Starting phenix.real_space_refine
on Wed Feb  4 02:28:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hvf_52434/02_2026/9hvf_52434.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hvf_52434/02_2026/9hvf_52434.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/9hvf_52434/02_2026/9hvf_52434.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hvf_52434/02_2026/9hvf_52434.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hvf_52434/02_2026/9hvf_52434.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hvf_52434/02_2026/9hvf_52434.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=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    5185      2.51       5
     N    1418      2.21       5
     O    1569      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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8225
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "E"
      Number of atoms: 3352
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 433, 3352
          Classifications: {'peptide': 433}
          Link IDs: {'PTRANS': 18, 'TRANS': 414}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 211
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 211
          Classifications: {'peptide': 27}
          Link IDs: {'PTRANS': 2, 'TRANS': 24}
    Chain: "C"
      Number of atoms: 198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 198
          Classifications: {'peptide': 23}
          Link IDs: {'TRANS': 22}
    Chain: "D"
      Number of atoms: 3451
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 453, 3451
          Classifications: {'peptide': 453}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 427}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1013
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 129, 1004
          Classifications: {'peptide': 129}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 124}
      Conformer: "B"
        Number of residues, atoms: 129, 1004
          Classifications: {'peptide': 129}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 124}
          bond proxies already assigned to first conformer: 1001
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AGLU B 283 " occ=0.64
      ... (16 atoms not shown)
      pdb=" OE2BGLU B 283 " occ=0.36
  Time building chain proxies: 1.93, per 1000 atoms: 0.23
  Number of scatterers: 8225
  At special positions: 0
  Unit cell: (113.3, 90.2, 102.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    1569      8.00
     N    1418      7.00
     C    5185      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  96 " - pdb=" SG  CYS D 101 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 384.8 milliseconds
  

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1984

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 12 sheets defined
      24.8% alpha, 16.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'E' and resid 15 through 19
      removed outlier: 3.925A  pdb=" N   ASP E  18 " --> pdb=" O   ARG E  15 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 29 through 33
      removed outlier: 3.640A  pdb=" N   ASN E  32 " --> pdb=" O   PRO E  29 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LYS E  33 " --> pdb=" O   VAL E  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 29 through 33'
    Processing helix  chain 'E' and resid 34 through 35
      No H-bonds generated for 'chain 'E' and resid 34 through 35'
    Processing helix  chain 'E' and resid 36 through 47
      removed outlier: 3.917A  pdb=" N   LEU E  40 " --> pdb=" O   ILE E  36 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASN E  41 " --> pdb=" O   TRP E  37 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU E  42 " --> pdb=" O   TYR E  38 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLY E  47 " --> pdb=" O   LEU E  43 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 56 through 63
    Processing helix  chain 'E' and resid 85 through 93
      removed outlier: 3.691A  pdb=" N   ILE E  93 " --> pdb=" O   SER E  89 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 114 through 125
      removed outlier: 3.873A  pdb=" N   VAL E 118 " --> pdb=" O   LEU E 114 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 184 through 189
    Processing helix  chain 'E' and resid 208 through 218
      removed outlier: 3.784A  pdb=" N   VAL E 212 " --> pdb=" O   LYS E 208 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   GLU E 217 " --> pdb=" O   ASP E 213 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 227 through 236
    Processing helix  chain 'E' and resid 239 through 244
    Processing helix  chain 'E' and resid 262 through 266
    Processing helix  chain 'E' and resid 316 through 326
    Processing helix  chain 'E' and resid 327 through 334
      removed outlier: 4.103A  pdb=" N   SER E 331 " --> pdb=" O   PRO E 327 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA E 332 " --> pdb=" O   LYS E 328 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 23
    Processing helix  chain 'D' and resid 32 through 37
      removed outlier: 3.943A  pdb=" N   SER D  37 " --> pdb=" O   HIS D  33 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 62
      removed outlier: 4.054A  pdb=" N   VAL D  57 " --> pdb=" O   GLY D  53 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ILE D  61 " --> pdb=" O   VAL D  57 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 137 through 147
      removed outlier: 3.974A  pdb=" N   LEU D 141 " --> pdb=" O   GLY D 137 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   MET D 142 " --> pdb=" O   HIS D 138 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ASN D 147 " --> pdb=" O   ALA D 143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 181
      removed outlier: 3.605A  pdb=" N   SER D 171 " --> pdb=" O   GLN D 167 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 212
      removed outlier: 3.790A  pdb=" N   GLN D 212 " --> pdb=" O   LEU D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 232 through 242
      removed outlier: 4.760A  pdb=" N   VAL D 240 " --> pdb=" O   CYS D 236 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 270 through 274
    Processing helix  chain 'D' and resid 344 through 349
      removed outlier: 3.671A  pdb=" N   CYS D 348 " --> pdb=" O   ASP D 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 216
      removed outlier: 3.744A  pdb=" N   VAL B 208 " --> pdb=" O   GLY B 204 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA B 214 " --> pdb=" O   GLU B 210 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLY B 215 " --> pdb=" O   ALA B 211 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LEU B 216 " --> pdb=" O   LEU B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 219
      No H-bonds generated for 'chain 'B' and resid 217 through 219'
    Processing helix  chain 'B' and resid 243 through 264
      removed outlier: 3.590A  pdb=" N   GLY B 247 " --> pdb=" O   GLU B 243 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 298
    Processing sheet with id=AA1, first strand: chain 'E' and resid 76 through 77
      removed outlier: 6.960A  pdb=" N   ALA E   5 " --> pdb=" O   ILE E  52 " (cutoff:3.500A)
      removed outlier: 8.095A  pdb=" N   VAL E  54 " --> pdb=" O   ALA E   5 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL E   7 " --> pdb=" O   VAL E  54 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   GLN E   4 " --> pdb=" O   LEU E 102 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   LEU E 104 " --> pdb=" O   GLN E   4 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   VAL E   6 " --> pdb=" O   LEU E 104 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 108 through 110
    Processing sheet with id=AA3, first strand: chain 'E' and resid 199 through 200
      removed outlier: 3.544A  pdb=" N   ALA E 129 " --> pdb=" O   CYS E 206 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 199 through 200
      removed outlier: 6.469A  pdb=" N   MET E 130 " --> pdb=" O   HIS E 303 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 167 through 171
      removed outlier: 4.157A  pdb=" N   PHE E 169 " --> pdb=" O   GLY E 159 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 362 through 363
    Processing sheet with id=AA7, first strand: chain 'D' and resid 82 through 88
      removed outlier: 4.028A  pdb=" N   ILE D  88 " --> pdb=" O   ARG D 128 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ARG D 128 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ILE D  42 " --> pdb=" O   SER D 131 " (cutoff:3.500A)
      removed outlier: 7.612A  pdb=" N   VAL D 133 " --> pdb=" O   ILE D  42 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ILE D  44 " --> pdb=" O   VAL D 133 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   ALA D 154 " --> pdb=" O   ASN D  43 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   ALA D 155 " --> pdb=" O   LEU D 186 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   LEU D 188 " --> pdb=" O   ALA D 155 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   LEU D 157 " --> pdb=" O   LEU D 188 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ASN D 190 " --> pdb=" O   LEU D 157 " (cutoff:3.500A)
      removed outlier: 9.376A  pdb=" N   ILE D 222 " --> pdb=" O   ILE D 185 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   ILE D 187 " --> pdb=" O   ILE D 222 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   ILE D 224 " --> pdb=" O   ILE D 187 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   GLN D 189 " --> pdb=" O   ILE D 224 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 68
    Processing sheet with id=AA9, first strand: chain 'D' and resid 113 through 114
    Processing sheet with id=AB1, first strand: chain 'D' and resid 318 through 322
      removed outlier: 4.022A  pdb=" N   SER D 320 " --> pdb=" O   GLY D 340 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   PHE D 322 " --> pdb=" O   GLY D 338 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   GLY D 338 " --> pdb=" O   PHE D 322 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   SER D 282 " --> pdb=" O   VAL D 258 " (cutoff:3.500A)
      removed outlier: 5.392A  pdb=" N   VAL D 258 " --> pdb=" O   SER D 282 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   LEU D 284 " --> pdb=" O   LEU D 256 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   LEU D 256 " --> pdb=" O   LEU D 284 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 370 through 377
      removed outlier: 3.528A  pdb=" N   GLY D 425 " --> pdb=" O   ILE D 373 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   LEU D 424 " --> pdb=" O   VAL D 420 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   VAL D 420 " --> pdb=" O   LEU D 424 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   LYS D 426 " --> pdb=" O   SER D 418 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   LEU D 404 " --> pdb=" O   GLY D 415 " (cutoff:3.500A)
      removed outlier: 8.826A  pdb=" N   VAL D 403 " --> pdb=" O   ARG D 446 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   ARG D 446 " --> pdb=" O   VAL D 403 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   ARG D 445 " --> pdb=" O   LEU D 453 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   LEU D 453 " --> pdb=" O   ARG D 445 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   VAL D 447 " --> pdb=" O   TRP D 451 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   TRP D 451 " --> pdb=" O   VAL D 447 " (cutoff:3.500A)
      removed outlier: 5.585A  pdb=" N   GLY D 457 " --> pdb=" O   PHE D 376 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   PHE D 376 " --> pdb=" O   GLY D 457 " (cutoff:3.500A)
      removed outlier: 5.429A  pdb=" N   ILE D 459 " --> pdb=" O   SER D 374 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   SER D 374 " --> pdb=" O   ILE D 459 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLU D 370 " --> pdb=" O   VAL D 463 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 225 through 231
      removed outlier: 6.728A  pdb=" N   ILE B 225 " --> pdb=" O   THR B 240 " (cutoff:3.500A)
      removed outlier: 8.317A  pdb=" N   THR B 240 " --> pdb=" O   ILE B 225 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   ILE B 227 " --> pdb=" O   THR B 238 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   THR B 238 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   LEU B 229 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   VAL B 236 " --> pdb=" O   LEU B 229 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ALA B 231 " --> pdb=" O   ARG B 234 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   LYS B 190 " --> pdb=" O   LYS B 276 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LYS B 276 " --> pdb=" O   LYS B 190 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   ARG B 192 " --> pdb=" O   GLU B 274 " (cutoff:3.500A)
      removed outlier: 5.757A  pdb=" N   GLU B 274 " --> pdb=" O   ARG B 192 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ASP B 194 " --> pdb=" O   GLN B 272 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLN B 272 " --> pdb=" O   ASP B 194 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA B 198 " --> pdb=" O   VAL B 268 " (cutoff:3.500A)

    209 hydrogen bonds defined for protein.
    571 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: 1.35

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2749
        1.34 -     1.46: 1599
        1.46 -     1.58: 3921
        1.58 -     1.70: 0
        1.70 -     1.82: 80
  Bond restraints: 8349
  Sorted by residual:
  bond pdb=" CA  LEU E 114 "
       pdb=" C   LEU E 114 "
    ideal  model  delta    sigma   weight residual
    1.524  1.495  0.028 2.25e-02 1.98e+03 1.58e+00
  bond pdb=" CA  ASP B 194 "
       pdb=" CB  ASP B 194 "
    ideal  model  delta    sigma   weight residual
    1.533  1.556 -0.023 1.90e-02 2.77e+03 1.48e+00
  bond pdb=" CG  MET B 255 "
       pdb=" SD  MET B 255 "
    ideal  model  delta    sigma   weight residual
    1.803  1.774  0.029 2.50e-02 1.60e+03 1.34e+00
  bond pdb=" CA  MET B 255 "
       pdb=" CB  MET B 255 "
    ideal  model  delta    sigma   weight residual
    1.529  1.549 -0.020 1.74e-02 3.30e+03 1.31e+00
  bond pdb=" N   VAL E 444 "
       pdb=" CA  VAL E 444 "
    ideal  model  delta    sigma   weight residual
    1.459  1.471 -0.012 1.25e-02 6.40e+03 9.40e-01
  ... (remaining 8344 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.76: 11146
        2.76 -     5.52: 113
        5.52 -     8.27: 22
        8.27 -    11.03: 2
       11.03 -    13.79: 4
  Bond angle restraints: 11287
  Sorted by residual:
  angle pdb=" CA  MET B 255 "
        pdb=" CB  MET B 255 "
        pdb=" CG  MET B 255 "
      ideal   model   delta    sigma   weight residual
     114.10  125.60  -11.50 2.00e+00 2.50e-01 3.31e+01
  angle pdb=" CB  MET B 255 "
        pdb=" CG  MET B 255 "
        pdb=" SD  MET B 255 "
      ideal   model   delta    sigma   weight residual
     112.70  126.49  -13.79 3.00e+00 1.11e-01 2.11e+01
  angle pdb=" N   MET B 255 "
        pdb=" CA  MET B 255 "
        pdb=" CB  MET B 255 "
      ideal   model   delta    sigma   weight residual
     110.39  117.33   -6.94 1.66e+00 3.63e-01 1.75e+01
  angle pdb=" C   THR D 144 "
        pdb=" N   MET D 145 "
        pdb=" CA  MET D 145 "
      ideal   model   delta    sigma   weight residual
     122.06  114.65    7.41 1.86e+00 2.89e-01 1.59e+01
  angle pdb=" C   ILE E 443 "
        pdb=" N   VAL E 444 "
        pdb=" CA  VAL E 444 "
      ideal   model   delta    sigma   weight residual
     121.97  129.09   -7.12 1.80e+00 3.09e-01 1.56e+01
  ... (remaining 11282 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 4483
       17.27 -    34.54: 503
       34.54 -    51.81: 129
       51.81 -    69.09: 43
       69.09 -    86.36: 9
  Dihedral angle restraints: 5167
    sinusoidal: 2098
      harmonic: 3069
  Sorted by residual:
  dihedral pdb=" CA  LEU A 477 "
           pdb=" C   LEU A 477 "
           pdb=" N   TRP A 478 "
           pdb=" CA  TRP A 478 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.95  -21.05     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  MET E 393 "
           pdb=" C   MET E 393 "
           pdb=" N   ASN E 394 "
           pdb=" CA  ASN E 394 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.17   19.83     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  LEU E 392 "
           pdb=" C   LEU E 392 "
           pdb=" N   MET E 393 "
           pdb=" CA  MET E 393 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.64  -18.36     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 5164 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1018
       0.052 -    0.104: 244
       0.104 -    0.156: 55
       0.156 -    0.207: 5
       0.207 -    0.259: 2
  Chirality restraints: 1324
  Sorted by residual:
  chirality pdb=" CG  LEU D 174 "
            pdb=" CB  LEU D 174 "
            pdb=" CD1 LEU D 174 "
            pdb=" CD2 LEU D 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CB  ILE E 387 "
            pdb=" CA  ILE E 387 "
            pdb=" CG1 ILE E 387 "
            pdb=" CG2 ILE E 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.88   -0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CB  ILE D 243 "
            pdb=" CA  ILE D 243 "
            pdb=" CG1 ILE D 243 "
            pdb=" CG2 ILE D 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.05e-01
  ... (remaining 1321 not shown)

  Planarity restraints: 1453
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 167 "    0.032 5.00e-02 4.00e+02   4.81e-02 3.71e+00
        pdb=" N   PRO D 168 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO D 168 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D 168 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D 246 "    0.031 5.00e-02 4.00e+02   4.74e-02 3.60e+00
        pdb=" N   PRO D 247 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO D 247 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 247 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU E  44 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.06e+00
        pdb=" CD  GLU E  44 "   -0.030 2.00e-02 2.50e+03
        pdb=" OE1 GLU E  44 "    0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU E  44 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1450 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 4224
        2.99 -     3.46: 8845
        3.46 -     3.94: 12625
        3.94 -     4.42: 14054
        4.42 -     4.90: 22417
  Nonbonded interactions: 62165
  Sorted by model distance:
  nonbonded pdb=" N   ASP E 355 "
            pdb=" OD1 ASP E 355 "
     model   vdw
     2.506 3.120
  nonbonded pdb=" O   TYR E 124 "
            pdb=" OD1 ASP E 125 "
     model   vdw
     2.522 3.040
  nonbonded pdb=" O   THR E 388 "
            pdb=" OD1 ASN E 389 "
     model   vdw
     2.538 3.040
  nonbonded pdb=" N   ILE E 387 "
            pdb=" N   THR E 388 "
     model   vdw
     2.568 2.560
  nonbonded pdb=" O   THR D 144 "
            pdb=" CA  MET D 145 "
     model   vdw
     2.601 2.776
  ... (remaining 62160 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=0.36 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.620
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
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      :  0.003   0.035   8350  Z= 0.137
  Angle     :  0.759  13.790  11289  Z= 0.384
  Chirality :  0.048   0.259   1324
  Planarity :  0.004   0.048   1453
  Dihedral  : 16.499  86.357   3180
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.86 %
    Allowed  :  9.23 %
    Favored  : 89.91 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 23.94 %
    Favored  : 73.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -2.52 (0.24), residues: 1054
  helix: -0.31 (0.35), residues: 223
  sheet: -1.55 (0.37), residues: 174
  loop : -2.32 (0.22), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 438 
 TYR   0.019   0.001   TYR D 238 
 PHE   0.012   0.001   PHE D 124 
 TRP   0.015   0.002   TRP E  37 
 HIS   0.006   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8349)
  covalent geometry    : angle       0.75912 (11287)
  SS BOND              : bond        0.00095 (    1)
  SS BOND              : angle       0.40165 (    2)
  hydrogen bonds       : bond        0.17079 (  207)
  hydrogen bonds       : angle       6.74099 (  571)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 83
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  216 MET cc_start: 0.8884 (tpp) cc_final: 0.8104 (tpp)
REVERT: E  231 TYR cc_start: 0.9140 (t80) cc_final: 0.8630 (t80)
REVERT: E  397 THR cc_start: 0.8912 (m) cc_final: 0.8618 (p)
REVERT: D   74 GLU cc_start: 0.6816 (mp0) cc_final: 0.5529 (mp0)
REVERT: D  100 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7739 (mm-30)
REVERT: D  238 TYR cc_start: 0.8900 (p90) cc_final: 0.8149 (p90)
REVERT: D  310 MET cc_start: 0.7418 (ttt) cc_final: 0.7057 (tmm)
REVERT: B  273 MET cc_start: 0.8788 (tmm) cc_final: 0.8249 (tmm)
  outliers start: 28
  outliers final: 24
  residues processed: 106
  average time/residue: 0.0892
  time to fit residues: 13.4828
Evaluate side-chains
  102 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   53 VAL
Chi-restraints excluded: chain E residue   68 LYS
Chi-restraints excluded: chain E residue  130 MET
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  186 ILE
Chi-restraints excluded: chain E residue  197 THR
Chi-restraints excluded: chain E residue  304 ILE
Chi-restraints excluded: chain E residue  370 ILE
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue  100 GLU
Chi-restraints excluded: chain D residue  101 CYS
Chi-restraints excluded: chain D residue  120 THR
Chi-restraints excluded: chain D residue  129 HIS
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  237 GLU
Chi-restraints excluded: chain D residue  245 VAL
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  315 PHE
Chi-restraints excluded: chain D residue  356 GLN
Chi-restraints excluded: chain D residue  451 TRP
Chi-restraints excluded: chain D residue  469 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    8.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** E 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 356 GLN ** 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 = 0.3854 r_free = 0.3854 target = 0.087841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.063666 restraints weight = 53661.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.066459 restraints weight = 26660.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.066407 restraints weight = 15233.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.066761 restraints weight = 15291.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.066842 restraints weight = 13441.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3328
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3328
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.083   8350  Z= 0.440
  Angle     :  0.946  10.975  11289  Z= 0.488
  Chirality :  0.054   0.207   1324
  Planarity :  0.006   0.049   1453
  Dihedral  :  8.343  73.450   1190
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 23.07
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  : 14.75 %
    Favored  : 84.30 %
  Rotamer:
    Outliers :  7.40 %
    Allowed  : 22.42 %
    Favored  : 70.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.12 (0.23), residues: 1054
  helix: -0.67 (0.33), residues: 222
  sheet: -2.48 (0.33), residues: 181
  loop : -2.58 (0.22), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E 438 
 TYR   0.023   0.003   TYR E  38 
 PHE   0.025   0.003   PHE D 368 
 TRP   0.037   0.003   TRP E  37 
 HIS   0.012   0.002   HIS E 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00992 ( 8349)
  covalent geometry    : angle       0.94608 (11287)
  SS BOND              : bond        0.00230 (    1)
  SS BOND              : angle       0.26133 (    2)
  hydrogen bonds       : bond        0.06073 (  207)
  hydrogen bonds       : angle       6.06463 (  571)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 67
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: E   37 TRP cc_start: 0.6455 (m100) cc_final: 0.5988 (m100)
REVERT: E  168 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8582 (mt)
REVERT: E  323 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7824 (t0)
REVERT: E  397 THR cc_start: 0.8792 (m) cc_final: 0.8475 (p)
REVERT: D   74 GLU cc_start: 0.6554 (mp0) cc_final: 0.5761 (mp0)
REVERT: D  238 TYR cc_start: 0.9210 (p90) cc_final: 0.8339 (p90)
REVERT: D  405 MET cc_start: 0.6972 (ppp) cc_final: 0.6733 (ppp)
REVERT: B  190 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8697 (pttm)
REVERT: B  273 MET cc_start: 0.8768 (tmm) cc_final: 0.8167 (tmm)
  outliers start: 68
  outliers final: 46
  residues processed: 128
  average time/residue: 0.0715
  time to fit residues: 13.8225
Evaluate side-chains
  105 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 56
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   17 THR
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   53 VAL
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue  100 ASP
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  130 MET
Chi-restraints excluded: chain E residue  131 LEU
Chi-restraints excluded: chain E residue  168 LEU
Chi-restraints excluded: chain E residue  186 ILE
Chi-restraints excluded: chain E residue  190 HIS
Chi-restraints excluded: chain E residue  197 THR
Chi-restraints excluded: chain E residue  206 CYS
Chi-restraints excluded: chain E residue  213 ASP
Chi-restraints excluded: chain E residue  263 ILE
Chi-restraints excluded: chain E residue  302 VAL
Chi-restraints excluded: chain E residue  304 ILE
Chi-restraints excluded: chain E residue  323 ASN
Chi-restraints excluded: chain E residue  351 LEU
Chi-restraints excluded: chain E residue  354 VAL
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain E residue  370 ILE
Chi-restraints excluded: chain E residue  387 ILE
Chi-restraints excluded: chain E residue  398 VAL
Chi-restraints excluded: chain E residue  407 SER
Chi-restraints excluded: chain E residue  410 CYS
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue   89 TYR
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue  100 GLU
Chi-restraints excluded: chain D residue  101 CYS
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  129 HIS
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  222 ILE
Chi-restraints excluded: chain D residue  245 VAL
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  330 TYR
Chi-restraints excluded: chain D residue  341 THR
Chi-restraints excluded: chain D residue  354 VAL
Chi-restraints excluded: chain D residue  356 GLN
Chi-restraints excluded: chain D residue  404 LEU
Chi-restraints excluded: chain D residue  451 TRP
Chi-restraints excluded: chain D residue  469 VAL
Chi-restraints excluded: chain B residue  190 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 43 optimal weight:    0.4980
   chunk 26 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 61 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
** E 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 253 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.090429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.065407 restraints weight = 62065.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.068928 restraints weight = 28001.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.069348 restraints weight = 14534.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.069619 restraints weight = 13861.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.069759 restraints weight = 12651.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3394
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3394
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8350  Z= 0.193
  Angle     :  0.738   9.530  11289  Z= 0.373
  Chirality :  0.049   0.197   1324
  Planarity :  0.005   0.045   1453
  Dihedral  :  7.666  67.643   1176
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.86 %
    Allowed  : 10.85 %
    Favored  : 88.30 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 23.83 %
    Favored  : 70.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.05 (0.23), residues: 1054
  helix: -0.60 (0.34), residues: 223
  sheet: -2.34 (0.33), residues: 185
  loop : -2.57 (0.22), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E 438 
 TYR   0.016   0.002   TYR D 238 
 PHE   0.016   0.002   PHE D 368 
 TRP   0.019   0.002   TRP E  37 
 HIS   0.007   0.001   HIS D 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 8349)
  covalent geometry    : angle       0.73839 (11287)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       0.35535 (    2)
  hydrogen bonds       : bond        0.04306 (  207)
  hydrogen bonds       : angle       5.61223 (  571)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 66
  time to evaluate  : 0.346 
Fit side-chains
REVERT: E   37 TRP cc_start: 0.6207 (m100) cc_final: 0.5876 (m100)
REVERT: E  397 THR cc_start: 0.8802 (m) cc_final: 0.8549 (p)
REVERT: D   74 GLU cc_start: 0.6139 (mp0) cc_final: 0.5105 (mp0)
REVERT: D  100 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7776 (mm-30)
REVERT: D  235 VAL cc_start: 0.9540 (OUTLIER) cc_final: 0.9193 (p)
REVERT: D  238 TYR cc_start: 0.9051 (p90) cc_final: 0.8361 (p90)
REVERT: D  439 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6784 (mt-10)
REVERT: B  273 MET cc_start: 0.8824 (tmm) cc_final: 0.8175 (tmm)
  outliers start: 56
  outliers final: 39
  residues processed: 113
  average time/residue: 0.0781
  time to fit residues: 13.0928
Evaluate side-chains
  105 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 63
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   17 THR
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   53 VAL
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue  127 SER
Chi-restraints excluded: chain E residue  130 MET
Chi-restraints excluded: chain E residue  131 LEU
Chi-restraints excluded: chain E residue  186 ILE
Chi-restraints excluded: chain E residue  197 THR
Chi-restraints excluded: chain E residue  206 CYS
Chi-restraints excluded: chain E residue  263 ILE
Chi-restraints excluded: chain E residue  302 VAL
Chi-restraints excluded: chain E residue  304 ILE
Chi-restraints excluded: chain E residue  351 LEU
Chi-restraints excluded: chain E residue  354 VAL
Chi-restraints excluded: chain E residue  356 SER
Chi-restraints excluded: chain E residue  370 ILE
Chi-restraints excluded: chain E residue  387 ILE
Chi-restraints excluded: chain E residue  398 VAL
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   89 TYR
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue  100 GLU
Chi-restraints excluded: chain D residue  101 CYS
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  120 THR
Chi-restraints excluded: chain D residue  129 HIS
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  222 ILE
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  330 TYR
Chi-restraints excluded: chain D residue  341 THR
Chi-restraints excluded: chain D residue  356 GLN
Chi-restraints excluded: chain D residue  404 LEU
Chi-restraints excluded: chain D residue  406 VAL
Chi-restraints excluded: chain D residue  439 GLU
Chi-restraints excluded: chain D residue  451 TRP
Chi-restraints excluded: chain D residue  469 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 9 optimal weight:    0.0770
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0980
   chunk 13 optimal weight:    0.0670
   chunk 6 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 67 optimal weight:   10.0000
   chunk 44 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0770
   chunk 22 optimal weight:    0.4980
   overall best weight:    0.1634

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

Flipped N/Q/H residues before XYZ refinement:
A 476 HIS
** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 356 GLN
B 253 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.093621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.067335 restraints weight = 76616.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.070481 restraints weight = 28830.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.072491 restraints weight = 16549.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.073705 restraints weight = 11833.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.074491 restraints weight = 9626.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3509
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3509 r_free = 0.3509    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3509 r_free = 0.3509    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3509
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8350  Z= 0.119
  Angle     :  0.689   9.591  11289  Z= 0.342
  Chirality :  0.048   0.190   1324
  Planarity :  0.004   0.046   1453
  Dihedral  :  6.967  59.237   1174
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.86 %
    Allowed  :  9.32 %
    Favored  : 89.82 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 25.57 %
    Favored  : 69.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -2.68 (0.24), residues: 1054
  helix: -0.30 (0.35), residues: 216
  sheet: -1.79 (0.36), residues: 170
  loop : -2.41 (0.22), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 438 
 TYR   0.020   0.001   TYR D 238 
 PHE   0.011   0.001   PHE D 124 
 TRP   0.006   0.001   TRP A 478 
 HIS   0.005   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8349)
  covalent geometry    : angle       0.68941 (11287)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       0.37006 (    2)
  hydrogen bonds       : bond        0.03544 (  207)
  hydrogen bonds       : angle       5.24286 (  571)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 73
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: E  157 PHE cc_start: 0.8593 (m-80) cc_final: 0.8385 (m-80)
REVERT: E  216 MET cc_start: 0.9064 (tpp) cc_final: 0.8100 (tpp)
REVERT: E  397 THR cc_start: 0.8773 (m) cc_final: 0.8476 (p)
REVERT: D   74 GLU cc_start: 0.6119 (mp0) cc_final: 0.5597 (mp0)
REVERT: D  100 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7856 (mm-30)
REVERT: D  235 VAL cc_start: 0.9505 (OUTLIER) cc_final: 0.9170 (p)
REVERT: D  238 TYR cc_start: 0.8958 (p90) cc_final: 0.8290 (p90)
REVERT: D  439 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6902 (mt-10)
REVERT: B  273 MET cc_start: 0.8894 (tmm) cc_final: 0.8336 (tmm)
  outliers start: 44
  outliers final: 22
  residues processed: 113
  average time/residue: 0.0781
  time to fit residues: 13.0212
Evaluate side-chains
  96 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue  127 SER
Chi-restraints excluded: chain E residue  186 ILE
Chi-restraints excluded: chain E residue  197 THR
Chi-restraints excluded: chain E residue  263 ILE
Chi-restraints excluded: chain E residue  304 ILE
Chi-restraints excluded: chain E residue  351 LEU
Chi-restraints excluded: chain E residue  387 ILE
Chi-restraints excluded: chain E residue  398 VAL
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue  100 GLU
Chi-restraints excluded: chain D residue  101 CYS
Chi-restraints excluded: chain D residue  120 THR
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  356 GLN
Chi-restraints excluded: chain D residue  406 VAL
Chi-restraints excluded: chain D residue  439 GLU
Chi-restraints excluded: chain D residue  451 TRP
Chi-restraints excluded: chain D residue  469 VAL
Chi-restraints excluded: chain B residue  286 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 69 optimal weight:    0.0470
   chunk 13 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 96 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0370
   chunk 41 optimal weight:    6.9990
   chunk 87 optimal weight:    9.9990
   chunk 66 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 70 optimal weight:    8.9990
   overall best weight:    1.8162

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

Flipped N/Q/H residues before XYZ refinement:
B 253 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.091423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.067297 restraints weight = 45895.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.070015 restraints weight = 23679.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.070201 restraints weight = 14439.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.070587 restraints weight = 14642.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.070848 restraints weight = 12638.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3424
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3424 r_free = 0.3424    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3424 r_free = 0.3424    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3424
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8350  Z= 0.175
  Angle     :  0.704   8.866  11289  Z= 0.353
  Chirality :  0.049   0.356   1324
  Planarity :  0.005   0.046   1453
  Dihedral  :  6.686  55.619   1164
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.86 %
    Allowed  : 11.23 %
    Favored  : 87.92 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 25.35 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -2.79 (0.24), residues: 1054
  helix: -0.50 (0.34), residues: 227
  sheet: -2.05 (0.34), residues: 182
  loop : -2.41 (0.22), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 438 
 TYR   0.021   0.002   TYR E 301 
 PHE   0.012   0.001   PHE D 368 
 TRP   0.016   0.001   TRP E  37 
 HIS   0.003   0.001   HIS D 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 8349)
  covalent geometry    : angle       0.70442 (11287)
  SS BOND              : bond        0.00190 (    1)
  SS BOND              : angle       0.28280 (    2)
  hydrogen bonds       : bond        0.03873 (  207)
  hydrogen bonds       : angle       5.20859 (  571)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 69
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: E   84 MET cc_start: 0.7495 (mmm) cc_final: 0.7267 (mmm)
REVERT: E  397 THR cc_start: 0.8760 (m) cc_final: 0.8548 (p)
REVERT: D   74 GLU cc_start: 0.6468 (mp0) cc_final: 0.5837 (mp0)
REVERT: D  100 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7906 (mm-30)
REVERT: D  129 HIS cc_start: 0.7989 (OUTLIER) cc_final: 0.6619 (m170)
REVERT: D  235 VAL cc_start: 0.9507 (OUTLIER) cc_final: 0.9109 (p)
REVERT: D  238 TYR cc_start: 0.9036 (p90) cc_final: 0.8355 (p90)
REVERT: D  310 MET cc_start: 0.7096 (ttt) cc_final: 0.6483 (tmm)
REVERT: D  439 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7021 (mt-10)
REVERT: B  273 MET cc_start: 0.8895 (tmm) cc_final: 0.8370 (tmm)
  outliers start: 50
  outliers final: 35
  residues processed: 112
  average time/residue: 0.0724
  time to fit residues: 12.2165
Evaluate side-chains
  104 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 65
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   53 VAL
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue  131 LEU
Chi-restraints excluded: chain E residue  186 ILE
Chi-restraints excluded: chain E residue  197 THR
Chi-restraints excluded: chain E residue  206 CYS
Chi-restraints excluded: chain E residue  263 ILE
Chi-restraints excluded: chain E residue  302 VAL
Chi-restraints excluded: chain E residue  304 ILE
Chi-restraints excluded: chain E residue  351 LEU
Chi-restraints excluded: chain E residue  354 VAL
Chi-restraints excluded: chain E residue  384 ARG
Chi-restraints excluded: chain E residue  387 ILE
Chi-restraints excluded: chain E residue  398 VAL
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue  100 GLU
Chi-restraints excluded: chain D residue  101 CYS
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  120 THR
Chi-restraints excluded: chain D residue  129 HIS
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  245 VAL
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  330 TYR
Chi-restraints excluded: chain D residue  341 THR
Chi-restraints excluded: chain D residue  356 GLN
Chi-restraints excluded: chain D residue  404 LEU
Chi-restraints excluded: chain D residue  406 VAL
Chi-restraints excluded: chain D residue  439 GLU
Chi-restraints excluded: chain D residue  451 TRP
Chi-restraints excluded: chain D residue  469 VAL
Chi-restraints excluded: chain B residue  286 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 94 optimal weight:    0.6980
   chunk 85 optimal weight:    3.9990
   chunk 84 optimal weight:    0.3980
   chunk 64 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   chunk 22 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
D 173 HIS
B 253 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.092482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.066023 restraints weight = 71304.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.069042 restraints weight = 28212.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.070925 restraints weight = 16615.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.072094 restraints weight = 12073.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.072806 restraints weight = 9930.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8350  Z= 0.136
  Angle     :  0.675   8.562  11289  Z= 0.338
  Chirality :  0.047   0.227   1324
  Planarity :  0.004   0.047   1453
  Dihedral  :  6.513  52.604   1164
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  : 10.09 %
    Favored  : 89.15 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 26.01 %
    Favored  : 68.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -2.73 (0.24), residues: 1054
  helix: -0.33 (0.34), residues: 219
  sheet: -1.88 (0.35), residues: 178
  loop : -2.44 (0.22), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 438 
 TYR   0.020   0.002   TYR E 301 
 PHE   0.009   0.001   PHE D 368 
 TRP   0.011   0.001   TRP E  37 
 HIS   0.003   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8349)
  covalent geometry    : angle       0.67536 (11287)
  SS BOND              : bond        0.00100 (    1)
  SS BOND              : angle       0.35076 (    2)
  hydrogen bonds       : bond        0.03595 (  207)
  hydrogen bonds       : angle       5.10726 (  571)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 67
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: E  397 THR cc_start: 0.8756 (m) cc_final: 0.8544 (p)
REVERT: D   74 GLU cc_start: 0.6207 (mp0) cc_final: 0.5589 (mp0)
REVERT: D  100 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7947 (mm-30)
REVERT: D  129 HIS cc_start: 0.7989 (OUTLIER) cc_final: 0.6846 (m170)
REVERT: D  235 VAL cc_start: 0.9523 (OUTLIER) cc_final: 0.9177 (p)
REVERT: D  238 TYR cc_start: 0.9051 (p90) cc_final: 0.8375 (p90)
REVERT: D  353 MET cc_start: 0.4601 (ttt) cc_final: 0.4336 (ttt)
REVERT: D  439 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6969 (mt-10)
REVERT: B  273 MET cc_start: 0.8900 (tmm) cc_final: 0.8336 (tmm)
  outliers start: 48
  outliers final: 29
  residues processed: 111
  average time/residue: 0.0678
  time to fit residues: 11.6142
Evaluate side-chains
  100 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 67
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    2 GLU
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   53 VAL
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue  131 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  197 THR
Chi-restraints excluded: chain E residue  263 ILE
Chi-restraints excluded: chain E residue  304 ILE
Chi-restraints excluded: chain E residue  351 LEU
Chi-restraints excluded: chain E residue  377 SER
Chi-restraints excluded: chain E residue  387 ILE
Chi-restraints excluded: chain E residue  398 VAL
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue  100 GLU
Chi-restraints excluded: chain D residue  101 CYS
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  120 THR
Chi-restraints excluded: chain D residue  129 HIS
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  245 VAL
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  341 THR
Chi-restraints excluded: chain D residue  406 VAL
Chi-restraints excluded: chain D residue  439 GLU
Chi-restraints excluded: chain D residue  451 TRP
Chi-restraints excluded: chain D residue  469 VAL
Chi-restraints excluded: chain B residue  286 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 14 optimal weight:    0.0010
   chunk 70 optimal weight:    1.9990
   chunk 32 optimal weight:    0.4980
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0670
   chunk 72 optimal weight:    3.9990
   chunk 98 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 50 optimal weight:   10.0000
   overall best weight:    0.6326

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 253 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.093379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.068267 restraints weight = 59046.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.072170 restraints weight = 27390.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.072280 restraints weight = 13289.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.072533 restraints weight = 13998.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.072711 restraints weight = 12260.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3462
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3462
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8350  Z= 0.118
  Angle     :  0.689   9.768  11289  Z= 0.342
  Chirality :  0.048   0.293   1324
  Planarity :  0.004   0.047   1453
  Dihedral  :  5.857  49.331   1157
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  :  9.99 %
    Favored  : 89.25 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 27.42 %
    Favored  : 68.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -2.66 (0.24), residues: 1054
  helix: -0.15 (0.35), residues: 216
  sheet: -1.81 (0.35), residues: 185
  loop : -2.44 (0.22), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 438 
 TYR   0.020   0.001   TYR D 238 
 PHE   0.009   0.001   PHE C  18 
 TRP   0.016   0.001   TRP E  37 
 HIS   0.003   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 8349)
  covalent geometry    : angle       0.68922 (11287)
  SS BOND              : bond        0.00097 (    1)
  SS BOND              : angle       0.34880 (    2)
  hydrogen bonds       : bond        0.03353 (  207)
  hydrogen bonds       : angle       4.99455 (  571)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 72
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  397 THR cc_start: 0.8780 (m) cc_final: 0.8574 (p)
REVERT: D   74 GLU cc_start: 0.6133 (mp0) cc_final: 0.5533 (mp0)
REVERT: D  100 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7937 (mm-30)
REVERT: D  129 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.6981 (m170)
REVERT: D  235 VAL cc_start: 0.9514 (OUTLIER) cc_final: 0.9157 (p)
REVERT: D  238 TYR cc_start: 0.9000 (p90) cc_final: 0.8323 (p90)
REVERT: D  310 MET cc_start: 0.7149 (ttt) cc_final: 0.6928 (tmm)
REVERT: D  439 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6912 (mt-10)
REVERT: B  273 MET cc_start: 0.8910 (tmm) cc_final: 0.8349 (tmm)
  outliers start: 39
  outliers final: 30
  residues processed: 107
  average time/residue: 0.0742
  time to fit residues: 11.9806
Evaluate side-chains
  101 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 67
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   53 VAL
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  186 ILE
Chi-restraints excluded: chain E residue  197 THR
Chi-restraints excluded: chain E residue  263 ILE
Chi-restraints excluded: chain E residue  304 ILE
Chi-restraints excluded: chain E residue  351 LEU
Chi-restraints excluded: chain E residue  384 ARG
Chi-restraints excluded: chain E residue  387 ILE
Chi-restraints excluded: chain E residue  398 VAL
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue  100 GLU
Chi-restraints excluded: chain D residue  101 CYS
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  120 THR
Chi-restraints excluded: chain D residue  129 HIS
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  234 VAL
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  315 PHE
Chi-restraints excluded: chain D residue  341 THR
Chi-restraints excluded: chain D residue  406 VAL
Chi-restraints excluded: chain D residue  439 GLU
Chi-restraints excluded: chain D residue  451 TRP
Chi-restraints excluded: chain D residue  469 VAL
Chi-restraints excluded: chain B residue  286 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 28 optimal weight:    0.2980
   chunk 90 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 70 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 253 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.093360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.067696 restraints weight = 76355.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.071778 restraints weight = 30551.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.072158 restraints weight = 15664.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.072381 restraints weight = 13804.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.072629 restraints weight = 12879.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3458
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3458 r_free = 0.3458    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3458 r_free = 0.3458    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3458
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8350  Z= 0.122
  Angle     :  0.685   9.325  11289  Z= 0.344
  Chirality :  0.048   0.229   1324
  Planarity :  0.004   0.049   1453
  Dihedral  :  5.796  47.648   1157
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  : 10.28 %
    Favored  : 88.96 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 27.20 %
    Favored  : 68.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -2.56 (0.24), residues: 1054
  helix: -0.04 (0.35), residues: 216
  sheet: -1.71 (0.36), residues: 180
  loop : -2.40 (0.22), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 295 
 TYR   0.019   0.001   TYR D 238 
 PHE   0.009   0.001   PHE C  18 
 TRP   0.016   0.001   TRP E  37 
 HIS   0.003   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8349)
  covalent geometry    : angle       0.68460 (11287)
  SS BOND              : bond        0.00101 (    1)
  SS BOND              : angle       0.34215 (    2)
  hydrogen bonds       : bond        0.03482 (  207)
  hydrogen bonds       : angle       4.97406 (  571)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 68
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  216 MET cc_start: 0.8948 (tpp) cc_final: 0.8008 (tpp)
REVERT: E  397 THR cc_start: 0.8788 (m) cc_final: 0.8584 (p)
REVERT: D   74 GLU cc_start: 0.6014 (mp0) cc_final: 0.5548 (mp0)
REVERT: D   89 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.6317 (p90)
REVERT: D  100 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7947 (mm-30)
REVERT: D  129 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7195 (m170)
REVERT: D  235 VAL cc_start: 0.9522 (OUTLIER) cc_final: 0.9173 (p)
REVERT: D  238 TYR cc_start: 0.9023 (p90) cc_final: 0.8341 (p90)
REVERT: D  310 MET cc_start: 0.7419 (ttt) cc_final: 0.7034 (tmm)
REVERT: D  439 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6969 (mt-10)
REVERT: B  255 MET cc_start: 0.9022 (pmm) cc_final: 0.8787 (pmm)
REVERT: B  273 MET cc_start: 0.8910 (tmm) cc_final: 0.8363 (tmm)
  outliers start: 44
  outliers final: 33
  residues processed: 110
  average time/residue: 0.0780
  time to fit residues: 12.8594
Evaluate side-chains
  104 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 66
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    2 GLU
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   53 VAL
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  186 ILE
Chi-restraints excluded: chain E residue  263 ILE
Chi-restraints excluded: chain E residue  304 ILE
Chi-restraints excluded: chain E residue  351 LEU
Chi-restraints excluded: chain E residue  354 VAL
Chi-restraints excluded: chain E residue  377 SER
Chi-restraints excluded: chain E residue  384 ARG
Chi-restraints excluded: chain E residue  387 ILE
Chi-restraints excluded: chain E residue  398 VAL
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue   89 TYR
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue  100 GLU
Chi-restraints excluded: chain D residue  101 CYS
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  120 THR
Chi-restraints excluded: chain D residue  129 HIS
Chi-restraints excluded: chain D residue  188 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  234 VAL
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  245 VAL
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  315 PHE
Chi-restraints excluded: chain D residue  341 THR
Chi-restraints excluded: chain D residue  406 VAL
Chi-restraints excluded: chain D residue  439 GLU
Chi-restraints excluded: chain D residue  451 TRP
Chi-restraints excluded: chain D residue  469 VAL
Chi-restraints excluded: chain B residue  286 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 59 optimal weight:    7.9990
   chunk 65 optimal weight:   20.0000
   chunk 53 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 11 optimal weight:    0.3980
   chunk 24 optimal weight:    5.9990
   chunk 61 optimal weight:    8.9990
   chunk 71 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 253 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.093750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.067442 restraints weight = 101123.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.071511 restraints weight = 37508.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.072297 restraints weight = 18312.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.072698 restraints weight = 13726.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.073102 restraints weight = 13767.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3478
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3478
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8350  Z= 0.117
  Angle     :  0.685  10.511  11289  Z= 0.340
  Chirality :  0.047   0.199   1324
  Planarity :  0.004   0.049   1453
  Dihedral  :  5.728  45.894   1156
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  :  9.51 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 27.75 %
    Favored  : 68.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -2.50 (0.24), residues: 1054
  helix: -0.07 (0.35), residues: 217
  sheet: -1.64 (0.36), residues: 180
  loop : -2.34 (0.22), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 438 
 TYR   0.020   0.001   TYR D 238 
 PHE   0.008   0.001   PHE D 124 
 TRP   0.012   0.001   TRP E  37 
 HIS   0.003   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8349)
  covalent geometry    : angle       0.68468 (11287)
  SS BOND              : bond        0.00091 (    1)
  SS BOND              : angle       0.34546 (    2)
  hydrogen bonds       : bond        0.03352 (  207)
  hydrogen bonds       : angle       4.87852 (  571)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 72
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: E  216 MET cc_start: 0.8998 (tpp) cc_final: 0.8031 (tpp)
REVERT: C    7 ASP cc_start: 0.8694 (t0) cc_final: 0.8466 (t0)
REVERT: D   74 GLU cc_start: 0.6130 (mp0) cc_final: 0.5646 (mp0)
REVERT: D   89 TYR cc_start: 0.6572 (OUTLIER) cc_final: 0.6295 (p90)
REVERT: D  100 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7899 (mm-30)
REVERT: D  129 HIS cc_start: 0.8145 (OUTLIER) cc_final: 0.7399 (m170)
REVERT: D  235 VAL cc_start: 0.9510 (OUTLIER) cc_final: 0.9160 (p)
REVERT: D  238 TYR cc_start: 0.9001 (p90) cc_final: 0.8296 (p90)
REVERT: D  310 MET cc_start: 0.7510 (ttt) cc_final: 0.7055 (tmm)
REVERT: D  439 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6998 (mt-10)
REVERT: B  273 MET cc_start: 0.8891 (tmm) cc_final: 0.8360 (tmm)
  outliers start: 38
  outliers final: 30
  residues processed: 109
  average time/residue: 0.0778
  time to fit residues: 12.6548
Evaluate side-chains
  103 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 68
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    2 GLU
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   53 VAL
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  186 ILE
Chi-restraints excluded: chain E residue  263 ILE
Chi-restraints excluded: chain E residue  304 ILE
Chi-restraints excluded: chain E residue  351 LEU
Chi-restraints excluded: chain E residue  377 SER
Chi-restraints excluded: chain E residue  384 ARG
Chi-restraints excluded: chain E residue  398 VAL
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue   88 ILE
Chi-restraints excluded: chain D residue   89 TYR
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue  100 GLU
Chi-restraints excluded: chain D residue  101 CYS
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  120 THR
Chi-restraints excluded: chain D residue  129 HIS
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  234 VAL
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  245 VAL
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  315 PHE
Chi-restraints excluded: chain D residue  341 THR
Chi-restraints excluded: chain D residue  406 VAL
Chi-restraints excluded: chain D residue  439 GLU
Chi-restraints excluded: chain D residue  451 TRP
Chi-restraints excluded: chain D residue  469 VAL
Chi-restraints excluded: chain B residue  286 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 101 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 96 optimal weight:    0.6980
   chunk 24 optimal weight:    8.9990
   chunk 3 optimal weight:    0.4980
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
E 389 ASN
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 253 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.092869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.066462 restraints weight = 71632.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.069449 restraints weight = 28473.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.071340 restraints weight = 16883.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.072455 restraints weight = 12345.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.073234 restraints weight = 10183.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3472
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3472
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8350  Z= 0.149
  Angle     :  0.710  12.492  11289  Z= 0.354
  Chirality :  0.048   0.202   1324
  Planarity :  0.004   0.050   1453
  Dihedral  :  5.742  44.961   1154
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  : 11.51 %
    Favored  : 87.73 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 28.40 %
    Favored  : 67.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -2.57 (0.24), residues: 1054
  helix: -0.06 (0.35), residues: 214
  sheet: -1.75 (0.35), residues: 185
  loop : -2.39 (0.22), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 438 
 TYR   0.018   0.002   TYR D 238 
 PHE   0.023   0.001   PHE A 481 
 TRP   0.018   0.001   TRP E  37 
 HIS   0.003   0.001   HIS E 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8349)
  covalent geometry    : angle       0.70975 (11287)
  SS BOND              : bond        0.00116 (    1)
  SS BOND              : angle       0.30197 (    2)
  hydrogen bonds       : bond        0.03639 (  207)
  hydrogen bonds       : angle       4.96294 (  571)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 68
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  216 MET cc_start: 0.9038 (tpp) cc_final: 0.8063 (tpp)
REVERT: C    7 ASP cc_start: 0.8664 (t0) cc_final: 0.8425 (t0)
REVERT: D   74 GLU cc_start: 0.5984 (mp0) cc_final: 0.5460 (mp0)
REVERT: D   89 TYR cc_start: 0.6624 (OUTLIER) cc_final: 0.6259 (p90)
REVERT: D  100 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7900 (mm-30)
REVERT: D  129 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7418 (m170)
REVERT: D  235 VAL cc_start: 0.9519 (OUTLIER) cc_final: 0.9173 (p)
REVERT: D  238 TYR cc_start: 0.9019 (p90) cc_final: 0.8341 (p90)
REVERT: D  310 MET cc_start: 0.7634 (ttt) cc_final: 0.7131 (tmm)
REVERT: D  439 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7030 (mt-10)
REVERT: B  273 MET cc_start: 0.8872 (tmm) cc_final: 0.8349 (tmm)
  outliers start: 39
  outliers final: 32
  residues processed: 104
  average time/residue: 0.0839
  time to fit residues: 12.6796
Evaluate side-chains
  104 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 67
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    2 GLU
Chi-restraints excluded: chain E residue   30 VAL
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   53 VAL
Chi-restraints excluded: chain E residue   56 THR
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  186 ILE
Chi-restraints excluded: chain E residue  263 ILE
Chi-restraints excluded: chain E residue  304 ILE
Chi-restraints excluded: chain E residue  351 LEU
Chi-restraints excluded: chain E residue  377 SER
Chi-restraints excluded: chain E residue  384 ARG
Chi-restraints excluded: chain E residue  387 ILE
Chi-restraints excluded: chain E residue  398 VAL
Chi-restraints excluded: chain D residue   78 THR
Chi-restraints excluded: chain D residue   89 TYR
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue  100 GLU
Chi-restraints excluded: chain D residue  101 CYS
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  120 THR
Chi-restraints excluded: chain D residue  129 HIS
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  234 VAL
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  245 VAL
Chi-restraints excluded: chain D residue  271 VAL
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  315 PHE
Chi-restraints excluded: chain D residue  341 THR
Chi-restraints excluded: chain D residue  406 VAL
Chi-restraints excluded: chain D residue  439 GLU
Chi-restraints excluded: chain D residue  451 TRP
Chi-restraints excluded: chain D residue  469 VAL
Chi-restraints excluded: chain B residue  286 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 96 optimal weight:    0.4980
   chunk 74 optimal weight:   10.0000
   chunk 73 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 98 optimal weight:    0.0670
   chunk 47 optimal weight:    0.9990
   chunk 66 optimal weight:    7.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.6120

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

Flipped N/Q/H residues before XYZ refinement:
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 253 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.094251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.069009 restraints weight = 81440.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.072725 restraints weight = 31678.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.073165 restraints weight = 17001.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.073257 restraints weight = 15536.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.073738 restraints weight = 13800.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3477
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3477
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8350  Z= 0.116
  Angle     :  0.690   9.293  11289  Z= 0.343
  Chirality :  0.047   0.198   1324
  Planarity :  0.004   0.049   1453
  Dihedral  :  5.593  44.195   1154
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  :  8.85 %
    Favored  : 90.39 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 28.18 %
    Favored  : 67.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -2.41 (0.24), residues: 1054
  helix:  0.09 (0.36), residues: 211
  sheet: -1.60 (0.36), residues: 180
  loop : -2.30 (0.22), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 438 
 TYR   0.019   0.001   TYR D 238 
 PHE   0.025   0.001   PHE A 481 
 TRP   0.011   0.001   TRP A 478 
 HIS   0.004   0.001   HIS D 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8349)
  covalent geometry    : angle       0.69000 (11287)
  SS BOND              : bond        0.00068 (    1)
  SS BOND              : angle       0.36319 (    2)
  hydrogen bonds       : bond        0.03354 (  207)
  hydrogen bonds       : angle       4.88099 (  571)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1977.72 seconds
wall clock time: 34 minutes 56.48 seconds (2096.48 seconds total)