0.69 (0.29), residues: 281
  loop : -0.09 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 339 
 HIS   0.002   0.001   HIS B  91 
 PHE   0.009   0.001   PHE B 151 
 TYR   0.010   0.001   TYR E 190 
 ARG   0.002   0.000   ARG R 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24293 (  483)
  hydrogen bonds       : angle       7.04319 ( 1365)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       0.70797 (    6)
  covalent geometry    : bond        0.00211 ( 9037)
  covalent geometry    : angle       0.38853 (12246)
  Misc. bond           : bond        0.09011 (    1)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 276
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8766 (mptm) cc_final: 0.7991 (mtmm)
REVERT: A   21 ARG cc_start: 0.8264 (ttm110) cc_final: 0.8021 (ttm110)
REVERT: A  186 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7872 (mm-30)
REVERT: A  208 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7707 (ttp80)
REVERT: A  251 ASP cc_start: 0.7961 (t70) cc_final: 0.7654 (OUTLIER)
REVERT: A  302 TYR cc_start: 0.8659 (t80) cc_final: 0.8423 (t80)
REVERT: A  331 ASN cc_start: 0.8857 (m-40) cc_final: 0.8531 (m-40)
REVERT: B   19 ARG cc_start: 0.8241 (ttp80) cc_final: 0.7995 (ttp80)
REVERT: B   46 ARG cc_start: 0.8142 (mtp-110) cc_final: 0.7846 (mtp85)
REVERT: B  172 GLU cc_start: 0.7598 (tp30) cc_final: 0.7189 (tp30)
REVERT: B  212 ASP cc_start: 0.8178 (t0) cc_final: 0.7856 (t0)
REVERT: B  219 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7918 (mtp180)
REVERT: B  259 GLN cc_start: 0.8659 (pt0) cc_final: 0.7949 (pt0)
REVERT: B  301 LYS cc_start: 0.8981 (mtpp) cc_final: 0.8670 (mtpt)
REVERT: C   17 GLU cc_start: 0.8560 (tp30) cc_final: 0.8227 (tp30)
REVERT: C   58 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7773 (mp0)
REVERT: E   18 ARG cc_start: 0.8002 (tpt-90) cc_final: 0.7691 (tpt-90)
REVERT: E   23 SER cc_start: 0.8537 (m) cc_final: 0.8300 (t)
REVERT: E   43 LYS cc_start: 0.8425 (mmtm) cc_final: 0.8141 (mmmm)
REVERT: E   46 GLU cc_start: 0.8152 (tt0) cc_final: 0.7703 (tm-30)
REVERT: E   78 THR cc_start: 0.8318 (m) cc_final: 0.8071 (p)
REVERT: R  203 MET cc_start: 0.8409 (pmm) cc_final: 0.8142 (pp-130)
  outliers start: 11
  outliers final: 10
  residues processed: 283
  average time/residue: 1.0665
  time to fit residues: 323.7340
Evaluate side-chains
  209 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 200
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  296 TYR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  142 ILE
Chi-restraints excluded: chain R residue  235 ILE
Chi-restraints excluded: chain R residue  255 PHE
Chi-restraints excluded: chain R residue  296 VAL
Chi-restraints excluded: chain R residue  300 TYR
Chi-restraints excluded: chain R residue  602 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0970
   chunk 87 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 101 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 255 ASN
B  75 GLN
E 171 ASN
E 179 GLN
E 186 GLN
R  83 HIS
** R  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.156519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.106279 restraints weight = 10971.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 2.24
r_work: 0.3014 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9041  Z= 0.139
  Angle     :  0.527   7.432  12252  Z= 0.285
  Chirality :  0.042   0.142   1408
  Planarity :  0.004   0.042   1534
  Dihedral  :  6.704  84.659   1331
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 12.91 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.89 (0.25), residues: 1118
  helix:  2.82 (0.24), residues: 403
  sheet:  0.79 (0.30), residues: 280
  loop :  0.13 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.011   0.001   PHE R 227 
 TYR   0.015   0.001   TYR E 190 
 ARG   0.004   0.000   ARG E 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04983 (  483)
  hydrogen bonds       : angle       4.67493 ( 1365)
  SS BOND              : bond        0.00399 (    3)
  SS BOND              : angle       0.98113 (    6)
  covalent geometry    : bond        0.00295 ( 9037)
  covalent geometry    : angle       0.52655 (12246)
  Misc. bond           : bond        0.00008 (    1)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 209
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8768 (mptm) cc_final: 0.7998 (mtmm)
REVERT: A   29 LYS cc_start: 0.8331 (tttt) cc_final: 0.7914 (tttp)
REVERT: A  208 ARG cc_start: 0.8036 (ttm-80) cc_final: 0.7798 (ttp80)
REVERT: A  302 TYR cc_start: 0.8597 (t80) cc_final: 0.8316 (t80)
REVERT: A  318 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7475 (pt0)
REVERT: B   17 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8361 (tp40)
REVERT: B   19 ARG cc_start: 0.8394 (ttp80) cc_final: 0.8155 (ttp80)
REVERT: B   46 ARG cc_start: 0.8386 (mtp-110) cc_final: 0.8081 (mtp85)
REVERT: B   59 TYR cc_start: 0.9065 (m-80) cc_final: 0.8589 (m-80)
REVERT: B  130 GLU cc_start: 0.8931 (mp0) cc_final: 0.8724 (mp0)
REVERT: B  172 GLU cc_start: 0.7975 (tp30) cc_final: 0.7602 (tp30)
REVERT: B  215 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7701 (mm-30)
REVERT: B  264 TYR cc_start: 0.9081 (m-80) cc_final: 0.8790 (m-80)
REVERT: B  301 LYS cc_start: 0.8895 (mtpp) cc_final: 0.8606 (mtpt)
REVERT: C   21 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7281 (ptm)
REVERT: C   58 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7984 (mp0)
REVERT: E   23 SER cc_start: 0.8502 (m) cc_final: 0.8249 (t)
REVERT: E   46 GLU cc_start: 0.8589 (tt0) cc_final: 0.8121 (tm-30)
REVERT: E   78 THR cc_start: 0.8090 (m) cc_final: 0.7787 (p)
REVERT: E   85 SER cc_start: 0.8753 (m) cc_final: 0.8356 (t)
REVERT: R   69 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8522 (tm)
REVERT: R   73 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8824 (pp)
REVERT: R  111 ILE cc_start: 0.7901 (pp) cc_final: 0.7527 (tp)
REVERT: R  304 ILE cc_start: 0.8592 (tp) cc_final: 0.8324 (tp)
REVERT: R  308 THR cc_start: 0.8899 (m) cc_final: 0.8664 (p)
  outliers start: 50
  outliers final: 23
  residues processed: 235
  average time/residue: 1.0758
  time to fit residues: 271.2891
Evaluate side-chains
  223 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 195
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain R residue   58 THR
Chi-restraints excluded: chain R residue   69 LEU
Chi-restraints excluded: chain R residue   73 ILE
Chi-restraints excluded: chain R residue  136 MET
Chi-restraints excluded: chain R residue  171 SER
Chi-restraints excluded: chain R residue  211 HIS
Chi-restraints excluded: chain R residue  235 ILE
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  255 PHE
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  280 VAL
Chi-restraints excluded: chain R residue  296 VAL
Chi-restraints excluded: chain R residue  300 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 105 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 101 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 79 optimal weight:    7.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 186 GLN
** R  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 114 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.156444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.106338 restraints weight = 11145.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 2.26
r_work: 0.2964 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   9041  Z= 0.131
  Angle     :  0.500   7.319  12252  Z= 0.270
  Chirality :  0.041   0.137   1408
  Planarity :  0.003   0.042   1534
  Dihedral  :  6.082  82.349   1324
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 15.11 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.96 (0.25), residues: 1118
  helix:  3.04 (0.23), residues: 403
  sheet:  0.58 (0.29), residues: 287
  loop :  0.17 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 114 
 PHE   0.011   0.001   PHE B 151 
 TYR   0.015   0.001   TYR R 113 
 ARG   0.003   0.000   ARG R 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04391 (  483)
  hydrogen bonds       : angle       4.40325 ( 1365)
  SS BOND              : bond        0.00338 (    3)
  SS BOND              : angle       0.73336 (    6)
  covalent geometry    : bond        0.00284 ( 9037)
  covalent geometry    : angle       0.49961 (12246)
  Misc. bond           : bond        0.00014 (    1)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 206
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8737 (mptm) cc_final: 0.7973 (mtmm)
REVERT: A   29 LYS cc_start: 0.8312 (tttt) cc_final: 0.7904 (tttp)
REVERT: A  208 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7795 (ttp80)
REVERT: A  273 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7842 (mp)
REVERT: A  296 TYR cc_start: 0.8602 (t80) cc_final: 0.8271 (t80)
REVERT: A  302 TYR cc_start: 0.8628 (t80) cc_final: 0.8341 (t80)
REVERT: A  354 PHE cc_start: 0.8465 (t80) cc_final: 0.8222 (t80)
REVERT: B   19 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8192 (ttp80)
REVERT: B   46 ARG cc_start: 0.8403 (mtp-110) cc_final: 0.8087 (mtp85)
REVERT: B  130 GLU cc_start: 0.8921 (mp0) cc_final: 0.8550 (mp0)
REVERT: B  172 GLU cc_start: 0.8048 (tp30) cc_final: 0.7738 (tp30)
REVERT: B  212 ASP cc_start: 0.8246 (t0) cc_final: 0.8003 (t0)
REVERT: B  215 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8013 (mm-30)
REVERT: B  264 TYR cc_start: 0.9106 (m-80) cc_final: 0.8838 (m-80)
REVERT: B  301 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8558 (mtpt)
REVERT: C   21 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7418 (ptm)
REVERT: C   58 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7974 (mp0)
REVERT: E   23 SER cc_start: 0.8505 (m) cc_final: 0.8231 (t)
REVERT: E   46 GLU cc_start: 0.8639 (tt0) cc_final: 0.8168 (tm-30)
REVERT: E   78 THR cc_start: 0.8055 (m) cc_final: 0.7714 (p)
REVERT: E   85 SER cc_start: 0.8825 (m) cc_final: 0.8370 (t)
REVERT: R  177 ILE cc_start: 0.7941 (mt) cc_final: 0.7733 (pt)
REVERT: R  206 HIS cc_start: 0.8143 (p-80) cc_final: 0.7728 (p-80)
REVERT: R  300 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.7943 (p90)
  outliers start: 54
  outliers final: 25
  residues processed: 230
  average time/residue: 1.1029
  time to fit residues: 271.4462
Evaluate side-chains
  221 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 193
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue   17 SER
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain R residue   58 THR
Chi-restraints excluded: chain R residue   73 ILE
Chi-restraints excluded: chain R residue  211 HIS
Chi-restraints excluded: chain R residue  235 ILE
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  255 PHE
Chi-restraints excluded: chain R residue  274 ILE
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  296 VAL
Chi-restraints excluded: chain R residue  300 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 84 optimal weight:    0.4980
   chunk 69 optimal weight:    2.9990
   chunk 104 optimal weight:    0.7980
   chunk 94 optimal weight:    4.9990
   chunk 101 optimal weight:    3.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 186 GLN
** R  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 114 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.153887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.103859 restraints weight = 11082.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.21
r_work: 0.3014 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9041  Z= 0.180
  Angle     :  0.529   8.260  12252  Z= 0.284
  Chirality :  0.042   0.153   1408
  Planarity :  0.003   0.043   1534
  Dihedral  :  6.147  86.329   1324
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 16.79 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.80 (0.25), residues: 1118
  helix:  2.87 (0.24), residues: 403
  sheet:  0.39 (0.29), residues: 284
  loop :  0.20 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.003   0.001   HIS C  44 
 PHE   0.012   0.001   PHE R 186 
 TYR   0.015   0.001   TYR R  92 
 ARG   0.003   0.000   ARG B 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04276 (  483)
  hydrogen bonds       : angle       4.38860 ( 1365)
  SS BOND              : bond        0.00348 (    3)
  SS BOND              : angle       1.16432 (    6)
  covalent geometry    : bond        0.00417 ( 9037)
  covalent geometry    : angle       0.52801 (12246)
  Misc. bond           : bond        0.00006 (    1)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 192
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8809 (mptm) cc_final: 0.8042 (mtmm)
REVERT: A   29 LYS cc_start: 0.8392 (tttt) cc_final: 0.7909 (tttp)
REVERT: A   32 ARG cc_start: 0.7523 (mtm110) cc_final: 0.7261 (mtm110)
REVERT: A  198 MET cc_start: 0.9054 (ttp) cc_final: 0.8769 (ttm)
REVERT: A  208 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7917 (ttp80)
REVERT: A  273 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7921 (mp)
REVERT: A  296 TYR cc_start: 0.8507 (t80) cc_final: 0.8177 (t80)
REVERT: A  302 TYR cc_start: 0.8725 (t80) cc_final: 0.8452 (t80)
REVERT: A  354 PHE cc_start: 0.8531 (t80) cc_final: 0.8277 (t80)
REVERT: B   19 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8216 (ttp80)
REVERT: B   42 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7824 (tpt-90)
REVERT: B   46 ARG cc_start: 0.8371 (mtp-110) cc_final: 0.8072 (mtp85)
REVERT: B   59 TYR cc_start: 0.9032 (m-80) cc_final: 0.8679 (m-80)
REVERT: B  130 GLU cc_start: 0.8921 (mp0) cc_final: 0.8605 (mp0)
REVERT: B  172 GLU cc_start: 0.8073 (tp30) cc_final: 0.7793 (tp30)
REVERT: B  212 ASP cc_start: 0.8288 (t0) cc_final: 0.8001 (t0)
REVERT: B  264 TYR cc_start: 0.9119 (m-80) cc_final: 0.8877 (m-80)
REVERT: C   21 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7462 (ptm)
REVERT: C   58 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7974 (mp0)
REVERT: C   59 ASN cc_start: 0.8751 (t0) cc_final: 0.8544 (t0)
REVERT: E   23 SER cc_start: 0.8513 (m) cc_final: 0.8245 (t)
REVERT: E   46 GLU cc_start: 0.8666 (tt0) cc_final: 0.8215 (tm-30)
REVERT: E   85 SER cc_start: 0.8821 (m) cc_final: 0.8345 (t)
REVERT: R  111 ILE cc_start: 0.7969 (pp) cc_final: 0.7629 (tp)
REVERT: R  206 HIS cc_start: 0.8188 (p-80) cc_final: 0.7893 (p-80)
REVERT: R  280 VAL cc_start: 0.8681 (t) cc_final: 0.8414 (t)
  outliers start: 53
  outliers final: 32
  residues processed: 218
  average time/residue: 1.3633
  time to fit residues: 317.3610
Evaluate side-chains
  225 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 190
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   17 SER
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain R residue   58 THR
Chi-restraints excluded: chain R residue   73 ILE
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  167 THR
Chi-restraints excluded: chain R residue  211 HIS
Chi-restraints excluded: chain R residue  235 ILE
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  255 PHE
Chi-restraints excluded: chain R residue  274 ILE
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  296 VAL
Chi-restraints excluded: chain R residue  326 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 95 optimal weight:    8.9990
   chunk 8 optimal weight:    0.6980
   chunk 109 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 114 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.154403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.104431 restraints weight = 11123.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 2.22
r_work: 0.2968 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2836 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9041  Z= 0.150
  Angle     :  0.505   6.767  12252  Z= 0.271
  Chirality :  0.042   0.134   1408
  Planarity :  0.003   0.043   1534
  Dihedral  :  5.853  87.873   1322
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 18.05 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.77 (0.25), residues: 1118
  helix:  2.88 (0.24), residues: 403
  sheet:  0.35 (0.30), residues: 283
  loop :  0.17 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.011   0.001   PHE R 186 
 TYR   0.016   0.001   TYR B  59 
 ARG   0.004   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04048 (  483)
  hydrogen bonds       : angle       4.30927 ( 1365)
  SS BOND              : bond        0.00353 (    3)
  SS BOND              : angle       1.01776 (    6)
  covalent geometry    : bond        0.00343 ( 9037)
  covalent geometry    : angle       0.50432 (12246)
  Misc. bond           : bond        0.00008 (    1)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 200
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8772 (mptm) cc_final: 0.8001 (mtmm)
REVERT: A   24 ARG cc_start: 0.7782 (ttp-110) cc_final: 0.7276 (mtm110)
REVERT: A   29 LYS cc_start: 0.8326 (tttt) cc_final: 0.7837 (tttp)
REVERT: A  198 MET cc_start: 0.8993 (ttp) cc_final: 0.8719 (ttm)
REVERT: A  208 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7862 (ttp80)
REVERT: A  273 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7886 (mp)
REVERT: A  296 TYR cc_start: 0.8530 (t80) cc_final: 0.8305 (t80)
REVERT: A  302 TYR cc_start: 0.8715 (t80) cc_final: 0.8436 (t80)
REVERT: A  354 PHE cc_start: 0.8532 (t80) cc_final: 0.8279 (t80)
REVERT: B   19 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8110 (ttp80)
REVERT: B   42 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7821 (tpt-90)
REVERT: B   46 ARG cc_start: 0.8380 (mtp-110) cc_final: 0.8059 (mtp85)
REVERT: B  130 GLU cc_start: 0.8893 (mp0) cc_final: 0.8548 (mp0)
REVERT: B  172 GLU cc_start: 0.8057 (tp30) cc_final: 0.7755 (tp30)
REVERT: B  212 ASP cc_start: 0.8199 (t0) cc_final: 0.7882 (t0)
REVERT: C   21 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7587 (ptm)
REVERT: C   58 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7997 (mp0)
REVERT: E   23 SER cc_start: 0.8477 (m) cc_final: 0.8226 (t)
REVERT: E   46 GLU cc_start: 0.8642 (tt0) cc_final: 0.8186 (tt0)
REVERT: E   85 SER cc_start: 0.8793 (m) cc_final: 0.8302 (t)
REVERT: R  111 ILE cc_start: 0.7989 (pp) cc_final: 0.7636 (tp)
REVERT: R  150 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8559 (tm)
REVERT: R  210 LYS cc_start: 0.8153 (ptpt) cc_final: 0.7837 (ptmt)
REVERT: R  280 VAL cc_start: 0.8644 (t) cc_final: 0.8372 (t)
  outliers start: 48
  outliers final: 28
  residues processed: 224
  average time/residue: 1.2909
  time to fit residues: 310.4442
Evaluate side-chains
  219 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 187
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain E residue   17 SER
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain R residue   73 ILE
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  211 HIS
Chi-restraints excluded: chain R residue  235 ILE
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  255 PHE
Chi-restraints excluded: chain R residue  274 ILE
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  296 VAL
Chi-restraints excluded: chain R residue  325 VAL
Chi-restraints excluded: chain R residue  326 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 17 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 83 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0980
   chunk 38 optimal weight:    3.9990
   chunk 10 optimal weight:   20.0000
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 113 GLN
** R  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 114 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.154143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.104334 restraints weight = 11136.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 2.21
r_work: 0.2956 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9041  Z= 0.129
  Angle     :  0.499   7.142  12252  Z= 0.267
  Chirality :  0.042   0.214   1408
  Planarity :  0.003   0.043   1534
  Dihedral  :  5.761  89.018   1322
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 19.10 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.74 (0.25), residues: 1118
  helix:  2.86 (0.25), residues: 403
  sheet:  0.34 (0.30), residues: 276
  loop :  0.14 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.012   0.001   PHE B 151 
 TYR   0.012   0.001   TYR E 190 
 ARG   0.003   0.000   ARG R 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03849 (  483)
  hydrogen bonds       : angle       4.25480 ( 1365)
  SS BOND              : bond        0.00334 (    3)
  SS BOND              : angle       0.84177 (    6)
  covalent geometry    : bond        0.00288 ( 9037)
  covalent geometry    : angle       0.49878 (12246)
  Misc. bond           : bond        0.00014 (    1)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 199
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8720 (mptm) cc_final: 0.7934 (mtmm)
REVERT: A   24 ARG cc_start: 0.7735 (ttp-110) cc_final: 0.7224 (mtm110)
REVERT: A   29 LYS cc_start: 0.8196 (tttt) cc_final: 0.7762 (tttp)
REVERT: A  198 MET cc_start: 0.8953 (ttp) cc_final: 0.8696 (ttm)
REVERT: A  208 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7743 (ttp80)
REVERT: A  273 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7874 (mp)
REVERT: A  302 TYR cc_start: 0.8693 (t80) cc_final: 0.8410 (t80)
REVERT: A  354 PHE cc_start: 0.8535 (t80) cc_final: 0.8280 (t80)
REVERT: B   19 ARG cc_start: 0.8360 (ttp80) cc_final: 0.8037 (ttp80)
REVERT: B   42 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7894 (tpt-90)
REVERT: B   46 ARG cc_start: 0.8403 (mtp-110) cc_final: 0.8074 (mtp85)
REVERT: B  130 GLU cc_start: 0.8875 (mp0) cc_final: 0.8599 (mp0)
REVERT: B  172 GLU cc_start: 0.8042 (tp30) cc_final: 0.7760 (tp30)
REVERT: B  212 ASP cc_start: 0.8119 (t0) cc_final: 0.7827 (t0)
REVERT: B  264 TYR cc_start: 0.9049 (m-80) cc_final: 0.8756 (m-80)
REVERT: C   21 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7647 (ptm)
REVERT: C   58 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7992 (mp0)
REVERT: E    6 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7473 (mt-10)
REVERT: E   23 SER cc_start: 0.8460 (m) cc_final: 0.8189 (t)
REVERT: E   46 GLU cc_start: 0.8645 (tt0) cc_final: 0.8161 (tt0)
REVERT: E   85 SER cc_start: 0.8814 (m) cc_final: 0.8322 (t)
REVERT: R  111 ILE cc_start: 0.8032 (pp) cc_final: 0.7647 (tp)
REVERT: R  203 MET cc_start: 0.8066 (pp-130) cc_final: 0.7830 (pp-130)
REVERT: R  206 HIS cc_start: 0.8094 (p-80) cc_final: 0.7713 (p-80)
REVERT: R  210 LYS cc_start: 0.8014 (ptpt) cc_final: 0.7808 (ptmt)
REVERT: R  280 VAL cc_start: 0.8603 (t) cc_final: 0.8334 (t)
  outliers start: 44
  outliers final: 29
  residues processed: 226
  average time/residue: 1.1003
  time to fit residues: 266.8200
Evaluate side-chains
  218 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 185
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   17 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain R residue   73 ILE
Chi-restraints excluded: chain R residue  115 ILE
Chi-restraints excluded: chain R residue  124 VAL
Chi-restraints excluded: chain R residue  178 VAL
Chi-restraints excluded: chain R residue  211 HIS
Chi-restraints excluded: chain R residue  235 ILE
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  255 PHE
Chi-restraints excluded: chain R residue  274 ILE
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  296 VAL
Chi-restraints excluded: chain R residue  325 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 107 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 75 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 62 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0570
   chunk 50 optimal weight:    3.9990
   chunk 71 optimal weight:    0.5980
   overall best weight:    0.8702

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 114 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.155701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.106252 restraints weight = 11234.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 2.21
r_work: 0.2962 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2828 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.3066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9041  Z= 0.124
  Angle     :  0.507   6.411  12252  Z= 0.271
  Chirality :  0.041   0.157   1408
  Planarity :  0.003   0.042   1534
  Dihedral  :  5.622  88.333   1322
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 19.62 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.78 (0.26), residues: 1118
  helix:  2.86 (0.25), residues: 403
  sheet:  0.37 (0.30), residues: 282
  loop :  0.20 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.011   0.001   PHE B 151 
 TYR   0.015   0.001   TYR A 296 
 ARG   0.004   0.000   ARG E 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03751 (  483)
  hydrogen bonds       : angle       4.23728 ( 1365)
  SS BOND              : bond        0.00323 (    3)
  SS BOND              : angle       0.78204 (    6)
  covalent geometry    : bond        0.00278 ( 9037)
  covalent geometry    : angle       0.50650 (12246)
  Misc. bond           : bond        0.00025 (    1)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 194
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8758 (mptm) cc_final: 0.7986 (mtmm)
REVERT: A   24 ARG cc_start: 0.7765 (ttp-110) cc_final: 0.7258 (mtm110)
REVERT: A   29 LYS cc_start: 0.8217 (tttt) cc_final: 0.7774 (tttp)
REVERT: A  198 MET cc_start: 0.8950 (ttp) cc_final: 0.8672 (ttm)
REVERT: A  208 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7751 (ttp80)
REVERT: A  302 TYR cc_start: 0.8727 (t80) cc_final: 0.8462 (t80)
REVERT: A  354 PHE cc_start: 0.8532 (t80) cc_final: 0.8295 (t80)
REVERT: B   19 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8107 (ttp80)
REVERT: B   42 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7889 (tpt-90)
REVERT: B   46 ARG cc_start: 0.8371 (mtp-110) cc_final: 0.8052 (mtp85)
REVERT: B  130 GLU cc_start: 0.8889 (mp0) cc_final: 0.8633 (mp0)
REVERT: B  172 GLU cc_start: 0.8044 (tp30) cc_final: 0.7767 (tp30)
REVERT: B  212 ASP cc_start: 0.8080 (t0) cc_final: 0.7792 (t0)
REVERT: B  264 TYR cc_start: 0.9031 (m-80) cc_final: 0.8767 (m-80)
REVERT: C   58 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8013 (mp0)
REVERT: E   23 SER cc_start: 0.8466 (m) cc_final: 0.8202 (t)
REVERT: E   46 GLU cc_start: 0.8650 (tt0) cc_final: 0.8174 (tt0)
REVERT: E   85 SER cc_start: 0.8854 (m) cc_final: 0.8371 (t)
REVERT: R  111 ILE cc_start: 0.8056 (pp) cc_final: 0.7664 (tp)
REVERT: R  280 VAL cc_start: 0.8608 (t) cc_final: 0.8351 (t)
  outliers start: 41
  outliers final: 32
  residues processed: 220
  average time/residue: 1.2815
  time to fit residues: 302.5949
Evaluate side-chains
  223 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 190
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   17 SER
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain R residue   73 ILE
Chi-restraints excluded: chain R residue  115 ILE
Chi-restraints excluded: chain R residue  124 VAL
Chi-restraints excluded: chain R residue  167 THR
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  211 HIS
Chi-restraints excluded: chain R residue  235 ILE
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  255 PHE
Chi-restraints excluded: chain R residue  274 ILE
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  296 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    0.1980
   chunk 80 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 111 optimal weight:    5.9990
   chunk 102 optimal weight:    0.9980
   chunk 108 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 GLN
** R  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 114 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.156029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.106588 restraints weight = 11292.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 2.22
r_work: 0.3016 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9041  Z= 0.120
  Angle     :  0.515   7.452  12252  Z= 0.273
  Chirality :  0.041   0.161   1408
  Planarity :  0.003   0.042   1534
  Dihedral  :  5.579  87.634   1322
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 20.67 %
    Favored  : 75.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.80 (0.26), residues: 1118
  helix:  2.90 (0.25), residues: 402
  sheet:  0.38 (0.30), residues: 282
  loop :  0.18 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 114 
 PHE   0.011   0.001   PHE R 219 
 TYR   0.024   0.001   TYR A 296 
 ARG   0.003   0.000   ARG E 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03678 (  483)
  hydrogen bonds       : angle       4.19096 ( 1365)
  SS BOND              : bond        0.00304 (    3)
  SS BOND              : angle       0.70569 (    6)
  covalent geometry    : bond        0.00267 ( 9037)
  covalent geometry    : angle       0.51528 (12246)
  Misc. bond           : bond        0.00018 (    1)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 194
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8777 (mptm) cc_final: 0.8005 (mtmm)
REVERT: A   24 ARG cc_start: 0.7759 (ttp-110) cc_final: 0.7256 (mtm110)
REVERT: A   29 LYS cc_start: 0.8216 (tttt) cc_final: 0.7780 (tttp)
REVERT: A  198 MET cc_start: 0.8921 (ttp) cc_final: 0.8649 (ttm)
REVERT: A  208 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7761 (ttp80)
REVERT: A  302 TYR cc_start: 0.8719 (t80) cc_final: 0.8433 (t80)
REVERT: A  354 PHE cc_start: 0.8539 (t80) cc_final: 0.8306 (t80)
REVERT: B   42 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7876 (tpt-90)
REVERT: B   46 ARG cc_start: 0.8341 (mtp-110) cc_final: 0.8021 (mtp85)
REVERT: B  130 GLU cc_start: 0.8886 (mp0) cc_final: 0.8627 (mp0)
REVERT: B  172 GLU cc_start: 0.8038 (tp30) cc_final: 0.7808 (tp30)
REVERT: B  212 ASP cc_start: 0.8062 (t0) cc_final: 0.7783 (t0)
REVERT: C   58 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8007 (mp0)
REVERT: E   23 SER cc_start: 0.8471 (m) cc_final: 0.8206 (t)
REVERT: E   46 GLU cc_start: 0.8649 (tt0) cc_final: 0.8178 (tt0)
REVERT: E   85 SER cc_start: 0.8863 (m) cc_final: 0.8392 (t)
REVERT: R  206 HIS cc_start: 0.8221 (p-80) cc_final: 0.7967 (p90)
REVERT: R  208 ARG cc_start: 0.8427 (mtp-110) cc_final: 0.8201 (mpp80)
REVERT: R  210 LYS cc_start: 0.7620 (ptmt) cc_final: 0.7369 (ptmt)
REVERT: R  280 VAL cc_start: 0.8629 (t) cc_final: 0.8377 (t)
REVERT: R  330 MET cc_start: 0.8490 (mmm) cc_final: 0.8037 (mmm)
  outliers start: 37
  outliers final: 29
  residues processed: 217
  average time/residue: 1.4521
  time to fit residues: 340.2731
Evaluate side-chains
  221 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 191
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue   17 SER
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  204 SER
Chi-restraints excluded: chain E residue  215 THR
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  124 VAL
Chi-restraints excluded: chain R residue  167 THR
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  211 HIS
Chi-restraints excluded: chain R residue  235 ILE
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  255 PHE
Chi-restraints excluded: chain R residue  296 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 85 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 62 optimal weight:    8.9990
   chunk 75 optimal weight:    0.4980
   chunk 72 optimal weight:    0.6980
   chunk 93 optimal weight:    1.9990
   chunk 107 optimal weight:   10.0000
   chunk 7 optimal weight:    0.4980
   chunk 89 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 35 optimal weight:    5.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 ASN
** R  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 114 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.156960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.107638 restraints weight = 11252.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 2.23
r_work: 0.3079 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.3260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9041  Z= 0.112
  Angle     :  0.517   8.426  12252  Z= 0.276
  Chirality :  0.041   0.200   1408
  Planarity :  0.003   0.041   1534
  Dihedral  :  5.486  87.088   1322
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.99 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.78 (0.26), residues: 1118
  helix:  2.82 (0.25), residues: 403
  sheet:  0.45 (0.31), residues: 281
  loop :  0.17 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.010   0.001   PHE B 151 
 TYR   0.024   0.001   TYR A 296 
 ARG   0.004   0.000   ARG E 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03625 (  483)
  hydrogen bonds       : angle       4.16795 ( 1365)
  SS BOND              : bond        0.00302 (    3)
  SS BOND              : angle       0.67285 (    6)
  covalent geometry    : bond        0.00247 ( 9037)
  covalent geometry    : angle       0.51728 (12246)
  Misc. bond           : bond        0.00024 (    1)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 192
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8777 (mptm) cc_final: 0.8022 (mtmm)
REVERT: A   24 ARG cc_start: 0.7779 (ttp-110) cc_final: 0.7277 (mtm110)
REVERT: A   29 LYS cc_start: 0.8270 (tttt) cc_final: 0.7833 (tttp)
REVERT: A  198 MET cc_start: 0.8851 (ttp) cc_final: 0.8596 (ttm)
REVERT: A  208 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7752 (ttp80)
REVERT: A  302 TYR cc_start: 0.8750 (t80) cc_final: 0.8487 (t80)
REVERT: A  354 PHE cc_start: 0.8566 (t80) cc_final: 0.8297 (t80)
REVERT: B   42 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7782 (tpt-90)
REVERT: B   46 ARG cc_start: 0.8216 (mtp-110) cc_final: 0.7892 (mtp85)
REVERT: B  130 GLU cc_start: 0.8874 (mp0) cc_final: 0.8648 (mp0)
REVERT: B  172 GLU cc_start: 0.8033 (tp30) cc_final: 0.7678 (tp30)
REVERT: B  212 ASP cc_start: 0.8026 (t0) cc_final: 0.7775 (t0)
REVERT: B  303 ASP cc_start: 0.7804 (m-30) cc_final: 0.7603 (m-30)
REVERT: C   58 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7994 (mp0)
REVERT: E   23 SER cc_start: 0.8530 (m) cc_final: 0.8301 (t)
REVERT: E   46 GLU cc_start: 0.8641 (tt0) cc_final: 0.8066 (tt0)
REVERT: E   62 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7880 (m-30)
REVERT: E   85 SER cc_start: 0.8844 (m) cc_final: 0.8360 (t)
REVERT: R  111 ILE cc_start: 0.8017 (pp) cc_final: 0.7663 (tp)
REVERT: R  206 HIS cc_start: 0.8213 (p-80) cc_final: 0.7985 (p90)
REVERT: R  208 ARG cc_start: 0.8392 (mtp-110) cc_final: 0.8170 (mpp80)
REVERT: R  280 VAL cc_start: 0.8635 (t) cc_final: 0.8398 (t)
REVERT: R  330 MET cc_start: 0.8446 (mmm) cc_final: 0.7994 (mmm)
  outliers start: 38
  outliers final: 23
  residues processed: 213
  average time/residue: 1.1399
  time to fit residues: 259.3887
Evaluate side-chains
  215 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 190
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain E residue   17 SER
Chi-restraints excluded: chain E residue   62 ASP
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  124 VAL
Chi-restraints excluded: chain R residue  167 THR
Chi-restraints excluded: chain R residue  211 HIS
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  255 PHE
Chi-restraints excluded: chain R residue  296 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    0.3980
   chunk 100 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 70 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 110 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 57 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 114 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.154431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.104659 restraints weight = 11260.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 2.22
r_work: 0.2915 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2783 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9041  Z= 0.175
  Angle     :  0.563   8.325  12252  Z= 0.298
  Chirality :  0.043   0.180   1408
  Planarity :  0.003   0.042   1534
  Dihedral  :  5.502  82.825   1320
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 22.56 %
    Favored  : 74.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.62 (0.25), residues: 1118
  helix:  2.63 (0.25), residues: 409
  sheet:  0.37 (0.31), residues: 271
  loop :  0.12 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.003   0.001   HIS R 114 
 PHE   0.012   0.001   PHE B 151 
 TYR   0.025   0.001   TYR A 296 
 ARG   0.005   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03899 (  483)
  hydrogen bonds       : angle       4.27204 ( 1365)
  SS BOND              : bond        0.00321 (    3)
  SS BOND              : angle       0.80454 (    6)
  covalent geometry    : bond        0.00409 ( 9037)
  covalent geometry    : angle       0.56273 (12246)
  Misc. bond           : bond        0.00015 (    1)

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 189
  time to evaluate  : 1.032 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8743 (mptm) cc_final: 0.7977 (mtmm)
REVERT: A   24 ARG cc_start: 0.7732 (ttp-110) cc_final: 0.7228 (mtm110)
REVERT: A   29 LYS cc_start: 0.8224 (tttt) cc_final: 0.7788 (tttp)
REVERT: A  198 MET cc_start: 0.8945 (ttp) cc_final: 0.8717 (ttm)
REVERT: A  208 ARG cc_start: 0.8107 (ttm-80) cc_final: 0.7856 (ttp80)
REVERT: A  302 TYR cc_start: 0.8722 (t80) cc_final: 0.8431 (t80)
REVERT: A  354 PHE cc_start: 0.8595 (t80) cc_final: 0.8334 (t80)
REVERT: B   42 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7886 (tpt-90)
REVERT: B   46 ARG cc_start: 0.8335 (mtp-110) cc_final: 0.8020 (mtp85)
REVERT: B  130 GLU cc_start: 0.8814 (mp0) cc_final: 0.8521 (mp0)
REVERT: B  172 GLU cc_start: 0.8049 (tp30) cc_final: 0.7776 (tp30)
REVERT: B  212 ASP cc_start: 0.8161 (t0) cc_final: 0.7844 (t0)
REVERT: C   58 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8013 (mp0)
REVERT: E    6 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7378 (mt-10)
REVERT: E   23 SER cc_start: 0.8421 (m) cc_final: 0.8200 (t)
REVERT: E   46 GLU cc_start: 0.8678 (tt0) cc_final: 0.8224 (tt0)
REVERT: E   62 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.8052 (m-30)
REVERT: E   85 SER cc_start: 0.8853 (m) cc_final: 0.8355 (t)
REVERT: E  119 VAL cc_start: 0.8183 (t) cc_final: 0.7861 (p)
REVERT: R  111 ILE cc_start: 0.8010 (pp) cc_final: 0.7664 (tp)
REVERT: R  206 HIS cc_start: 0.8252 (p-80) cc_final: 0.7995 (p90)
REVERT: R  208 ARG cc_start: 0.8525 (mtp-110) cc_final: 0.8255 (mpp80)
REVERT: R  210 LYS cc_start: 0.7874 (ptmt) cc_final: 0.7539 (ptmt)
REVERT: R  330 MET cc_start: 0.8431 (mmm) cc_final: 0.7923 (mmm)
  outliers start: 25
  outliers final: 18
  residues processed: 204
  average time/residue: 1.1893
  time to fit residues: 258.6092
Evaluate side-chains
  208 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 187
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain E residue    6 GLU
Chi-restraints excluded: chain E residue   17 SER
Chi-restraints excluded: chain E residue   62 ASP
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue   86 ARG
Chi-restraints excluded: chain R residue  124 VAL
Chi-restraints excluded: chain R residue  167 THR
Chi-restraints excluded: chain R residue  255 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 39 optimal weight:    0.4980
   chunk 51 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    0.3980
   chunk 63 optimal weight:    0.5980
   chunk 91 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
** R  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 114 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.156968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.107396 restraints weight = 11266.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.23
r_work: 0.3072 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.3363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9041  Z= 0.112
  Angle     :  0.521   8.351  12252  Z= 0.277
  Chirality :  0.041   0.180   1408
  Planarity :  0.003   0.041   1534
  Dihedral  :  5.305  82.336   1319
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 22.56 %
    Favored  : 74.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  1.71 (0.26), residues: 1118
  helix:  2.70 (0.25), residues: 409
  sheet:  0.40 (0.31), residues: 277
  loop :  0.18 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.011   0.001   PHE R 328 
 TYR   0.022   0.001   TYR A 296 
 ARG   0.005   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03571 (  483)
  hydrogen bonds       : angle       4.15941 ( 1365)
  SS BOND              : bond        0.00320 (    3)
  SS BOND              : angle       0.67128 (    6)
  covalent geometry    : bond        0.00247 ( 9037)
  covalent geometry    : angle       0.52134 (12246)
  Misc. bond           : bond        0.00026 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9489.61 seconds
wall clock time: 165 minutes 22.58 seconds (9922.58 seconds total)