Starting phenix.real_space_refine
on Fri Sep 11 10:05:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vms_21243/09_2026/6vms_21243.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vms_21243/09_2026/6vms_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_21243/09_2026/6vms_21243.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vms_21243/09_2026/6vms_21243.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vms_21243/09_2026/6vms_21243.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vms_21243/09_2026/6vms_21243.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 1.94, per 1000 atoms: 0.22
  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: 0.75
  Conformation dependent library (CDL) restraints added in 325.3 milliseconds
  

  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: 0.27
  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: 1.51

  Time building geometry restraints manager: 0.99 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:             1.320
  Set stop_for_unknowns flag:              0.010
  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:          0.190
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.030
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
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   9145  Z= 0.201
  Angle     :  0.706   9.108  12409  Z= 0.394
  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 : 5.77
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (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
 ARG   0.011   0.001   ARG B 314 
 TYR   0.012   0.002   TYR R 146 
 PHE   0.016   0.002   PHE B 234 
 TRP   0.025   0.003   TRP B  82 
 HIS   0.005   0.001   HIS R 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00469 /  0.20 ( 9141)
  covalent geometry    : angle       0.70438 /  0.39 (12401)
  SS BOND              : bond        0.00368 /  0.24 (    4)
  SS BOND              : angle       1.92235 /  1.14 (    8)
  hydrogen bonds       : bond        0.16323 / 10.98 (  449)
  hydrogen bonds       : angle       7.69191 /  5.49 ( 1269)

*********************** 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  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 PHE cc_start: 0.7740 (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: 0.1141
  time to fit residues: 46.9362
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  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0770
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   overall best weight:    0.9740

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.4034 r_free = 0.4034 target = 0.172523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.144409 restraints weight = 12257.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.144691 restraints weight = 12992.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.146038 restraints weight = 10853.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.146362 restraints weight = 8748.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.146821 restraints weight = 7900.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9145  Z= 0.163
  Angle     :  0.666   7.778  12409  Z= 0.358
  Chirality :  0.046   0.196   1419
  Planarity :  0.005   0.055   1557
  Dihedral  :  5.736  65.439   1312
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 11.43 %
    Favored  : 85.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.25), residues: 1121
  helix:  0.80 (0.26), residues: 393
  sheet:  0.85 (0.29), residues: 277
  loop :  0.12 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 314 
 TYR   0.019   0.002   TYR B  59 
 PHE   0.028   0.002   PHE R 390 
 TRP   0.019   0.002   TRP R 100 
 HIS   0.014   0.002   HIS R 393 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.16 ( 9141)
  covalent geometry    : angle       0.66393 /  0.36 (12401)
  SS BOND              : bond        0.00452 /  0.28 (    4)
  SS BOND              : angle       2.07852 /  1.24 (    8)
  hydrogen bonds       : bond        0.04497 /  2.97 (  449)
  hydrogen bonds       : angle       5.50946 /  3.89 ( 1269)

*********************** 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
  239 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 209
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  273 LEU cc_start: 0.8230 (mt) cc_final: 0.7857 (tt)
REVERT: A  345 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7901 (mttm)
REVERT: B   59 TYR cc_start: 0.8499 (m-80) cc_final: 0.8200 (m-80)
REVERT: B   76 ASP cc_start: 0.6536 (t0) cc_final: 0.6268 (t0)
REVERT: B  188 MET cc_start: 0.8601 (mmm) cc_final: 0.8321 (mmm)
REVERT: B  191 SER cc_start: 0.8132 (t) cc_final: 0.7906 (t)
REVERT: B  266 HIS cc_start: 0.6341 (t-170) cc_final: 0.6038 (t70)
REVERT: B  334 SER cc_start: 0.8194 (m) cc_final: 0.7918 (p)
  outliers start: 30
  outliers final: 17
  residues processed: 226
  average time/residue: 0.1098
  time to fit residues: 33.2367
Evaluate side-chains
  183 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
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  213 THR
Chi-restraints excluded: chain R residue   74 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 33 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 51 optimal weight:    0.2980
   chunk 43 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 93 optimal weight:    0.0670
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.5718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3974 r_free = 0.3974 target = 0.166878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.135207 restraints weight = 12339.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.136415 restraints weight = 11614.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.137470 restraints weight = 9287.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.137721 restraints weight = 8095.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.140635 restraints weight = 7071.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.4406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9145  Z= 0.125
  Angle     :  0.589   8.305  12409  Z= 0.316
  Chirality :  0.044   0.166   1419
  Planarity :  0.004   0.038   1557
  Dihedral  :  5.454  62.064   1312
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.67 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.25), residues: 1121
  helix:  1.18 (0.27), residues: 392
  sheet:  0.71 (0.29), residues: 269
  loop : -0.06 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 217 
 TYR   0.019   0.001   TYR A 287 
 PHE   0.021   0.002   PHE R 172 
 TRP   0.023   0.002   TRP R 100 
 HIS   0.009   0.001   HIS R 393 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.13 ( 9141)
  covalent geometry    : angle       0.58840 /  0.32 (12401)
  SS BOND              : bond        0.00430 /  0.30 (    4)
  SS BOND              : angle       1.48806 /  0.83 (    8)
  hydrogen bonds       : bond        0.03853 /  2.54 (  449)
  hydrogen bonds       : angle       5.23038 /  3.69 ( 1269)

*********************** 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
  205 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  273 LEU cc_start: 0.8271 (mt) cc_final: 0.7943 (tt)
REVERT: B   10 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6753 (pt0)
REVERT: B   76 ASP cc_start: 0.6477 (t0) cc_final: 0.6206 (t0)
REVERT: B  175 GLN cc_start: 0.7507 (mm-40) cc_final: 0.7254 (mm110)
REVERT: B  334 SER cc_start: 0.8389 (m) cc_final: 0.8185 (p)
REVERT: E  192 MET cc_start: 0.8477 (ptt) cc_final: 0.8094 (ptt)
REVERT: R   93 TYR cc_start: 0.7235 (t80) cc_final: 0.6692 (t80)
REVERT: R  100 TRP cc_start: 0.4919 (t60) cc_final: 0.3892 (t60)
REVERT: R  220 ARG cc_start: 0.5884 (ttt-90) cc_final: 0.5384 (ttt90)
  outliers start: 20
  outliers final: 13
  residues processed: 198
  average time/residue: 0.1027
  time to fit residues: 27.6739
Evaluate side-chains
  168 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 155
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain B residue  189 SER
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 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 94 optimal weight:    9.9990
   chunk 70 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 91 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.3984

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.159324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.127107 restraints weight = 12236.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.128755 restraints weight = 11118.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.130433 restraints weight = 9207.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.130774 restraints weight = 6952.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.131164 restraints weight = 6491.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.5187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9145  Z= 0.166
  Angle     :  0.601   6.473  12409  Z= 0.320
  Chirality :  0.045   0.196   1419
  Planarity :  0.004   0.040   1557
  Dihedral  :  5.371  60.432   1312
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 14.59 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.25), residues: 1121
  helix:  1.40 (0.28), residues: 383
  sheet:  0.42 (0.28), residues: 291
  loop : -0.14 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 217 
 TYR   0.017   0.001   TYR E 190 
 PHE   0.019   0.002   PHE R 389 
 TRP   0.013   0.002   TRP R 100 
 HIS   0.004   0.001   HIS A 244 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.17 ( 9141)
  covalent geometry    : angle       0.60046 /  0.32 (12401)
  SS BOND              : bond        0.00330 /  0.22 (    4)
  SS BOND              : angle       1.50300 /  0.86 (    8)
  hydrogen bonds       : bond        0.03796 /  2.52 (  449)
  hydrogen bonds       : angle       5.03095 /  3.54 ( 1269)

*********************** 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
  222 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 189
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.7611 (m-30) cc_final: 0.7298 (m-30)
REVERT: A   33 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7381 (mt-10)
REVERT: A  273 LEU cc_start: 0.8234 (mt) cc_final: 0.7976 (tt)
REVERT: A  313 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7214 (mtm-85)
REVERT: B   76 ASP cc_start: 0.6567 (t0) cc_final: 0.6329 (t0)
REVERT: B   88 ASN cc_start: 0.8406 (m-40) cc_final: 0.8122 (m110)
REVERT: B  175 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7432 (mm110)
REVERT: E  192 MET cc_start: 0.8596 (ptt) cc_final: 0.8070 (ptt)
REVERT: R  108 ASP cc_start: 0.6561 (m-30) cc_final: 0.6200 (m-30)
REVERT: R  148 SER cc_start: 0.8752 (m) cc_final: 0.8113 (t)
REVERT: R  403 ILE cc_start: 0.8096 (tp) cc_final: 0.7532 (mm)
  outliers start: 33
  outliers final: 22
  residues processed: 205
  average time/residue: 0.0998
  time to fit residues: 27.9527
Evaluate side-chains
  192 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 169
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
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  313 ARG
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  187 LEU
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  103 SER
Chi-restraints excluded: chain R residue  136 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  391 ILE
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 36 optimal weight:    2.9990
   chunk 16 optimal weight:   10.0000
   chunk 49 optimal weight:    3.9990
   chunk 89 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 92 optimal weight:    0.7980
   chunk 74 optimal weight:   10.0000
   chunk 100 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 244 HIS
** 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 = 0.3893 r_free = 0.3893 target = 0.160107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.128517 restraints weight = 12118.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.129075 restraints weight = 11790.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.130339 restraints weight = 9928.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.130471 restraints weight = 8476.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.131163 restraints weight = 7538.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.5643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9145  Z= 0.142
  Angle     :  0.583   8.324  12409  Z= 0.310
  Chirality :  0.044   0.177   1419
  Planarity :  0.004   0.040   1557
  Dihedral  :  5.259  57.010   1312
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 16.22 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.25), residues: 1121
  helix:  1.31 (0.28), residues: 384
  sheet:  0.28 (0.28), residues: 291
  loop : -0.31 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG R 220 
 TYR   0.017   0.001   TYR E 190 
 PHE   0.020   0.002   PHE R 390 
 TRP   0.015   0.001   TRP R 100 
 HIS   0.002   0.001   HIS A 188 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.14 ( 9141)
  covalent geometry    : angle       0.58189 /  0.31 (12401)
  SS BOND              : bond        0.00292 /  0.20 (    4)
  SS BOND              : angle       1.39064 /  0.81 (    8)
  hydrogen bonds       : bond        0.03639 /  2.44 (  449)
  hydrogen bonds       : angle       4.94234 /  3.49 ( 1269)

*********************** 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
  215 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 181
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.7711 (m-30) cc_final: 0.7407 (m-30)
REVERT: A  228 SER cc_start: 0.7574 (OUTLIER) cc_final: 0.7212 (t)
REVERT: A  273 LEU cc_start: 0.8347 (mt) cc_final: 0.8130 (tt)
REVERT: A  313 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7251 (mtm-85)
REVERT: B   76 ASP cc_start: 0.6592 (t0) cc_final: 0.6313 (t0)
REVERT: B   88 ASN cc_start: 0.8489 (m-40) cc_final: 0.8234 (m110)
REVERT: B  175 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7546 (mm110)
REVERT: C   11 GLN cc_start: 0.6237 (mp10) cc_final: 0.4775 (mt0)
REVERT: E   93 MET cc_start: 0.8663 (tpp) cc_final: 0.8057 (ttt)
REVERT: E  192 MET cc_start: 0.8607 (ptt) cc_final: 0.7950 (ptt)
REVERT: R  108 ASP cc_start: 0.6653 (m-30) cc_final: 0.6363 (m-30)
  outliers start: 34
  outliers final: 23
  residues processed: 203
  average time/residue: 0.1088
  time to fit residues: 29.7034
Evaluate side-chains
  192 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 167
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
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  228 SER
Chi-restraints excluded: chain A residue  313 ARG
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain E residue   21 SER
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  187 LEU
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  103 SER
Chi-restraints excluded: chain R residue  136 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  219 ARG
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 53 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 87 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   chunk 71 optimal weight:    0.7980
   chunk 57 optimal weight:    7.9990
   chunk 73 optimal weight:    0.6980
   chunk 82 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.9844 > 50:)
   chunk 102 optimal weight:    6.9990
   overall best weight:    1.2582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 220 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.159029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.127794 restraints weight = 12070.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.127698 restraints weight = 13222.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.130283 restraints weight = 11049.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.130179 restraints weight = 7944.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.131087 restraints weight = 8317.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.6162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9145  Z= 0.154
  Angle     :  0.594   8.913  12409  Z= 0.314
  Chirality :  0.045   0.249   1419
  Planarity :  0.004   0.033   1557
  Dihedral  :  5.229  57.843   1312
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 16.53 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.25), residues: 1121
  helix:  1.20 (0.27), residues: 390
  sheet:  0.25 (0.28), residues: 286
  loop : -0.36 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  32 
 TYR   0.021   0.001   TYR E 190 
 PHE   0.021   0.002   PHE B 199 
 TRP   0.014   0.001   TRP R 100 
 HIS   0.003   0.001   HIS C  44 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.15 ( 9141)
  covalent geometry    : angle       0.59317 /  0.31 (12401)
  SS BOND              : bond        0.00281 /  0.19 (    4)
  SS BOND              : angle       1.50035 /  0.86 (    8)
  hydrogen bonds       : bond        0.03553 /  2.37 (  449)
  hydrogen bonds       : angle       4.94478 /  3.48 ( 1269)

*********************** 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
  220 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 180
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.7787 (m-30) cc_final: 0.7507 (m-30)
REVERT: A  228 SER cc_start: 0.7664 (OUTLIER) cc_final: 0.7319 (t)
REVERT: A  273 LEU cc_start: 0.8303 (mt) cc_final: 0.8067 (tt)
REVERT: A  313 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7274 (mtm-85)
REVERT: B   76 ASP cc_start: 0.6768 (t0) cc_final: 0.6456 (t0)
REVERT: B   88 ASN cc_start: 0.8566 (m-40) cc_final: 0.8359 (m110)
REVERT: E   93 MET cc_start: 0.8681 (tpp) cc_final: 0.8144 (ttt)
REVERT: E  192 MET cc_start: 0.8578 (ptt) cc_final: 0.7910 (ptt)
REVERT: R  140 MET cc_start: 0.7760 (mmm) cc_final: 0.7202 (mmm)
REVERT: R  369 LYS cc_start: 0.6225 (mmmt) cc_final: 0.5657 (tptt)
REVERT: R  403 ILE cc_start: 0.8073 (tp) cc_final: 0.7537 (mm)
  outliers start: 40
  outliers final: 29
  residues processed: 203
  average time/residue: 0.1089
  time to fit residues: 29.7908
Evaluate side-chains
  195 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 164
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
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  313 ARG
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  249 THR
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  147 VAL
Chi-restraints excluded: chain E residue  187 LEU
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   78 VAL
Chi-restraints excluded: chain R residue  103 SER
Chi-restraints excluded: chain R residue  136 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  181 GLU
Chi-restraints excluded: chain R residue  219 ARG
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 43 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 98 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 106 optimal weight:   20.0000
   chunk 41 optimal weight:    0.9990
   chunk 95 optimal weight:    0.7980
   overall best weight:    0.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 259 GLN
** 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 = 0.3824 r_free = 0.3824 target = 0.154025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.122117 restraints weight = 12297.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.122500 restraints weight = 11088.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.124390 restraints weight = 10288.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.124940 restraints weight = 7403.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.125385 restraints weight = 6900.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.6441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9145  Z= 0.131
  Angle     :  0.571   9.170  12409  Z= 0.304
  Chirality :  0.044   0.236   1419
  Planarity :  0.004   0.042   1557
  Dihedral  :  5.082  55.476   1312
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 18.88 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.25), residues: 1121
  helix:  1.19 (0.27), residues: 391
  sheet:  0.37 (0.29), residues: 274
  loop : -0.40 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  32 
 TYR   0.019   0.001   TYR E 190 
 PHE   0.019   0.001   PHE R 389 
 TRP   0.015   0.001   TRP R 100 
 HIS   0.002   0.001   HIS R 393 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 9141)
  covalent geometry    : angle       0.57049 /  0.30 (12401)
  SS BOND              : bond        0.00290 /  0.19 (    4)
  SS BOND              : angle       1.42815 /  0.83 (    8)
  hydrogen bonds       : bond        0.03472 /  2.35 (  449)
  hydrogen bonds       : angle       4.85135 /  3.43 ( 1269)

*********************** 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
  214 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 178
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.7824 (m-30) cc_final: 0.7616 (m-30)
REVERT: A  197 LYS cc_start: 0.8611 (mttt) cc_final: 0.8309 (mttp)
REVERT: A  287 TYR cc_start: 0.7565 (m-80) cc_final: 0.7249 (m-80)
REVERT: B   76 ASP cc_start: 0.6739 (t0) cc_final: 0.6464 (t0)
REVERT: B  215 GLU cc_start: 0.7119 (tp30) cc_final: 0.6599 (tp30)
REVERT: C   15 LEU cc_start: 0.7430 (mp) cc_final: 0.7132 (tp)
REVERT: E   93 MET cc_start: 0.8682 (tpp) cc_final: 0.8185 (ttt)
REVERT: E  192 MET cc_start: 0.8497 (ptt) cc_final: 0.7665 (ptt)
REVERT: R  140 MET cc_start: 0.7835 (mmm) cc_final: 0.7322 (mmm)
REVERT: R  369 LYS cc_start: 0.6170 (mmmt) cc_final: 0.5465 (tptt)
REVERT: R  403 ILE cc_start: 0.8063 (tp) cc_final: 0.7548 (mm)
  outliers start: 36
  outliers final: 23
  residues processed: 199
  average time/residue: 0.1033
  time to fit residues: 27.6395
Evaluate side-chains
  188 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 165
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  187 THR
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  249 THR
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  147 VAL
Chi-restraints excluded: chain E residue  187 LEU
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  136 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  219 ARG
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 71 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 77 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  66 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.151803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.119844 restraints weight = 12252.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.119685 restraints weight = 11306.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.121840 restraints weight = 10535.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.122422 restraints weight = 7557.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.122743 restraints weight = 7793.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.6783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9145  Z= 0.162
  Angle     :  0.600   9.694  12409  Z= 0.319
  Chirality :  0.045   0.245   1419
  Planarity :  0.004   0.032   1557
  Dihedral  :  5.086  53.213   1312
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.49 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.25), residues: 1121
  helix:  1.18 (0.27), residues: 392
  sheet:  0.28 (0.29), residues: 280
  loop : -0.50 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  32 
 TYR   0.023   0.001   TYR E 190 
 PHE   0.027   0.002   PHE R 390 
 TRP   0.019   0.001   TRP R 100 
 HIS   0.003   0.001   HIS A 188 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00380 /  0.16 ( 9141)
  covalent geometry    : angle       0.59925 /  0.32 (12401)
  SS BOND              : bond        0.00315 /  0.21 (    4)
  SS BOND              : angle       1.53356 /  0.88 (    8)
  hydrogen bonds       : bond        0.03570 /  2.38 (  449)
  hydrogen bonds       : angle       4.87198 /  3.45 ( 1269)

*********************** 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
  211 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 179
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7907 (m-30) cc_final: 0.7707 (m-30)
REVERT: A   14 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7409 (tt0)
REVERT: A  228 SER cc_start: 0.7746 (OUTLIER) cc_final: 0.7329 (t)
REVERT: B   67 SER cc_start: 0.9360 (m) cc_final: 0.8638 (t)
REVERT: B   76 ASP cc_start: 0.6958 (t0) cc_final: 0.6674 (t0)
REVERT: C   11 GLN cc_start: 0.5780 (mp10) cc_final: 0.4639 (mt0)
REVERT: C   15 LEU cc_start: 0.7483 (mp) cc_final: 0.7202 (tp)
REVERT: E  192 MET cc_start: 0.8476 (ptt) cc_final: 0.7666 (ptt)
REVERT: R  140 MET cc_start: 0.7875 (mmm) cc_final: 0.7368 (mmm)
REVERT: R  369 LYS cc_start: 0.6197 (mmmt) cc_final: 0.5512 (tptt)
  outliers start: 32
  outliers final: 29
  residues processed: 199
  average time/residue: 0.1111
  time to fit residues: 29.5396
Evaluate side-chains
  196 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 166
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
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  309 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  210 LEU
Chi-restraints excluded: chain B residue  249 THR
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  147 VAL
Chi-restraints excluded: chain E residue  187 LEU
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   78 VAL
Chi-restraints excluded: chain R residue  136 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  208 VAL
Chi-restraints excluded: chain R residue  219 ARG
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 59 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 94 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3822 r_free = 0.3822 target = 0.153854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.121939 restraints weight = 12192.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.121958 restraints weight = 11083.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.124402 restraints weight = 10218.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.124259 restraints weight = 7262.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.124755 restraints weight = 7525.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.6961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9145  Z= 0.128
  Angle     :  0.595  10.697  12409  Z= 0.313
  Chirality :  0.045   0.207   1419
  Planarity :  0.004   0.081   1557
  Dihedral  :  5.045  54.586   1312
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 20.61 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.25), residues: 1121
  helix:  1.28 (0.27), residues: 387
  sheet:  0.25 (0.29), residues: 283
  loop : -0.53 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  32 
 TYR   0.019   0.001   TYR E 190 
 PHE   0.025   0.001   PHE R 390 
 TRP   0.018   0.001   TRP B 211 
 HIS   0.003   0.001   HIS A 188 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.13 ( 9141)
  covalent geometry    : angle       0.59366 /  0.31 (12401)
  SS BOND              : bond        0.00336 /  0.22 (    4)
  SS BOND              : angle       1.41921 /  0.83 (    8)
  hydrogen bonds       : bond        0.03482 /  2.32 (  449)
  hydrogen bonds       : angle       4.83339 /  3.42 ( 1269)

*********************** 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
  207 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 180
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6759 (tt0)
REVERT: A  197 LYS cc_start: 0.8622 (mttt) cc_final: 0.7888 (mtmm)
REVERT: A  228 SER cc_start: 0.7734 (p) cc_final: 0.7405 (t)
REVERT: A  232 LEU cc_start: 0.8033 (mt) cc_final: 0.7825 (mt)
REVERT: B   67 SER cc_start: 0.9335 (m) cc_final: 0.8586 (t)
REVERT: B   76 ASP cc_start: 0.6766 (t0) cc_final: 0.6482 (t0)
REVERT: C   11 GLN cc_start: 0.5523 (mp10) cc_final: 0.4630 (mt0)
REVERT: E   52 SER cc_start: 0.8805 (m) cc_final: 0.8345 (t)
REVERT: E  192 MET cc_start: 0.8516 (ptt) cc_final: 0.7683 (ptt)
REVERT: R   42 THR cc_start: 0.5860 (m) cc_final: 0.5339 (p)
REVERT: R  140 MET cc_start: 0.7748 (mmm) cc_final: 0.7273 (mmm)
REVERT: R  369 LYS cc_start: 0.5939 (mmmt) cc_final: 0.5300 (tptt)
REVERT: R  403 ILE cc_start: 0.8037 (tp) cc_final: 0.7554 (mm)
  outliers start: 27
  outliers final: 23
  residues processed: 198
  average time/residue: 0.1102
  time to fit residues: 29.2049
Evaluate side-chains
  190 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 167
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
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  309 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  249 THR
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  138 ILE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  190 TYR
Chi-restraints excluded: chain E residue  193 SER
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  208 VAL
Chi-restraints excluded: chain R residue  219 ARG
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 89 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 108 optimal weight:    0.5980
   chunk 85 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 107 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 220 GLN
** 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 = 0.3824 r_free = 0.3824 target = 0.154019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.121579 restraints weight = 12108.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.122250 restraints weight = 11432.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.123888 restraints weight = 9945.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.124714 restraints weight = 7571.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.125013 restraints weight = 6847.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.7129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9145  Z= 0.132
  Angle     :  0.601  10.878  12409  Z= 0.316
  Chirality :  0.045   0.214   1419
  Planarity :  0.004   0.034   1557
  Dihedral  :  5.042  55.485   1312
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.02 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.25), residues: 1121
  helix:  1.16 (0.27), residues: 391
  sheet:  0.33 (0.30), residues: 275
  loop : -0.52 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  13 
 TYR   0.022   0.001   TYR A 287 
 PHE   0.035   0.002   PHE R 390 
 TRP   0.018   0.001   TRP R 100 
 HIS   0.003   0.001   HIS A 188 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.13 ( 9141)
  covalent geometry    : angle       0.59961 /  0.32 (12401)
  SS BOND              : bond        0.00289 /  0.19 (    4)
  SS BOND              : angle       1.44011 /  0.84 (    8)
  hydrogen bonds       : bond        0.03460 /  2.31 (  449)
  hydrogen bonds       : angle       4.80893 /  3.40 ( 1269)

********************** 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
  207 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 185
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7552 (mt-10) cc_final: 0.6902 (tt0)
REVERT: A  197 LYS cc_start: 0.8632 (mttt) cc_final: 0.7853 (mtmm)
REVERT: A  228 SER cc_start: 0.7815 (p) cc_final: 0.7475 (t)
REVERT: A  232 LEU cc_start: 0.8049 (mt) cc_final: 0.7848 (mt)
REVERT: B   67 SER cc_start: 0.9365 (m) cc_final: 0.8647 (t)
REVERT: B   76 ASP cc_start: 0.6937 (t0) cc_final: 0.6656 (t0)
REVERT: B  211 TRP cc_start: 0.8809 (m100) cc_final: 0.8387 (m100)
REVERT: C   11 GLN cc_start: 0.5377 (mp10) cc_final: 0.4770 (mt0)
REVERT: E   52 SER cc_start: 0.8848 (m) cc_final: 0.8403 (t)
REVERT: E  192 MET cc_start: 0.8529 (ptt) cc_final: 0.7696 (ptt)
REVERT: R   42 THR cc_start: 0.5998 (m) cc_final: 0.5441 (p)
REVERT: R   93 TYR cc_start: 0.7192 (t80) cc_final: 0.6985 (t80)
REVERT: R  140 MET cc_start: 0.7823 (mmm) cc_final: 0.7431 (mmm)
REVERT: R  369 LYS cc_start: 0.5968 (mmmt) cc_final: 0.5349 (tptt)
REVERT: R  403 ILE cc_start: 0.8157 (tp) cc_final: 0.7633 (mm)
  outliers start: 22
  outliers final: 21
  residues processed: 199
  average time/residue: 0.1095
  time to fit residues: 29.0267
Evaluate side-chains
  196 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 175
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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  309 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain E residue  138 ILE
Chi-restraints excluded: chain E residue  150 THR
Chi-restraints excluded: chain E residue  187 LEU
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   78 VAL
Chi-restraints excluded: chain R residue  208 VAL
Chi-restraints excluded: chain R residue  219 ARG
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 79 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0170
   chunk 100 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   chunk 102 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 99 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 96 optimal weight:    7.9990
   overall best weight:    0.6818

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.155224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.123243 restraints weight = 11993.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.124671 restraints weight = 10634.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.126499 restraints weight = 9224.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.126510 restraints weight = 7141.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.126920 restraints weight = 6547.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.7273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9145  Z= 0.123
  Angle     :  0.596  10.733  12409  Z= 0.316
  Chirality :  0.044   0.209   1419
  Planarity :  0.004   0.044   1557
  Dihedral  :  5.000  56.383   1312
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 20.51 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.25), residues: 1121
  helix:  1.17 (0.27), residues: 395
  sheet:  0.34 (0.30), residues: 280
  loop : -0.51 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  13 
 TYR   0.024   0.001   TYR A 287 
 PHE   0.024   0.001   PHE R 390 
 TRP   0.016   0.001   TRP B 211 
 HIS   0.003   0.001   HIS A 188 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 9141)
  covalent geometry    : angle       0.59531 /  0.32 (12401)
  SS BOND              : bond        0.00297 /  0.20 (    4)
  SS BOND              : angle       1.38674 /  0.81 (    8)
  hydrogen bonds       : bond        0.03460 /  2.30 (  449)
  hydrogen bonds       : angle       4.77058 /  3.38 ( 1269)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1544.89 seconds
wall clock time: 27 minutes 36.01 seconds (1656.01 seconds total)