Starting phenix.real_space_refine
on Thu Mar 13 13:50:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vms_21243/03_2025/6vms_21243.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vms_21243/03_2025/6vms_21243.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vms_21243/03_2025/6vms_21243.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vms_21243/03_2025/6vms_21243.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vms_21243/03_2025/6vms_21243.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vms_21243/03_2025/6vms_21243.cif"
  }
  resolution = 3.8
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Br      1      7.06       5
     S      65      5.16       5
     C    5705      2.51       5
     N    1512      2.21       5
     O    1670      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8953
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1823
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 224}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "C"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 454
          Classifications: {'peptide': 59}
          Link IDs: {'PTRANS': 4, 'TRANS': 54}
    Chain: "E"
      Number of atoms: 1782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1782
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "R"
      Number of atoms: 2244
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2244
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 9, 'TRANS': 268}
    Chain: "R"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'08Y': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.76, per 1000 atoms: 0.64
  Number of scatterers: 8953
  At special positions: 0
  Unit cell: (103.75, 117.86, 128.65, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Br      1     34.99
     S      65     16.00
     O    1670      8.00
     N    1512      7.00
     C    5705      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 107 " - pdb=" SG  CYS R 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 399 " - pdb=" SG  CYS R 401 " 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: 2.46
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2138

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 14 sheets defined
      38.4% alpha, 24.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 3.839A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
      removed outlier: 3.527A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 213 through 216'
    Processing helix  chain 'A' and resid 228 through 232
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 273 through 281
      removed outlier: 3.864A  pdb=" N   LYS A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.589A  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 330 through 351
    Processing helix  chain 'B' and resid 3 through 24
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.518A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'C' and resid 8 through 24
      removed outlier: 3.507A  pdb=" N   ALA C  12 " --> pdb=" O   SER C   8 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   LYS C  14 " --> pdb=" O   ALA C  10 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 3.668A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 48'
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 74 through 76
      No H-bonds generated for 'chain 'E' and resid 74 through 76'
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'E' and resid 220 through 224
    Processing helix  chain 'R' and resid 35 through 40
      removed outlier: 3.515A  pdb=" N   LEU R  40 " --> pdb=" O   TYR R  37 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 41 through 62
      removed outlier: 3.547A  pdb=" N   ILE R  45 " --> pdb=" O   LEU R  41 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LEU R  54 " --> pdb=" O   PHE R  50 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   VAL R  55 " --> pdb=" O   GLY R  51 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   CYS R  56 " --> pdb=" O   ASN R  52 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 87
      removed outlier: 3.555A  pdb=" N   TYR R  71 " --> pdb=" O   THR R  67 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 87 through 97
    Processing helix  chain 'R' and resid 105 through 138
    Processing helix  chain 'R' and resid 144 through 168
      removed outlier: 3.670A  pdb=" N   LYS R 149 " --> pdb=" O   ARG R 145 " (cutoff:3.500A)
      removed outlier: 5.161A  pdb=" N   ARG R 150 " --> pdb=" O   TYR R 146 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 169 through 171
      No H-bonds generated for 'chain 'R' and resid 169 through 171'
    Processing helix  chain 'R' and resid 186 through 198
      removed outlier: 3.675A  pdb=" N   VAL R 190 " --> pdb=" O   ASN R 186 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ILE R 195 " --> pdb=" O   VAL R 191 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   VAL R 196 " --> pdb=" O   TYR R 192 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 198 through 224
      removed outlier: 4.453A  pdb=" N   ASN R 224 " --> pdb=" O   ARG R 220 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 363 through 399
      removed outlier: 3.526A  pdb=" N   LYS R 369 " --> pdb=" O   GLN R 365 " (cutoff:3.500A)
      Proline residue:  R 388  - end of helix
      removed outlier: 3.609A  pdb=" N   ILE R 397 " --> pdb=" O   HIS R 393 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   HIS R 398 " --> pdb=" O   ILE R 394 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 404 through 426
      removed outlier: 4.127A  pdb=" N   TYR R 408 " --> pdb=" O   PRO R 404 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ALA R 410 " --> pdb=" O   VAL R 406 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ASN R 418 " --> pdb=" O   LEU R 414 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   SER R 419 " --> pdb=" O   GLY R 415 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ALA R 420 " --> pdb=" O   TYR R 416 " (cutoff:3.500A)
      Proline residue:  R 423  - end of helix
    Processing helix  chain 'R' and resid 430 through 441
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.737A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.527A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 5.136A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.985A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.399A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.818A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.924A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.319A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.804A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.773A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 5.894A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.366A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.943A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.624A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 4.176A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.822A  pdb=" N   GLU E 246 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 5.163A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.822A  pdb=" N   GLU E 246 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   THR E 238 " --> pdb=" O   GLN E 231 " (cutoff:3.500A)

    459 hydrogen bonds defined for protein.
    1269 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.75

  Time building geometry restraints manager: 2.78 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2875
        1.34 -     1.47: 2292
        1.47 -     1.60: 3880
        1.60 -     1.73: 0
        1.73 -     1.86: 94
  Bond restraints: 9141
  Sorted by residual:
  bond pdb=" C25 08Y R 601 "
       pdb=" C29 08Y R 601 "
    ideal  model  delta    sigma   weight residual
    1.367  1.403 -0.036 2.00e-02 2.50e+03 3.17e+00
  bond pdb=" C   LEU R 407 "
       pdb=" N   TYR R 408 "
    ideal  model  delta    sigma   weight residual
    1.335  1.351 -0.017 1.25e-02 6.40e+03 1.84e+00
  bond pdb=" C2  08Y R 601 "
       pdb=" O1  08Y R 601 "
    ideal  model  delta    sigma   weight residual
    1.398  1.425 -0.027 2.00e-02 2.50e+03 1.76e+00
  bond pdb=" CB  VAL A 342 "
       pdb=" CG2 VAL A 342 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.36e+00
  bond pdb=" CG  LEU B 336 "
       pdb=" CD2 LEU B 336 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.31e+00
  ... (remaining 9136 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 12050
        1.82 -     3.64: 304
        3.64 -     5.47: 41
        5.47 -     7.29: 5
        7.29 -     9.11: 1
  Bond angle restraints: 12401
  Sorted by residual:
  angle pdb=" CB  LYS C  32 "
        pdb=" CG  LYS C  32 "
        pdb=" CD  LYS C  32 "
      ideal   model   delta    sigma   weight residual
     111.30  120.41   -9.11 2.30e+00 1.89e-01 1.57e+01
  angle pdb=" N   MET E 192 "
        pdb=" CA  MET E 192 "
        pdb=" C   MET E 192 "
      ideal   model   delta    sigma   weight residual
     110.80  117.44   -6.64 2.13e+00 2.20e-01 9.71e+00
  angle pdb=" N   ARG R 361 "
        pdb=" CA  ARG R 361 "
        pdb=" C   ARG R 361 "
      ideal   model   delta    sigma   weight residual
     110.80  117.11   -6.31 2.13e+00 2.20e-01 8.77e+00
  angle pdb=" N   GLY E  33 "
        pdb=" CA  GLY E  33 "
        pdb=" C   GLY E  33 "
      ideal   model   delta    sigma   weight residual
     112.89  108.41    4.48 1.58e+00 4.01e-01 8.05e+00
  angle pdb=" C   ILE B 338 "
        pdb=" N   TRP B 339 "
        pdb=" CA  TRP B 339 "
      ideal   model   delta    sigma   weight residual
     123.05  126.75   -3.70 1.40e+00 5.10e-01 7.00e+00
  ... (remaining 12396 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 5249
       17.47 -    34.94: 195
       34.94 -    52.41: 35
       52.41 -    69.88: 18
       69.88 -    87.35: 6
  Dihedral angle restraints: 5503
    sinusoidal: 2192
      harmonic: 3311
  Sorted by residual:
  dihedral pdb=" CB  CYS R 399 "
           pdb=" SG  CYS R 399 "
           pdb=" SG  CYS R 401 "
           pdb=" CB  CYS R 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -145.68   59.68     1      1.00e+01 1.00e-02 4.75e+01
  dihedral pdb=" CB  CYS E 159 "
           pdb=" SG  CYS E 159 "
           pdb=" SG  CYS E 229 "
           pdb=" CB  CYS E 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  149.27  -56.27     1      1.00e+01 1.00e-02 4.27e+01
  dihedral pdb=" CA  PRO R 139 "
           pdb=" C   PRO R 139 "
           pdb=" N   MET R 140 "
           pdb=" CA  MET R 140 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.66   22.34     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 5500 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 765
       0.029 -    0.058: 431
       0.058 -    0.087: 140
       0.087 -    0.116: 70
       0.116 -    0.145: 13
  Chirality restraints: 1419
  Sorted by residual:
  chirality pdb=" CA  ILE A 221 "
            pdb=" N   ILE A 221 "
            pdb=" C   ILE A 221 "
            pdb=" CB  ILE A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.25e-01
  chirality pdb=" CA  ILE A 265 "
            pdb=" N   ILE A 265 "
            pdb=" C   ILE A 265 "
            pdb=" CB  ILE A 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.59e-01
  chirality pdb=" CA  VAL B 135 "
            pdb=" N   VAL B 135 "
            pdb=" C   VAL B 135 "
            pdb=" CB  VAL B 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.12e-01
  ... (remaining 1416 not shown)

  Planarity restraints: 1557
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C21 08Y R 601 "   -0.099 2.00e-02 2.50e+03   8.71e-02 2.28e+02
        pdb=" C23 08Y R 601 "    0.157 2.00e-02 2.50e+03
        pdb=" C24 08Y R 601 "   -0.063 2.00e-02 2.50e+03
        pdb=" C25 08Y R 601 "   -0.032 2.00e-02 2.50e+03
        pdb=" C26 08Y R 601 "   -0.107 2.00e-02 2.50e+03
        pdb=" C28 08Y R 601 "   -0.087 2.00e-02 2.50e+03
        pdb=" C29 08Y R 601 "   -0.021 2.00e-02 2.50e+03
        pdb=" C30 08Y R 601 "    0.092 2.00e-02 2.50e+03
        pdb=" C31 08Y R 601 "    0.023 2.00e-02 2.50e+03
        pdb=" C32 08Y R 601 "    0.122 2.00e-02 2.50e+03
        pdb=" N5  08Y R 601 "   -0.056 2.00e-02 2.50e+03
        pdb="BR   08Y R 601 "    0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  08Y R 601 "    0.060 2.00e-02 2.50e+03   5.54e-02 4.61e+01
        pdb=" C3  08Y R 601 "   -0.071 2.00e-02 2.50e+03
        pdb=" C6  08Y R 601 "   -0.074 2.00e-02 2.50e+03
        pdb=" C9  08Y R 601 "    0.008 2.00e-02 2.50e+03
        pdb=" N2  08Y R 601 "    0.011 2.00e-02 2.50e+03
        pdb=" O4  08Y R 601 "    0.065 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  08Y R 601 "   -0.067 2.00e-02 2.50e+03   4.51e-02 3.05e+01
        pdb=" C3  08Y R 601 "    0.035 2.00e-02 2.50e+03
        pdb=" C5  08Y R 601 "    0.055 2.00e-02 2.50e+03
        pdb=" C8  08Y R 601 "   -0.000 2.00e-02 2.50e+03
        pdb=" N1  08Y R 601 "    0.028 2.00e-02 2.50e+03
        pdb=" O3  08Y R 601 "   -0.051 2.00e-02 2.50e+03
  ... (remaining 1554 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 112
        2.65 -     3.21: 8326
        3.21 -     3.77: 13346
        3.77 -     4.34: 19193
        4.34 -     4.90: 31065
  Nonbonded interactions: 72042
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.082 3.040
  nonbonded pdb=" O   ALA A  41 "
            pdb=" OG  SER A  44 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" O   SER E  30 "
            pdb=" OG  SER E  53 "
     model   vdw
     2.116 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" OG  SER E 106 "
            pdb=" OH  TYR E 190 "
     model   vdw
     2.227 3.040
  ... (remaining 72037 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 group one per residue
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:             1.420
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.750
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6893
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9141  Z= 0.306
  Angle     :  0.704   9.108  12401  Z= 0.393
  Chirality :  0.043   0.145   1419
  Planarity :  0.005   0.087   1557
  Dihedral  : 11.035  87.351   3353
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.27 (0.24), residues: 1121
  helix: -0.49 (0.24), residues: 380
  sheet:  0.63 (0.29), residues: 275
  loop : -0.23 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP B  82 
 HIS   0.005   0.001   HIS R 106 
 PHE   0.016   0.002   PHE B 234 
 TYR   0.012   0.002   TYR R 146 
 ARG   0.011   0.001   ARG B 314 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 312
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 PHE cc_start: 0.7739 (t80) cc_final: 0.7508 (t80)
REVERT: A  228 SER cc_start: 0.7575 (p) cc_final: 0.6988 (p)
REVERT: A  273 LEU cc_start: 0.8501 (mt) cc_final: 0.8101 (tt)
REVERT: B   76 ASP cc_start: 0.6632 (t0) cc_final: 0.6373 (t0)
REVERT: B  171 ILE cc_start: 0.7446 (tp) cc_final: 0.7173 (tp)
REVERT: E   60 TYR cc_start: 0.7906 (m-80) cc_final: 0.7482 (m-80)
REVERT: E   68 PHE cc_start: 0.7615 (m-10) cc_final: 0.7041 (m-10)
REVERT: E   71 SER cc_start: 0.6618 (t) cc_final: 0.6020 (p)
REVERT: E   83 MET cc_start: 0.8704 (mtt) cc_final: 0.8474 (mtm)
REVERT: E  234 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7945 (mm-30)
REVERT: R  164 PHE cc_start: 0.7718 (t80) cc_final: 0.7498 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 312
  average time/residue: 0.2528
  time to fit residues: 102.1528
Evaluate side-chains
  175 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 44 optimal weight:    4.9990
   chunk 86 optimal weight:    0.0970
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
B 220 GLN
B 266 HIS
B 295 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  18 GLN
C  44 HIS
** E  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 179 GLN
R 106 HIS
R 179 GLN
** R 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.170733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.142251 restraints weight = 12004.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.142444 restraints weight = 13019.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.143285 restraints weight = 11892.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9141  Z= 0.263
  Angle     :  0.683   7.998  12401  Z= 0.369
  Chirality :  0.047   0.208   1419
  Planarity :  0.005   0.058   1557
  Dihedral  :  5.787  65.932   1312
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 11.02 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: 1121
  helix:  0.76 (0.26), residues: 394
  sheet:  0.76 (0.29), residues: 279
  loop :  0.14 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 100 
 HIS   0.013   0.002   HIS R 393 
 PHE   0.029   0.002   PHE R 390 
 TYR   0.021   0.002   TYR B  59 
 ARG   0.006   0.001   ARG A  32 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 210
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  273 LEU cc_start: 0.8394 (mt) cc_final: 0.7998 (tt)
REVERT: A  345 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7875 (mttm)
REVERT: B   59 TYR cc_start: 0.8556 (m-80) cc_final: 0.8230 (m-80)
REVERT: B   76 ASP cc_start: 0.6703 (t0) cc_final: 0.6428 (t0)
REVERT: B  188 MET cc_start: 0.8670 (mmm) cc_final: 0.8298 (mmm)
REVERT: B  191 SER cc_start: 0.8235 (t) cc_final: 0.8013 (t)
REVERT: B  266 HIS cc_start: 0.6528 (t-170) cc_final: 0.6161 (t70)
REVERT: B  334 SER cc_start: 0.8323 (m) cc_final: 0.8088 (p)
REVERT: R   91 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8232 (p)
REVERT: R  369 LYS cc_start: 0.6124 (tttp) cc_final: 0.5909 (mmmt)
  outliers start: 32
  outliers final: 18
  residues processed: 229
  average time/residue: 0.2402
  time to fit residues: 72.9079
Evaluate side-chains
  186 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 167
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain C residue   24 ASN
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue   21 SER
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain R residue   74 VAL
Chi-restraints excluded: chain R residue   91 VAL
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  103 SER
Chi-restraints excluded: chain R residue  153 THR
Chi-restraints excluded: chain R residue  399 CYS
Chi-restraints excluded: chain R residue  408 TYR
Chi-restraints excluded: chain R residue  433 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 78 optimal weight:    0.0970
   chunk 72 optimal weight:    7.9990
   chunk 37 optimal weight:    0.3980
   chunk 74 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0870
   chunk 61 optimal weight:   20.0000
   chunk 96 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 10 optimal weight:    0.1980
   overall best weight:    0.2956

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 220 GLN
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 179 GLN
** R 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.167261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.136425 restraints weight = 12340.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.137701 restraints weight = 11324.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.139808 restraints weight = 9003.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.4334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9141  Z= 0.167
  Angle     :  0.587   7.895  12401  Z= 0.314
  Chirality :  0.044   0.146   1419
  Planarity :  0.004   0.040   1557
  Dihedral  :  5.482  62.552   1312
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.29 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.84 (0.25), residues: 1121
  helix:  1.18 (0.27), residues: 392
  sheet:  0.81 (0.29), residues: 275
  loop : -0.04 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 100 
 HIS   0.008   0.001   HIS R 393 
 PHE   0.020   0.002   PHE R 172 
 TYR   0.018   0.001   TYR A 287 
 ARG   0.006   0.001   ARG A 242 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  273 LEU cc_start: 0.8197 (mt) cc_final: 0.7873 (tt)
REVERT: B   76 ASP cc_start: 0.6413 (t0) cc_final: 0.6155 (t0)
REVERT: B  290 ASP cc_start: 0.8561 (m-30) cc_final: 0.8347 (m-30)
REVERT: B  334 SER cc_start: 0.8296 (m) cc_final: 0.8078 (p)
REVERT: C   28 ILE cc_start: 0.7270 (pt) cc_final: 0.7052 (pt)
REVERT: E  192 MET cc_start: 0.8487 (ptt) cc_final: 0.8223 (ptt)
REVERT: R   93 TYR cc_start: 0.7092 (t80) cc_final: 0.6861 (t80)
REVERT: R  220 ARG cc_start: 0.5899 (ttt-90) cc_final: 0.5455 (ttt90)
REVERT: R  413 TRP cc_start: 0.7238 (m100) cc_final: 0.6086 (m-10)
  outliers start: 19
  outliers final: 15
  residues processed: 198
  average time/residue: 0.2362
  time to fit residues: 62.9233
Evaluate side-chains
  175 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 160
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain E residue   21 SER
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain R residue   74 VAL
Chi-restraints excluded: chain R residue  103 SER
Chi-restraints excluded: chain R residue  399 CYS
Chi-restraints excluded: chain R residue  408 TYR
Chi-restraints excluded: chain R residue  433 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 95 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0370
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    0.7980
   chunk 108 optimal weight:    0.0870
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 68 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
A 269 ASN
B 176 GLN
** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  13 GLN
E 179 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.165262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.133895 restraints weight = 12212.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.134824 restraints weight = 11746.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.136087 restraints weight = 9487.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.4804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9141  Z= 0.164
  Angle     :  0.563   7.279  12401  Z= 0.299
  Chirality :  0.043   0.182   1419
  Planarity :  0.003   0.037   1557
  Dihedral  :  5.250  59.485   1312
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.31 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.84 (0.25), residues: 1121
  helix:  1.37 (0.28), residues: 389
  sheet:  0.70 (0.29), residues: 277
  loop : -0.15 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 100 
 HIS   0.002   0.001   HIS E 167 
 PHE   0.022   0.001   PHE R 389 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.007   0.001   ARG R 217 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 178
  time to evaluate  : 1.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7314 (mt-10)
REVERT: A  273 LEU cc_start: 0.8174 (mt) cc_final: 0.7907 (tt)
REVERT: B   76 ASP cc_start: 0.6451 (t0) cc_final: 0.6146 (t0)
REVERT: B  175 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7276 (mm110)
REVERT: B  334 SER cc_start: 0.8405 (m) cc_final: 0.8168 (p)
REVERT: E   18 ARG cc_start: 0.7671 (tpp-160) cc_final: 0.7307 (tpp-160)
REVERT: E  192 MET cc_start: 0.8645 (ptt) cc_final: 0.8148 (ptt)
  outliers start: 25
  outliers final: 16
  residues processed: 191
  average time/residue: 0.2972
  time to fit residues: 77.0700
Evaluate side-chains
  180 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 164
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain R residue   74 VAL
Chi-restraints excluded: chain R residue  103 SER
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  399 CYS
Chi-restraints excluded: chain R residue  408 TYR
Chi-restraints excluded: chain R residue  433 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   chunk 101 optimal weight:    0.6980
   chunk 44 optimal weight:    6.9990
   chunk 54 optimal weight:    8.9990
   chunk 95 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.156419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.126011 restraints weight = 12086.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.126091 restraints weight = 11679.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.127390 restraints weight = 11754.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.6006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9141  Z= 0.310
  Angle     :  0.658   6.607  12401  Z= 0.349
  Chirality :  0.047   0.220   1419
  Planarity :  0.004   0.036   1557
  Dihedral  :  5.418  57.686   1312
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 16.02 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.53 (0.25), residues: 1121
  helix:  1.28 (0.27), residues: 385
  sheet:  0.25 (0.28), residues: 293
  loop : -0.29 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 100 
 HIS   0.009   0.001   HIS A 244 
 PHE   0.032   0.002   PHE R 172 
 TYR   0.029   0.002   TYR E 190 
 ARG   0.007   0.001   ARG C  13 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 195
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.7961 (m-30) cc_final: 0.7682 (m-30)
REVERT: A  228 SER cc_start: 0.7798 (p) cc_final: 0.7391 (t)
REVERT: A  273 LEU cc_start: 0.8441 (mt) cc_final: 0.8229 (tt)
REVERT: B   76 ASP cc_start: 0.6982 (t0) cc_final: 0.6731 (t0)
REVERT: B  175 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7632 (mm110)
REVERT: B  191 SER cc_start: 0.8747 (t) cc_final: 0.8225 (t)
REVERT: B  234 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8561 (m-80)
REVERT: E   93 MET cc_start: 0.8706 (tpp) cc_final: 0.8130 (ttt)
REVERT: E  192 MET cc_start: 0.8498 (ptt) cc_final: 0.7867 (ptt)
REVERT: R   48 ILE cc_start: 0.6591 (OUTLIER) cc_final: 0.6346 (pp)
REVERT: R  140 MET cc_start: 0.7779 (mmm) cc_final: 0.7246 (mmm)
REVERT: R  369 LYS cc_start: 0.5279 (tppt) cc_final: 0.4846 (tptt)
  outliers start: 33
  outliers final: 24
  residues processed: 217
  average time/residue: 0.2267
  time to fit residues: 66.1603
Evaluate side-chains
  194 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  337 ASP
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  253 PHE
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue   21 SER
Chi-restraints excluded: chain E residue  190 TYR
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain R residue   48 ILE
Chi-restraints excluded: chain R residue   74 VAL
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue  103 SER
Chi-restraints excluded: chain R residue  130 ILE
Chi-restraints excluded: chain R residue  136 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  399 CYS
Chi-restraints excluded: chain R residue  408 TYR
Chi-restraints excluded: chain R residue  433 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 107 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 66 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 84 optimal weight:    7.9990
   chunk 101 optimal weight:    0.8980
   chunk 56 optimal weight:    9.9990
   chunk 24 optimal weight:   20.0000
   chunk 83 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
B 220 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.146863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.114675 restraints weight = 12055.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.114145 restraints weight = 11838.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.116259 restraints weight = 11022.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.6721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   9141  Z= 0.368
  Angle     :  0.664   8.674  12401  Z= 0.353
  Chirality :  0.048   0.238   1419
  Planarity :  0.004   0.035   1557
  Dihedral  :  5.476  57.873   1312
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 17.86 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.28 (0.25), residues: 1121
  helix:  1.01 (0.27), residues: 386
  sheet:  0.22 (0.28), residues: 285
  loop : -0.45 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.007   0.001   HIS E 232 
 PHE   0.028   0.002   PHE R 390 
 TYR   0.023   0.002   TYR E 190 
 ARG   0.006   0.001   ARG A 313 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 186
  time to evaluate  : 0.954 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7939 (m-30) cc_final: 0.7725 (m-30)
REVERT: A   33 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7718 (mt-10)
REVERT: A  228 SER cc_start: 0.7848 (OUTLIER) cc_final: 0.7447 (t)
REVERT: B   76 ASP cc_start: 0.7097 (t0) cc_final: 0.6870 (t0)
REVERT: B  191 SER cc_start: 0.8815 (t) cc_final: 0.8418 (t)
REVERT: B  234 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8814 (m-80)
REVERT: C   15 LEU cc_start: 0.7330 (mp) cc_final: 0.7044 (tp)
REVERT: E   93 MET cc_start: 0.8689 (tpp) cc_final: 0.8060 (ttt)
REVERT: E  192 MET cc_start: 0.8571 (ptt) cc_final: 0.7896 (ptt)
REVERT: R  367 LYS cc_start: 0.6855 (tptt) cc_final: 0.6643 (tppt)
REVERT: R  377 ILE cc_start: 0.8581 (mm) cc_final: 0.8365 (mt)
  outliers start: 40
  outliers final: 29
  residues processed: 210
  average time/residue: 0.2463
  time to fit residues: 69.1038
Evaluate side-chains
  199 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 168
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  253 PHE
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain C residue   24 ASN
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue   21 SER
Chi-restraints excluded: chain E residue  138 ILE
Chi-restraints excluded: chain E residue  190 TYR
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain R residue   39 THR
Chi-restraints excluded: chain R residue   74 VAL
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  136 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  193 SER
Chi-restraints excluded: chain R residue  399 CYS
Chi-restraints excluded: chain R residue  408 TYR
Chi-restraints excluded: chain R residue  433 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 179 GLN
R  66 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.151756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.119735 restraints weight = 12010.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.119621 restraints weight = 11400.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.121963 restraints weight = 10679.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.7013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9141  Z= 0.237
  Angle     :  0.600   8.536  12401  Z= 0.318
  Chirality :  0.045   0.207   1419
  Planarity :  0.004   0.038   1557
  Dihedral  :  5.234  55.761   1312
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 19.49 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.27 (0.25), residues: 1121
  helix:  1.08 (0.27), residues: 391
  sheet:  0.23 (0.28), residues: 283
  loop : -0.57 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 100 
 HIS   0.003   0.001   HIS R 393 
 PHE   0.028   0.002   PHE R 390 
 TYR   0.021   0.001   TYR E 190 
 ARG   0.006   0.001   ARG A  32 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 190
  time to evaluate  : 0.924 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7784 (m-30) cc_final: 0.7552 (m-30)
REVERT: A   33 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7662 (mt-10)
REVERT: A  228 SER cc_start: 0.7760 (OUTLIER) cc_final: 0.7186 (t)
REVERT: A  287 TYR cc_start: 0.7527 (m-80) cc_final: 0.7268 (m-80)
REVERT: B   76 ASP cc_start: 0.6975 (t0) cc_final: 0.6714 (t0)
REVERT: B  191 SER cc_start: 0.8750 (t) cc_final: 0.8307 (t)
REVERT: B  234 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8801 (m-80)
REVERT: C   58 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6581 (tt0)
REVERT: E   93 MET cc_start: 0.8681 (tpp) cc_final: 0.8044 (ttt)
REVERT: E  192 MET cc_start: 0.8603 (ptt) cc_final: 0.7563 (ptt)
REVERT: R  171 LEU cc_start: 0.7720 (mt) cc_final: 0.7186 (mp)
REVERT: R  367 LYS cc_start: 0.6745 (tptt) cc_final: 0.6331 (tppt)
REVERT: R  369 LYS cc_start: 0.6201 (mmmt) cc_final: 0.5633 (tptt)
  outliers start: 34
  outliers final: 25
  residues processed: 206
  average time/residue: 0.2397
  time to fit residues: 65.7703
Evaluate side-chains
  201 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 174
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue   21 SER
Chi-restraints excluded: chain E residue  138 ILE
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  190 TYR
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain R residue   74 VAL
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  193 SER
Chi-restraints excluded: chain R residue  399 CYS
Chi-restraints excluded: chain R residue  408 TYR
Chi-restraints excluded: chain R residue  433 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 40 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 109 optimal weight:    4.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 398 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.150706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.117959 restraints weight = 12056.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.118531 restraints weight = 11957.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.120666 restraints weight = 9888.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.7214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9141  Z= 0.251
  Angle     :  0.604   8.302  12401  Z= 0.322
  Chirality :  0.045   0.199   1419
  Planarity :  0.004   0.047   1557
  Dihedral  :  5.263  56.352   1312
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 19.80 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.26 (0.25), residues: 1121
  helix:  1.20 (0.27), residues: 389
  sheet:  0.07 (0.28), residues: 285
  loop : -0.58 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 100 
 HIS   0.004   0.001   HIS R 393 
 PHE   0.031   0.002   PHE R 390 
 TYR   0.020   0.001   TYR E 190 
 ARG   0.006   0.000   ARG A  32 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 183
  time to evaluate  : 0.950 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7771 (m-30) cc_final: 0.7569 (m-30)
REVERT: A   33 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7689 (mt-10)
REVERT: A  228 SER cc_start: 0.7844 (OUTLIER) cc_final: 0.7500 (t)
REVERT: A  256 ASN cc_start: 0.8349 (t0) cc_final: 0.7965 (m-40)
REVERT: A  313 ARG cc_start: 0.7594 (mtm-85) cc_final: 0.7346 (ttm110)
REVERT: B   67 SER cc_start: 0.9334 (m) cc_final: 0.8646 (t)
REVERT: B   76 ASP cc_start: 0.7023 (t0) cc_final: 0.6776 (t0)
REVERT: B  191 SER cc_start: 0.8772 (t) cc_final: 0.8349 (t)
REVERT: B  234 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8871 (m-80)
REVERT: B  254 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7365 (m-30)
REVERT: C   58 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6510 (tt0)
REVERT: E   93 MET cc_start: 0.8698 (tpp) cc_final: 0.8067 (ttt)
REVERT: R  140 MET cc_start: 0.7716 (mmm) cc_final: 0.7158 (mmm)
REVERT: R  367 LYS cc_start: 0.6713 (tptt) cc_final: 0.6299 (tppt)
REVERT: R  369 LYS cc_start: 0.6341 (mmmt) cc_final: 0.5707 (tptt)
  outliers start: 38
  outliers final: 30
  residues processed: 205
  average time/residue: 0.2480
  time to fit residues: 67.3649
Evaluate side-chains
  206 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 173
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue   21 SER
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue  138 ILE
Chi-restraints excluded: chain E residue  150 THR
Chi-restraints excluded: chain E residue  190 TYR
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain R residue   74 VAL
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  136 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  193 SER
Chi-restraints excluded: chain R residue  399 CYS
Chi-restraints excluded: chain R residue  408 TYR
Chi-restraints excluded: chain R residue  433 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 8 optimal weight:    0.6980
   chunk 42 optimal weight:    7.9990
   chunk 75 optimal weight:    0.1980
   chunk 85 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 99 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.150913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.118382 restraints weight = 11886.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.118719 restraints weight = 10979.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.120687 restraints weight = 10264.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.7403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9141  Z= 0.236
  Angle     :  0.616  10.627  12401  Z= 0.329
  Chirality :  0.045   0.201   1419
  Planarity :  0.004   0.034   1557
  Dihedral  :  5.245  56.086   1312
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 20.51 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.25 (0.25), residues: 1121
  helix:  1.24 (0.27), residues: 389
  sheet:  0.06 (0.29), residues: 284
  loop : -0.63 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP R 100 
 HIS   0.004   0.001   HIS R 393 
 PHE   0.033   0.002   PHE R 390 
 TYR   0.020   0.001   TYR E 190 
 ARG   0.005   0.000   ARG C  13 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 183
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7681 (mt-10)
REVERT: A  228 SER cc_start: 0.7857 (OUTLIER) cc_final: 0.7533 (t)
REVERT: A  256 ASN cc_start: 0.8327 (t0) cc_final: 0.7983 (m-40)
REVERT: A  313 ARG cc_start: 0.7574 (mtm-85) cc_final: 0.7354 (ttm110)
REVERT: B   67 SER cc_start: 0.9331 (m) cc_final: 0.8659 (t)
REVERT: B   76 ASP cc_start: 0.7011 (t0) cc_final: 0.6757 (t0)
REVERT: B  191 SER cc_start: 0.8769 (t) cc_final: 0.8365 (t)
REVERT: B  234 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.8881 (m-80)
REVERT: B  254 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7366 (m-30)
REVERT: C   15 LEU cc_start: 0.7452 (tp) cc_final: 0.7251 (tp)
REVERT: C   32 LYS cc_start: 0.7576 (ptmm) cc_final: 0.7198 (ttpp)
REVERT: E   93 MET cc_start: 0.8702 (tpp) cc_final: 0.8036 (ttt)
REVERT: R  140 MET cc_start: 0.7744 (mmm) cc_final: 0.7262 (mmm)
REVERT: R  367 LYS cc_start: 0.6652 (tptt) cc_final: 0.6290 (tppt)
REVERT: R  369 LYS cc_start: 0.6235 (mmmt) cc_final: 0.5633 (tptt)
REVERT: R  403 ILE cc_start: 0.8009 (tp) cc_final: 0.7512 (mm)
  outliers start: 35
  outliers final: 29
  residues processed: 203
  average time/residue: 0.2529
  time to fit residues: 67.6855
Evaluate side-chains
  205 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 173
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue   21 SER
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue  138 ILE
Chi-restraints excluded: chain E residue  150 THR
Chi-restraints excluded: chain E residue  190 TYR
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain R residue   74 VAL
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue   96 VAL
Chi-restraints excluded: chain R residue  136 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  193 SER
Chi-restraints excluded: chain R residue  208 VAL
Chi-restraints excluded: chain R residue  399 CYS
Chi-restraints excluded: chain R residue  408 TYR
Chi-restraints excluded: chain R residue  433 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 86 optimal weight:    0.1980
   chunk 96 optimal weight:    4.9990
   chunk 104 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 73 optimal weight:    0.1980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.153845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.121175 restraints weight = 11937.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.121728 restraints weight = 11380.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.123240 restraints weight = 11309.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.7519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9141  Z= 0.174
  Angle     :  0.594  11.268  12401  Z= 0.318
  Chirality :  0.044   0.190   1419
  Planarity :  0.004   0.069   1557
  Dihedral  :  5.124  56.470   1312
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 21.43 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.35 (0.25), residues: 1121
  helix:  1.31 (0.27), residues: 392
  sheet:  0.18 (0.29), residues: 283
  loop : -0.62 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 100 
 HIS   0.003   0.001   HIS R 393 
 PHE   0.027   0.001   PHE R 390 
 TYR   0.020   0.001   TYR A 287 
 ARG   0.008   0.001   ARG A  32 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 189
  time to evaluate  : 1.066 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7537 (tt0) cc_final: 0.7257 (tt0)
REVERT: A   33 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7673 (mt-10)
REVERT: A  228 SER cc_start: 0.7848 (OUTLIER) cc_final: 0.7528 (t)
REVERT: A  256 ASN cc_start: 0.8335 (t0) cc_final: 0.7991 (m-40)
REVERT: B   67 SER cc_start: 0.9293 (m) cc_final: 0.8677 (t)
REVERT: B   76 ASP cc_start: 0.6892 (t0) cc_final: 0.6618 (t0)
REVERT: C   11 GLN cc_start: 0.5622 (mp10) cc_final: 0.4792 (mt0)
REVERT: C   32 LYS cc_start: 0.7722 (ptmm) cc_final: 0.7309 (ttpp)
REVERT: E   93 MET cc_start: 0.8722 (tpp) cc_final: 0.8126 (ttt)
REVERT: E  192 MET cc_start: 0.8287 (ptt) cc_final: 0.7168 (ptt)
REVERT: E  237 LEU cc_start: 0.9032 (mp) cc_final: 0.8829 (mp)
REVERT: R  140 MET cc_start: 0.7758 (mmm) cc_final: 0.7244 (mmm)
REVERT: R  367 LYS cc_start: 0.6537 (tptt) cc_final: 0.6251 (tppt)
REVERT: R  369 LYS cc_start: 0.6082 (mmmt) cc_final: 0.5522 (tptt)
REVERT: R  403 ILE cc_start: 0.8078 (tp) cc_final: 0.7570 (mm)
  outliers start: 28
  outliers final: 24
  residues processed: 206
  average time/residue: 0.2488
  time to fit residues: 67.7327
Evaluate side-chains
  200 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 175
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue  138 ILE
Chi-restraints excluded: chain E residue  150 THR
Chi-restraints excluded: chain E residue  190 TYR
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain R residue   74 VAL
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  193 SER
Chi-restraints excluded: chain R residue  208 VAL
Chi-restraints excluded: chain R residue  399 CYS
Chi-restraints excluded: chain R residue  408 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 60 optimal weight:    8.9990
   chunk 83 optimal weight:    0.0070
   chunk 84 optimal weight:    0.0470
   chunk 89 optimal weight:    0.0270
   chunk 14 optimal weight:    0.0470
   chunk 25 optimal weight:    6.9990
   overall best weight:    0.1852

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.153627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.120837 restraints weight = 12041.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.121498 restraints weight = 10511.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.123333 restraints weight = 9202.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.7614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9141  Z= 0.153
  Angle     :  0.601  11.590  12401  Z= 0.321
  Chirality :  0.044   0.264   1419
  Planarity :  0.004   0.035   1557
  Dihedral  :  5.050  56.436   1312
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 23.27 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.43 (0.25), residues: 1121
  helix:  1.42 (0.27), residues: 388
  sheet:  0.31 (0.29), residues: 282
  loop : -0.66 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 211 
 HIS   0.005   0.001   HIS R 393 
 PHE   0.027   0.001   PHE R 390 
 TYR   0.015   0.001   TYR E 190 
 ARG   0.014   0.001   ARG C  13 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2974.70 seconds
wall clock time: 53 minutes 14.89 seconds (3194.89 seconds total)