Starting phenix.real_space_refine
on Thu Mar 13 13:57:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g05_29645/03_2025/8g05_29645_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g05_29645/03_2025/8g05_29645.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g05_29645/03_2025/8g05_29645.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g05_29645/03_2025/8g05_29645.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g05_29645/03_2025/8g05_29645_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g05_29645/03_2025/8g05_29645_neut.cif"
  }
  resolution = 3.0
  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: 4
    Type Number    sf(0)   Gaussians
     S      61      5.16       5
     C    5701      2.51       5
     N    1525      2.21       5
     O    1657      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8944
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2256
          Classifications: {'peptide': 286}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 274}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1806
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
    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: "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: "G"
      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: "R"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'CLR': 1, 'YI9': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.41, per 1000 atoms: 0.60
  Number of scatterers: 8944
  At special positions: 0
  Unit cell: (109.14, 128.4, 113.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      61     16.00
     O    1657      8.00
     N    1525      7.00
     C    5701      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  11 " - pdb=" SG  CYS R 166 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R  93 " - pdb=" SG  CYS R 168 " distance=2.03
    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=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.39
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2126

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 13 sheets defined
      35.9% alpha, 22.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'R' and resid 15 through 34
      removed outlier: 4.648A  pdb=" N   TYR R  19 " --> pdb=" O   SER R  15 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   TYR R  21 " --> pdb=" O   LEU R  17 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   VAL R  22 " --> pdb=" O   GLY R  18 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   TRP R  26 " --> pdb=" O   VAL R  22 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   VAL R  29 " --> pdb=" O   SER R  25 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL R  32 " --> pdb=" O   VAL R  28 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 36 through 48
      removed outlier: 3.514A  pdb=" N   LEU R  40 " --> pdb=" O   VAL R  36 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   THR R  41 " --> pdb=" O   GLY R  37 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU R  42 " --> pdb=" O   ASN R  38 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLN R  48 " --> pdb=" O   ALA R  44 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 49 through 52
      removed outlier: 3.801A  pdb=" N   ARG R  52 " --> pdb=" O   PRO R  49 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 49 through 52'
    Processing helix  chain 'R' and resid 55 through 66
      removed outlier: 3.627A  pdb=" N   ILE R  59 " --> pdb=" O   PHE R  55 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASP R  66 " --> pdb=" O   LEU R  62 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 72
    Processing helix  chain 'R' and resid 79 through 84
    Processing helix  chain 'R' and resid 89 through 120
      removed outlier: 3.821A  pdb=" N   VAL R  95 " --> pdb=" O   THR R  91 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LEU R  98 " --> pdb=" O   ARG R  94 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   PHE R 101 " --> pdb=" O   GLY R  97 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ASN R 104 " --> pdb=" O   LEU R 100 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   SER R 107 " --> pdb=" O   SER R 103 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU R 116 " --> pdb=" O   CYS R 112 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 127 through 132
    Processing helix  chain 'R' and resid 135 through 149
      removed outlier: 3.798A  pdb=" N   THR R 144 " --> pdb=" O   ALA R 140 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   TRP R 145 " --> pdb=" O   LEU R 141 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   VAL R 147 " --> pdb=" O   SER R 143 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 189
    Processing helix  chain 'R' and resid 196 through 210
      removed outlier: 3.771A  pdb=" N   HIS R 202 " --> pdb=" O   TYR R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 315 through 330
      removed outlier: 3.787A  pdb=" N   ARG R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   PHE R 325 " --> pdb=" O   CYS R 321 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   CYS R 327 " --> pdb=" O   ALA R 323 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   PHE R 328 " --> pdb=" O   VAL R 324 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 331 through 342
      removed outlier: 4.267A  pdb=" N   PHE R 335 " --> pdb=" O   SER R 331 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE R 340 " --> pdb=" O   LEU R 336 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LEU R 341 " --> pdb=" O   LEU R 337 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 348 through 358
      removed outlier: 3.562A  pdb=" N   HIS R 352 " --> pdb=" O   PRO R 348 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 360 through 364
    Processing helix  chain 'R' and resid 365 through 370
    Processing helix  chain 'R' and resid 374 through 387
    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 211
    Processing helix  chain 'A' and resid 212 through 216
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.614A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 4.085A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.958A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 331 through 352
    Processing helix  chain 'B' and resid 3 through 26
      removed outlier: 3.638A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.578A  pdb=" N   PHE E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 3.965A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.883A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 220 through 224
      removed outlier: 3.729A  pdb=" N   ASP E 223 " --> pdb=" O   GLU E 220 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL E 224 " --> pdb=" O   ALA E 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 220 through 224'
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 43
    Processing helix  chain 'G' and resid 44 through 48
    Processing sheet with id=AA1, first strand: chain 'R' and resid 159 through 162
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191
      removed outlier: 5.990A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51
      removed outlier: 6.607A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.669A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.000A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.537A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.923A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.458A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.837A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.398A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12
      removed outlier: 6.752A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.970A  pdb=" N   GLU E 246 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 155 through 160

    395 hydrogen bonds defined for protein.
    1104 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: 4.28

  Time building geometry restraints manager: 2.81 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: 1442
        1.31 -     1.43: 2517
        1.43 -     1.56: 5085
        1.56 -     1.69: 1
        1.69 -     1.81: 86
  Bond restraints: 9131
  Sorted by residual:
  bond pdb=" C11 YI9 R 401 "
       pdb=" C12 YI9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.506  1.365  0.141 2.00e-02 2.50e+03 4.94e+01
  bond pdb=" C10 YI9 R 401 "
       pdb=" C11 YI9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.501  1.371  0.130 2.00e-02 2.50e+03 4.24e+01
  bond pdb=" C10 YI9 R 401 "
       pdb=" N09 YI9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.325  1.445 -0.120 2.00e-02 2.50e+03 3.58e+01
  bond pdb=" C15 YI9 R 401 "
       pdb=" N14 YI9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.408  1.323  0.085 2.00e-02 2.50e+03 1.81e+01
  bond pdb=" C   ASN R 366 "
       pdb=" N   PRO R 367 "
    ideal  model  delta    sigma   weight residual
    1.337  1.366 -0.029 1.11e-02 8.12e+03 6.93e+00
  ... (remaining 9126 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.43: 12261
        3.43 -     6.87: 99
        6.87 -    10.30: 11
       10.30 -    13.73: 3
       13.73 -    17.16: 1
  Bond angle restraints: 12375
  Sorted by residual:
  angle pdb=" C   ASN A 269 "
        pdb=" N   LYS A 270 "
        pdb=" CA  LYS A 270 "
      ideal   model   delta    sigma   weight residual
     122.82  128.48   -5.66 1.42e+00 4.96e-01 1.59e+01
  angle pdb=" CA  ARG E 218 "
        pdb=" CB  ARG E 218 "
        pdb=" CG  ARG E 218 "
      ideal   model   delta    sigma   weight residual
     114.10  120.96   -6.86 2.00e+00 2.50e-01 1.18e+01
  angle pdb=" C   ARG E 191 "
        pdb=" N   MET E 192 "
        pdb=" CA  MET E 192 "
      ideal   model   delta    sigma   weight residual
     121.54  127.87   -6.33 1.91e+00 2.74e-01 1.10e+01
  angle pdb=" N   VAL R 146 "
        pdb=" CA  VAL R 146 "
        pdb=" C   VAL R 146 "
      ideal   model   delta    sigma   weight residual
     112.29  109.25    3.04 9.40e-01 1.13e+00 1.05e+01
  angle pdb=" CA  LEU B  70 "
        pdb=" CB  LEU B  70 "
        pdb=" CG  LEU B  70 "
      ideal   model   delta    sigma   weight residual
     116.30  127.58  -11.28 3.50e+00 8.16e-02 1.04e+01
  ... (remaining 12370 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 4918
       17.83 -    35.67: 450
       35.67 -    53.50: 70
       53.50 -    71.33: 13
       71.33 -    89.17: 13
  Dihedral angle restraints: 5464
    sinusoidal: 2163
      harmonic: 3301
  Sorted by residual:
  dihedral pdb=" CB  CYS R  11 "
           pdb=" SG  CYS R  11 "
           pdb=" SG  CYS R 166 "
           pdb=" CB  CYS R 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -150.17   64.17     1      1.00e+01 1.00e-02 5.42e+01
  dihedral pdb=" CA  LYS R 135 "
           pdb=" C   LYS R 135 "
           pdb=" N   GLY R 136 "
           pdb=" CA  GLY R 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.21   23.79     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" CA  THR E 172 "
           pdb=" C   THR E 172 "
           pdb=" N   TYR E 173 "
           pdb=" CA  TYR E 173 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.59  -22.41     0      5.00e+00 4.00e-02 2.01e+01
  ... (remaining 5461 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.991: 1409
       0.991 -    1.981: 0
       1.981 -    2.972: 0
       2.972 -    3.962: 0
       3.962 -    4.953: 1
  Chirality restraints: 1410
  Sorted by residual:
  chirality pdb=" C17 CLR R 402 "
            pdb=" C13 CLR R 402 "
            pdb=" C16 CLR R 402 "
            pdb=" C20 CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55   -2.40    4.95 2.00e-01 2.50e+01 6.13e+02
  chirality pdb=" CB  VAL A 339 "
            pdb=" CA  VAL A 339 "
            pdb=" CG1 VAL A 339 "
            pdb=" CG2 VAL A 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CB  ILE B 232 "
            pdb=" CA  ILE B 232 "
            pdb=" CG1 ILE B 232 "
            pdb=" CG2 ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.24e+00
  ... (remaining 1407 not shown)

  Planarity restraints: 1559
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C08 YI9 R 401 "   -0.082 2.00e-02 2.50e+03   3.84e-02 3.32e+01
        pdb=" C10 YI9 R 401 "    0.034 2.00e-02 2.50e+03
        pdb=" C11 YI9 R 401 "    0.028 2.00e-02 2.50e+03
        pdb=" C12 YI9 R 401 "    0.004 2.00e-02 2.50e+03
        pdb=" C15 YI9 R 401 "   -0.012 2.00e-02 2.50e+03
        pdb=" N09 YI9 R 401 "    0.057 2.00e-02 2.50e+03
        pdb=" N14 YI9 R 401 "   -0.011 2.00e-02 2.50e+03
        pdb=" N17 YI9 R 401 "    0.012 2.00e-02 2.50e+03
        pdb=" O16 YI9 R 401 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA R 153 "    0.043 5.00e-02 4.00e+02   6.47e-02 6.69e+00
        pdb=" N   PRO R 154 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO R 154 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R 154 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 366 "   -0.041 5.00e-02 4.00e+02   6.17e-02 6.09e+00
        pdb=" N   PRO R 367 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO R 367 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO R 367 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1556 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2156
        2.79 -     3.31: 7662
        3.31 -     3.84: 15070
        3.84 -     4.37: 18207
        4.37 -     4.90: 31481
  Nonbonded interactions: 74576
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR E 175 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   VAL R 106 "
            pdb=" OG1 THR R 110 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" OD1 ASP B 290 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OG  SER R 105 "
            pdb=" OH  TYR R 186 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.316 3.040
  ... (remaining 74571 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:             0.320
  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:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     24.450
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:30.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   56.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
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      :  0.007   0.141   9131  Z= 0.418
  Angle     :  0.908  17.165  12375  Z= 0.491
  Chirality :  0.143   4.953   1410
  Planarity :  0.007   0.065   1559
  Dihedral  : 14.307  89.168   3326
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  7.33 %
    Favored  : 92.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -3.23 (0.21), residues: 1124
  helix: -3.16 (0.19), residues: 359
  sheet: -0.93 (0.29), residues: 284
  loop : -1.91 (0.24), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP B  82 
 HIS   0.006   0.001   HIS B  91 
 PHE   0.023   0.002   PHE B 199 
 TYR   0.019   0.002   TYR B  59 
 ARG   0.014   0.001   ARG E  98 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 196
  time to evaluate  : 1.030 
Fit side-chains
REVERT: R  186 TYR cc_start: 0.6991 (m-80) cc_final: 0.6775 (m-80)
REVERT: R  316 LYS cc_start: 0.8052 (mtmm) cc_final: 0.7323 (tttm)
REVERT: A  204 GLN cc_start: 0.7891 (mt0) cc_final: 0.7583 (mm-40)
REVERT: B   16 ASN cc_start: 0.7828 (m110) cc_final: 0.7602 (m110)
REVERT: B   46 ARG cc_start: 0.6933 (mtp-110) cc_final: 0.6647 (mmt180)
REVERT: B  188 MET cc_start: 0.8124 (mmm) cc_final: 0.7846 (mmp)
REVERT: B  214 ARG cc_start: 0.6800 (mmp-170) cc_final: 0.5932 (mmm-85)
REVERT: G   38 MET cc_start: 0.7873 (ttp) cc_final: 0.7515 (ttp)
  outliers start: 6
  outliers final: 2
  residues processed: 201
  average time/residue: 1.2755
  time to fit residues: 273.8020
Evaluate side-chains
  151 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 149
  time to evaluate  : 1.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  344 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0570
   chunk 65 optimal weight:    0.6980
   chunk 101 optimal weight:    0.8980
   overall best weight:    1.1302

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

Flipped N/Q/H residues before XYZ refinement:
R  74 GLN
R  83 HIS
R  85 HIS
R 357 ASN
R 379 GLN
A  22 ASN
A 241 ASN
A 256 ASN
A 306 GLN
B  91 HIS
B 156 GLN
B 259 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.161883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.122412 restraints weight = 10524.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 2.15
r_work: 0.3257 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.1655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9131  Z= 0.212
  Angle     :  0.599   8.739  12375  Z= 0.312
  Chirality :  0.043   0.163   1410
  Planarity :  0.004   0.046   1559
  Dihedral  :  6.964  59.794   1314
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 14.36 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -1.88 (0.24), residues: 1124
  helix: -1.54 (0.25), residues: 368
  sheet: -0.61 (0.30), residues: 279
  loop : -1.22 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.006   0.001   HIS R  85 
 PHE   0.015   0.001   PHE A 334 
 TYR   0.011   0.001   TYR E  94 
 ARG   0.005   0.000   ARG B 150 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 165
  time to evaluate  : 0.984 
Fit side-chains
REVERT: R   94 ARG cc_start: 0.6042 (mtt180) cc_final: 0.5412 (tpp80)
REVERT: R  186 TYR cc_start: 0.7037 (m-80) cc_final: 0.6821 (m-80)
REVERT: R  316 LYS cc_start: 0.7988 (mtmm) cc_final: 0.7053 (tttm)
REVERT: R  344 ARG cc_start: 0.7691 (mtm110) cc_final: 0.7410 (mtm110)
REVERT: R  376 GLN cc_start: 0.7922 (mp10) cc_final: 0.7482 (mm-40)
REVERT: A  204 GLN cc_start: 0.7867 (mt0) cc_final: 0.7334 (mm-40)
REVERT: A  298 GLU cc_start: 0.7788 (tp30) cc_final: 0.7147 (tm-30)
REVERT: B   10 GLU cc_start: 0.8945 (tp30) cc_final: 0.8389 (tp30)
REVERT: B   16 ASN cc_start: 0.7857 (m110) cc_final: 0.7522 (m110)
REVERT: B   42 ARG cc_start: 0.7529 (tpt170) cc_final: 0.7144 (tpp-160)
REVERT: B   46 ARG cc_start: 0.7872 (mtp-110) cc_final: 0.6984 (mmt180)
REVERT: B  214 ARG cc_start: 0.6644 (mmp-170) cc_final: 0.5765 (mmm160)
REVERT: E   17 SER cc_start: 0.8315 (m) cc_final: 0.7874 (p)
REVERT: G   42 GLU cc_start: 0.7210 (mp0) cc_final: 0.6880 (tm-30)
  outliers start: 30
  outliers final: 12
  residues processed: 184
  average time/residue: 1.2025
  time to fit residues: 236.4228
Evaluate side-chains
  159 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 147
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  169 SER
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  139 VAL
Chi-restraints excluded: chain E residue  210 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 85 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 80 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 102 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
R  61 ASN
R  85 HIS
R 357 ASN
R 379 GLN
A 241 ASN
A 256 ASN
B 156 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.161371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.121986 restraints weight = 10626.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 2.23
r_work: 0.3195 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9131  Z= 0.257
  Angle     :  0.612   8.847  12375  Z= 0.314
  Chirality :  0.043   0.139   1410
  Planarity :  0.004   0.052   1559
  Dihedral  :  6.526  57.728   1312
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 16.12 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -1.39 (0.24), residues: 1124
  helix: -0.86 (0.27), residues: 369
  sheet: -0.44 (0.30), residues: 279
  loop : -1.10 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.005   0.001   HIS R  85 
 PHE   0.015   0.002   PHE A 334 
 TYR   0.011   0.001   TYR G  40 
 ARG   0.005   0.000   ARG R 375 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 157
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
REVERT: R   94 ARG cc_start: 0.5842 (mtt180) cc_final: 0.5172 (tpp80)
REVERT: R  316 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7023 (tttm)
REVERT: R  344 ARG cc_start: 0.7473 (mtm110) cc_final: 0.7260 (mtm110)
REVERT: R  373 MET cc_start: 0.7919 (mmp) cc_final: 0.7712 (mmp)
REVERT: R  376 GLN cc_start: 0.7991 (mp10) cc_final: 0.7573 (mm-40)
REVERT: A  298 GLU cc_start: 0.8127 (tp30) cc_final: 0.7341 (tm-30)
REVERT: B   42 ARG cc_start: 0.7541 (tpt170) cc_final: 0.7186 (tpp-160)
REVERT: B   46 ARG cc_start: 0.7933 (mtp-110) cc_final: 0.7029 (mmt180)
REVERT: B  175 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8165 (mt0)
REVERT: B  214 ARG cc_start: 0.6605 (mmp-170) cc_final: 0.5759 (mmm160)
REVERT: E   17 SER cc_start: 0.8201 (m) cc_final: 0.7877 (p)
  outliers start: 41
  outliers final: 25
  residues processed: 182
  average time/residue: 1.0767
  time to fit residues: 210.5259
Evaluate side-chains
  178 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   22 VAL
Chi-restraints excluded: chain R residue   71 THR
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  169 SER
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  199 CYS
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  139 VAL
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  210 THR
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain E residue  226 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 80 optimal weight:    8.9990
   chunk 42 optimal weight:    8.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** R  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  85 HIS
R 379 GLN
A 204 GLN
A 241 ASN
A 256 ASN
A 306 GLN
A 311 ASN
B 156 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.160129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.121135 restraints weight = 10637.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.19
r_work: 0.3209 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9131  Z= 0.279
  Angle     :  0.617   8.844  12375  Z= 0.316
  Chirality :  0.044   0.138   1410
  Planarity :  0.004   0.040   1559
  Dihedral  :  6.401  58.489   1312
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 17.36 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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: -1.17 (0.25), residues: 1124
  helix: -0.57 (0.28), residues: 370
  sheet: -0.34 (0.30), residues: 274
  loop : -1.06 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.005   0.001   HIS R  85 
 PHE   0.014   0.002   PHE A 334 
 TYR   0.011   0.002   TYR B 105 
 ARG   0.006   0.000   ARG B 150 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 157
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
REVERT: R   94 ARG cc_start: 0.5870 (mtt180) cc_final: 0.5204 (tpp80)
REVERT: R  344 ARG cc_start: 0.7521 (mtm110) cc_final: 0.7228 (mtm110)
REVERT: R  373 MET cc_start: 0.7941 (mmp) cc_final: 0.7736 (mmp)
REVERT: R  376 GLN cc_start: 0.8078 (mp10) cc_final: 0.7693 (mm-40)
REVERT: A  204 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7048 (mm-40)
REVERT: A  298 GLU cc_start: 0.8294 (tp30) cc_final: 0.7479 (tm-30)
REVERT: B   42 ARG cc_start: 0.7547 (tpt170) cc_final: 0.7118 (tpp-160)
REVERT: B   46 ARG cc_start: 0.7978 (mtp-110) cc_final: 0.7112 (mmt180)
REVERT: B  175 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8192 (mt0)
REVERT: B  214 ARG cc_start: 0.6596 (mmp-170) cc_final: 0.5759 (mmm-85)
REVERT: B  338 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8332 (mm)
REVERT: E   17 SER cc_start: 0.8214 (m) cc_final: 0.7916 (p)
REVERT: E   67 ARG cc_start: 0.6620 (mtm110) cc_final: 0.6301 (ttm110)
REVERT: E  218 ARG cc_start: 0.7061 (mmp-170) cc_final: 0.6520 (mtm-85)
REVERT: G   42 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6840 (tm-30)
  outliers start: 45
  outliers final: 31
  residues processed: 185
  average time/residue: 1.1571
  time to fit residues: 228.9345
Evaluate side-chains
  188 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 153
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   22 VAL
Chi-restraints excluded: chain R residue   88 THR
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  169 SER
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  199 CYS
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain A residue  204 GLN
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  139 VAL
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  210 THR
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 72 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 80 optimal weight:    6.9990
   chunk 106 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 83 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** R  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  85 HIS
R 379 GLN
A 204 GLN
A 241 ASN
A 256 ASN
A 311 ASN
B  16 ASN
B 156 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.161752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.123226 restraints weight = 10633.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.19
r_work: 0.3250 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9131  Z= 0.203
  Angle     :  0.582   8.055  12375  Z= 0.297
  Chirality :  0.042   0.139   1410
  Planarity :  0.003   0.038   1559
  Dihedral  :  6.174  59.778   1312
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 18.90 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.25), residues: 1124
  helix: -0.31 (0.28), residues: 371
  sheet: -0.22 (0.31), residues: 270
  loop : -0.92 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R  85 
 PHE   0.013   0.001   PHE A 334 
 TYR   0.009   0.001   TYR E 190 
 ARG   0.007   0.000   ARG B 314 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 158
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   94 ARG cc_start: 0.5818 (mtt180) cc_final: 0.5195 (tpp80)
REVERT: R  316 LYS cc_start: 0.8026 (mtmm) cc_final: 0.7105 (tttm)
REVERT: R  344 ARG cc_start: 0.7554 (mtm110) cc_final: 0.7138 (mtm110)
REVERT: R  376 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7719 (mm-40)
REVERT: A   53 MET cc_start: 0.6197 (mtm) cc_final: 0.5962 (mtp)
REVERT: A  204 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6925 (mm-40)
REVERT: A  298 GLU cc_start: 0.8251 (tp30) cc_final: 0.7500 (tm-30)
REVERT: A  339 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8308 (m)
REVERT: B   42 ARG cc_start: 0.7544 (tpt170) cc_final: 0.7163 (tpp-160)
REVERT: B   46 ARG cc_start: 0.7906 (mtp-110) cc_final: 0.7083 (mmt180)
REVERT: B  175 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8166 (mt0)
REVERT: B  214 ARG cc_start: 0.6589 (mmp-170) cc_final: 0.5773 (mmm-85)
REVERT: B  303 ASP cc_start: 0.7935 (m-30) cc_final: 0.7705 (m-30)
REVERT: B  338 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8307 (mm)
REVERT: E   17 SER cc_start: 0.8165 (m) cc_final: 0.7909 (p)
REVERT: E   18 ARG cc_start: 0.7652 (tpt170) cc_final: 0.7268 (tpt90)
REVERT: E   46 GLU cc_start: 0.7767 (pt0) cc_final: 0.7504 (pt0)
REVERT: E   67 ARG cc_start: 0.6515 (mtm110) cc_final: 0.6301 (ttm110)
REVERT: G   42 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6938 (tm-30)
  outliers start: 36
  outliers final: 24
  residues processed: 185
  average time/residue: 1.1415
  time to fit residues: 225.9355
Evaluate side-chains
  177 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 147
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   22 VAL
Chi-restraints excluded: chain R residue   35 THR
Chi-restraints excluded: chain R residue   71 THR
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue  149 VAL
Chi-restraints excluded: chain R residue  169 SER
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  199 CYS
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  376 GLN
Chi-restraints excluded: chain A residue  204 GLN
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  149 VAL
Chi-restraints excluded: chain E residue  210 THR
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 11 optimal weight:    0.4980
   chunk 91 optimal weight:    0.2980
   chunk 52 optimal weight:    7.9990
   chunk 59 optimal weight:    0.6980
   chunk 24 optimal weight:    6.9990
   chunk 42 optimal weight:    9.9990
   chunk 76 optimal weight:    0.0870
   overall best weight:    0.7160

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

Flipped N/Q/H residues before XYZ refinement:
** R  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  85 HIS
R 379 GLN
A 256 ASN
B 156 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.163913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.125725 restraints weight = 10548.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 2.18
r_work: 0.3290 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9131  Z= 0.166
  Angle     :  0.564   8.548  12375  Z= 0.288
  Chirality :  0.042   0.151   1410
  Planarity :  0.003   0.037   1559
  Dihedral  :  5.837  55.019   1312
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 18.70 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.25), residues: 1124
  helix: -0.11 (0.28), residues: 371
  sheet: -0.11 (0.31), residues: 272
  loop : -0.79 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.022   0.001   PHE R  92 
 TYR   0.008   0.001   TYR E 190 
 ARG   0.004   0.000   ARG R 176 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 154
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   94 ARG cc_start: 0.5794 (mtt180) cc_final: 0.5208 (tpp80)
REVERT: R  316 LYS cc_start: 0.8014 (mtmm) cc_final: 0.7098 (tttm)
REVERT: R  344 ARG cc_start: 0.7533 (mtm110) cc_final: 0.6925 (mtm110)
REVERT: R  376 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7712 (mm-40)
REVERT: A  204 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.6805 (mm-40)
REVERT: A  298 GLU cc_start: 0.8246 (tp30) cc_final: 0.7512 (tm-30)
REVERT: B   46 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7092 (mmt180)
REVERT: B  214 ARG cc_start: 0.6573 (mmp-170) cc_final: 0.5766 (mmm-85)
REVERT: B  338 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8301 (mm)
REVERT: E   17 SER cc_start: 0.8068 (m) cc_final: 0.7788 (p)
REVERT: E   46 GLU cc_start: 0.7731 (pt0) cc_final: 0.7499 (pt0)
REVERT: E  218 ARG cc_start: 0.7005 (mmp-170) cc_final: 0.6672 (mmp-170)
  outliers start: 38
  outliers final: 22
  residues processed: 181
  average time/residue: 1.1536
  time to fit residues: 223.7970
Evaluate side-chains
  171 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 146
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   22 VAL
Chi-restraints excluded: chain R residue   35 THR
Chi-restraints excluded: chain R residue   71 THR
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue  169 SER
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  199 CYS
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  376 GLN
Chi-restraints excluded: chain A residue  204 GLN
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  210 THR
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain E residue  226 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0870
   chunk 17 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 50 optimal weight:   20.0000
   chunk 14 optimal weight:    0.4980
   chunk 80 optimal weight:    6.9990
   overall best weight:    1.1162

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

Flipped N/Q/H residues before XYZ refinement:
** R  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  85 HIS
R 357 ASN
R 379 GLN
A 204 GLN
A 241 ASN
A 256 ASN
A 306 GLN
A 311 ASN
B 156 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.162839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.124336 restraints weight = 10668.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.19
r_work: 0.3253 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9131  Z= 0.206
  Angle     :  0.593  10.139  12375  Z= 0.302
  Chirality :  0.043   0.197   1410
  Planarity :  0.003   0.036   1559
  Dihedral  :  5.602  56.125   1311
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 19.83 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.25), residues: 1124
  helix: -0.02 (0.28), residues: 371
  sheet:  0.02 (0.31), residues: 274
  loop : -0.73 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 332 
 HIS   0.004   0.001   HIS R  85 
 PHE   0.013   0.001   PHE A 334 
 TYR   0.010   0.001   TYR E 190 
 ARG   0.005   0.000   ARG R 375 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 147
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   94 ARG cc_start: 0.5749 (mtt180) cc_final: 0.5177 (tpp80)
REVERT: R  316 LYS cc_start: 0.8011 (mtmm) cc_final: 0.7091 (tttm)
REVERT: R  344 ARG cc_start: 0.7560 (mtm110) cc_final: 0.6967 (mtm110)
REVERT: R  376 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7726 (mt0)
REVERT: A  298 GLU cc_start: 0.8255 (tp30) cc_final: 0.7515 (tm-30)
REVERT: B   46 ARG cc_start: 0.7990 (mtp-110) cc_final: 0.7139 (mmt180)
REVERT: B   75 GLN cc_start: 0.8244 (pt0) cc_final: 0.8014 (pt0)
REVERT: B  175 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8120 (mt0)
REVERT: B  214 ARG cc_start: 0.6618 (mmp-170) cc_final: 0.5800 (mmm-85)
REVERT: B  338 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8318 (mm)
REVERT: E   46 GLU cc_start: 0.7765 (pt0) cc_final: 0.7531 (pt0)
REVERT: E  218 ARG cc_start: 0.7050 (mmp-170) cc_final: 0.6634 (mmp-170)
REVERT: G   27 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7548 (mpt180)
  outliers start: 31
  outliers final: 22
  residues processed: 170
  average time/residue: 1.2414
  time to fit residues: 225.8502
Evaluate side-chains
  169 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   22 VAL
Chi-restraints excluded: chain R residue   35 THR
Chi-restraints excluded: chain R residue  169 SER
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  199 CYS
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  376 GLN
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  210 THR
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain E residue  226 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 108 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 80 optimal weight:    5.9990
   chunk 87 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** R  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  85 HIS
R 379 GLN
A 241 ASN
A 256 ASN
A 306 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.161255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.123425 restraints weight = 10772.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.17
r_work: 0.3245 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9131  Z= 0.254
  Angle     :  0.618  12.017  12375  Z= 0.313
  Chirality :  0.044   0.202   1410
  Planarity :  0.004   0.036   1559
  Dihedral  :  5.673  58.822   1311
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 19.01 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.25), residues: 1124
  helix: -0.07 (0.28), residues: 371
  sheet:  0.01 (0.31), residues: 271
  loop : -0.77 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R  85 
 PHE   0.026   0.002   PHE R  92 
 TYR   0.011   0.001   TYR E 190 
 ARG   0.006   0.000   ARG R 375 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 150
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   94 ARG cc_start: 0.5755 (mtt180) cc_final: 0.5053 (ttm110)
REVERT: R  316 LYS cc_start: 0.8050 (mtmm) cc_final: 0.7830 (mptt)
REVERT: R  344 ARG cc_start: 0.7600 (mtm110) cc_final: 0.7071 (mtm110)
REVERT: R  376 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7725 (mm-40)
REVERT: A  298 GLU cc_start: 0.8261 (tp30) cc_final: 0.7528 (tm-30)
REVERT: B   46 ARG cc_start: 0.7956 (mtp-110) cc_final: 0.7124 (mmt180)
REVERT: B  175 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8152 (mt0)
REVERT: B  214 ARG cc_start: 0.6570 (mmp-170) cc_final: 0.5678 (mmm-85)
REVERT: B  338 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8324 (mm)
REVERT: E   17 SER cc_start: 0.7948 (m) cc_final: 0.7602 (p)
REVERT: E   18 ARG cc_start: 0.7390 (ttt90) cc_final: 0.7169 (ttt90)
REVERT: E  178 LEU cc_start: 0.8874 (tt) cc_final: 0.8671 (tt)
REVERT: E  191 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7908 (mtt180)
REVERT: E  218 ARG cc_start: 0.7018 (mmp-170) cc_final: 0.6698 (mmp-170)
REVERT: G   19 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7958 (mp)
  outliers start: 39
  outliers final: 25
  residues processed: 177
  average time/residue: 1.1315
  time to fit residues: 214.3228
Evaluate side-chains
  179 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 149
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   22 VAL
Chi-restraints excluded: chain R residue   35 THR
Chi-restraints excluded: chain R residue   71 THR
Chi-restraints excluded: chain R residue  169 SER
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  199 CYS
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  376 GLN
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  191 ARG
Chi-restraints excluded: chain E residue  210 THR
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   19 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 107 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 68 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 109 optimal weight:    9.9990
   chunk 46 optimal weight:    0.0670
   overall best weight:    0.7322

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

Flipped N/Q/H residues before XYZ refinement:
R  61 ASN
R  85 HIS
R 379 GLN
A 241 ASN
A 256 ASN
A 306 GLN
A 311 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.164010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.125964 restraints weight = 10610.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.17
r_work: 0.3286 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.2797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9131  Z= 0.174
  Angle     :  0.589  12.461  12375  Z= 0.298
  Chirality :  0.042   0.146   1410
  Planarity :  0.003   0.036   1559
  Dihedral  :  5.475  55.699   1311
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 20.66 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.26), residues: 1124
  helix:  0.15 (0.28), residues: 371
  sheet:  0.14 (0.31), residues: 278
  loop : -0.66 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.012   0.001   PHE A 334 
 TYR   0.008   0.001   TYR E 190 
 ARG   0.005   0.000   ARG R 375 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 160
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   94 ARG cc_start: 0.5737 (mtt180) cc_final: 0.5217 (mmt-90)
REVERT: R  316 LYS cc_start: 0.8032 (mtmm) cc_final: 0.7136 (tttm)
REVERT: R  344 ARG cc_start: 0.7591 (mtm110) cc_final: 0.7061 (mtm110)
REVERT: R  376 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7756 (mm-40)
REVERT: A  298 GLU cc_start: 0.8257 (tp30) cc_final: 0.7544 (tm-30)
REVERT: B   46 ARG cc_start: 0.7996 (mtp-110) cc_final: 0.7133 (mmt180)
REVERT: B  175 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8119 (mt0)
REVERT: B  214 ARG cc_start: 0.6591 (mmp-170) cc_final: 0.5694 (mmm-85)
REVERT: B  338 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8375 (mm)
REVERT: E   90 ASP cc_start: 0.8515 (m-30) cc_final: 0.8300 (m-30)
REVERT: E  178 LEU cc_start: 0.8895 (tt) cc_final: 0.8684 (tt)
REVERT: E  191 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8044 (mpp80)
REVERT: E  218 ARG cc_start: 0.7016 (mmp-170) cc_final: 0.6595 (mmp-170)
REVERT: G   19 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8023 (mp)
REVERT: G   27 ARG cc_start: 0.8116 (mtt90) cc_final: 0.7543 (mpt180)
  outliers start: 29
  outliers final: 20
  residues processed: 182
  average time/residue: 1.1027
  time to fit residues: 215.3151
Evaluate side-chains
  172 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 147
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   22 VAL
Chi-restraints excluded: chain R residue   35 THR
Chi-restraints excluded: chain R residue   71 THR
Chi-restraints excluded: chain R residue  169 SER
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  199 CYS
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain R residue  376 GLN
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  191 ARG
Chi-restraints excluded: chain E residue  210 THR
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   19 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 106 optimal weight:    0.2980
   chunk 86 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   chunk 28 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   chunk 111 optimal weight:    6.9990
   chunk 110 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 59 optimal weight:    0.2980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
R  85 HIS
R 379 GLN
A 241 ASN
A 256 ASN
A 306 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.163332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.125023 restraints weight = 10648.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.19
r_work: 0.3269 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9131  Z= 0.205
  Angle     :  0.616  13.468  12375  Z= 0.311
  Chirality :  0.043   0.155   1410
  Planarity :  0.003   0.036   1559
  Dihedral  :  5.477  56.694   1311
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 21.69 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.26), residues: 1124
  helix:  0.19 (0.28), residues: 372
  sheet:  0.08 (0.31), residues: 281
  loop : -0.65 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.005   0.001   HIS R  85 
 PHE   0.031   0.001   PHE R  92 
 TYR   0.012   0.001   TYR B 289 
 ARG   0.005   0.000   ARG R 375 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 153
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   94 ARG cc_start: 0.5746 (mtt180) cc_final: 0.5215 (mmt-90)
REVERT: R  316 LYS cc_start: 0.8016 (mtmm) cc_final: 0.7118 (tttm)
REVERT: R  376 GLN cc_start: 0.8032 (mp10) cc_final: 0.7693 (mm-40)
REVERT: A  298 GLU cc_start: 0.8258 (tp30) cc_final: 0.7543 (tm-30)
REVERT: B   46 ARG cc_start: 0.8013 (mtp-110) cc_final: 0.7149 (mmt180)
REVERT: B  175 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8155 (mt0)
REVERT: B  214 ARG cc_start: 0.6585 (mmp-170) cc_final: 0.5694 (mmm-85)
REVERT: B  338 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8373 (mm)
REVERT: E   18 ARG cc_start: 0.7253 (tpt170) cc_final: 0.6950 (ttm-80)
REVERT: E  178 LEU cc_start: 0.8908 (tt) cc_final: 0.8702 (tt)
REVERT: E  191 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7910 (mtt180)
REVERT: E  218 ARG cc_start: 0.6977 (mmp-170) cc_final: 0.6539 (mmm160)
REVERT: G   19 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7988 (mp)
  outliers start: 27
  outliers final: 20
  residues processed: 174
  average time/residue: 1.3134
  time to fit residues: 246.3970
Evaluate side-chains
  174 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   22 VAL
Chi-restraints excluded: chain R residue   35 THR
Chi-restraints excluded: chain R residue   71 THR
Chi-restraints excluded: chain R residue  169 SER
Chi-restraints excluded: chain R residue  189 LEU
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  199 CYS
Chi-restraints excluded: chain R residue  350 VAL
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  191 ARG
Chi-restraints excluded: chain E residue  210 THR
Chi-restraints excluded: chain E residue  224 VAL
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   19 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:    4.9990
   chunk 44 optimal weight:    8.9990
   chunk 108 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 97 optimal weight:   30.0000
   chunk 78 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
R  85 HIS
R 379 GLN
A 241 ASN
A 256 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.158948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.120734 restraints weight = 10856.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.19
r_work: 0.3204 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   9131  Z= 0.403
  Angle     :  0.730  13.916  12375  Z= 0.372
  Chirality :  0.048   0.238   1410
  Planarity :  0.004   0.035   1559
  Dihedral  :  5.949  61.726   1311
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 21.69 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.25), residues: 1124
  helix: -0.12 (0.28), residues: 370
  sheet: -0.03 (0.30), residues: 285
  loop : -0.85 (0.29), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 169 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.018   0.002   PHE B 199 
 TYR   0.015   0.002   TYR B 105 
 ARG   0.008   0.001   ARG R 375 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7867.84 seconds
wall clock time: 137 minutes 28.72 seconds (8248.72 seconds total)