Starting phenix.real_space_refine
on Wed Mar  4 23:20:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xta_33444/03_2026/7xta_33444_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xta_33444/03_2026/7xta_33444.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xta_33444/03_2026/7xta_33444.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xta_33444/03_2026/7xta_33444.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xta_33444/03_2026/7xta_33444_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xta_33444/03_2026/7xta_33444_neut_trim.cif"
  }
  resolution = 3.2
  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=   0.003 sd=   0.034
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      70      5.16       5
     C    5607      2.51       5
     N    1476      2.21       5
     O    1618      1.98       5
     H    8707      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17478
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 3538
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 216}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 5026
          Classifications: {'peptide': 333}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
    Chain: "E"
      Number of atoms: 3472
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 3472
          Classifications: {'peptide': 230}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 794
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
    Chain: "R"
      Number of atoms: 4635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 4635
          Classifications: {'peptide': 283}
          Link IDs: {'PTRANS': 11, 'TRANS': 271}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Unusual residues: {'SRO': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.31, per 1000 atoms: 0.19
  Number of scatterers: 17478
  At special positions: 0
  Unit cell: (115.668, 128.52, 110.313, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      70     16.00
     O    1618      8.00
     N    1476      7.00
     C    5607      6.00
     H    8707      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.16
  Conformation dependent library (CDL) restraints added in 608.0 milliseconds
  

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2088

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 12 sheets defined
      40.0% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.649A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 4.068A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU A 232 " --> pdb=" O   ASP A 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 232'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.861A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 4.205A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 281
      No H-bonds generated for 'chain 'A' and resid 280 through 281'
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.868A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 351
    Processing helix  chain 'B' and resid 9 through 25
      removed outlier: 4.063A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 3.641A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 62 through 65
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'G' and resid 14 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.570A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'R' and resid 19 through 46
    Processing helix  chain 'R' and resid 46 through 51
    Processing helix  chain 'R' and resid 53 through 72
      removed outlier: 4.329A  pdb=" N   PHE R  57 " --> pdb=" O   LYS R  53 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE R  58 " --> pdb=" O   THR R  54 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 72 through 83
      removed outlier: 3.664A  pdb=" N   VAL R  81 " --> pdb=" O   ALA R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 87 through 123
      removed outlier: 4.297A  pdb=" N   PHE R  91 " --> pdb=" O   TYR R  87 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 127 through 132
    Processing helix  chain 'R' and resid 133 through 153
      removed outlier: 3.542A  pdb=" N   ILE R 137 " --> pdb=" O   THR R 133 " (cutoff:3.500A)
      Proline residue:  R 148  - end of helix
      removed outlier: 3.912A  pdb=" N   ILE R 151 " --> pdb=" O   ILE R 147 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 153 through 158
      removed outlier: 3.654A  pdb=" N   GLN R 158 " --> pdb=" O   LEU R 154 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 165 through 174
      removed outlier: 3.848A  pdb=" N   PHE R 174 " --> pdb=" O   GLU R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 188 through 200
    Processing helix  chain 'R' and resid 200 through 222
    Processing helix  chain 'R' and resid 255 through 281
      Proline residue:  R 273  - end of helix
    Processing helix  chain 'R' and resid 282 through 284
      No H-bonds generated for 'chain 'R' and resid 282 through 284'
    Processing helix  chain 'R' and resid 289 through 312
      removed outlier: 3.770A  pdb=" N   ASN R 303 " --> pdb=" O   LEU R 299 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   SER R 304 " --> pdb=" O   GLY R 300 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   GLY R 305 " --> pdb=" O   TYR R 301 " (cutoff:3.500A)
      Proline residue:  R 308  - end of helix
    Processing helix  chain 'R' and resid 317 through 328
      removed outlier: 3.942A  pdb=" N   ALA R 321 " --> pdb=" O   SER R 317 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.880A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.609A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.903A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.726A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.559A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.656A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.243A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.729A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.964A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.350A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.969A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.511A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7
      removed outlier: 3.594A  pdb=" N   VAL E   5 " --> pdb=" O   SER E  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 7.156A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.128A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   LEU E 187 " --> pdb=" O   LEU E 178 " (cutoff:3.500A)

    426 hydrogen bonds defined for protein.
    1194 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.47

  Time building geometry restraints manager: 1.66 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8668
        1.03 -     1.23: 40
        1.23 -     1.42: 3793
        1.42 -     1.62: 5066
        1.62 -     1.81: 99
  Bond restraints: 17666
  Sorted by residual:
  bond pdb=" CZ2 SRO R 401 "
       pdb=" CH2 SRO R 401 "
    ideal  model  delta    sigma   weight residual
    1.386  1.521 -0.135 2.00e-02 2.50e+03 4.59e+01
  bond pdb=" CG  SRO R 401 "
       pdb=" CD2 SRO R 401 "
    ideal  model  delta    sigma   weight residual
    1.438  1.508 -0.070 2.00e-02 2.50e+03 1.22e+01
  bond pdb=" CD1 SRO R 401 "
       pdb=" NE1 SRO R 401 "
    ideal  model  delta    sigma   weight residual
    1.377  1.315  0.062 2.00e-02 2.50e+03 9.71e+00
  bond pdb=" CE2 SRO R 401 "
       pdb=" CZ2 SRO R 401 "
    ideal  model  delta    sigma   weight residual
    1.393  1.352  0.041 2.00e-02 2.50e+03 4.17e+00
  bond pdb=" CD2 SRO R 401 "
       pdb=" CE3 SRO R 401 "
    ideal  model  delta    sigma   weight residual
    1.404  1.366  0.038 2.00e-02 2.50e+03 3.66e+00
  ... (remaining 17661 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 31668
        2.09 -     4.17: 120
        4.17 -     6.26: 16
        6.26 -     8.34: 2
        8.34 -    10.43: 1
  Bond angle restraints: 31807
  Sorted by residual:
  angle pdb=" CD1 SRO R 401 "
        pdb=" NE1 SRO R 401 "
        pdb=" CE2 SRO R 401 "
      ideal   model   delta    sigma   weight residual
     109.10  119.53  -10.43 3.00e+00 1.11e-01 1.21e+01
  angle pdb=" CG  SRO R 401 "
        pdb=" CD1 SRO R 401 "
        pdb=" NE1 SRO R 401 "
      ideal   model   delta    sigma   weight residual
     110.16  102.15    8.01 3.00e+00 1.11e-01 7.12e+00
  angle pdb=" CB  LYS R 171 "
        pdb=" CG  LYS R 171 "
        pdb=" CD  LYS R 171 "
      ideal   model   delta    sigma   weight residual
     111.30  116.87   -5.57 2.30e+00 1.89e-01 5.86e+00
  angle pdb=" C   LEU R  80 "
        pdb=" N   VAL R  81 "
        pdb=" CA  VAL R  81 "
      ideal   model   delta    sigma   weight residual
     123.16  120.63    2.53 1.06e+00 8.90e-01 5.71e+00
  angle pdb=" CA  HIS R 223 "
        pdb=" C   HIS R 223 "
        pdb=" N   GLN R 224 "
      ideal   model   delta    sigma   weight residual
     117.21  120.56   -3.35 1.42e+00 4.96e-01 5.56e+00
  ... (remaining 31802 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.10: 7598
       17.10 -    34.21: 542
       34.21 -    51.31: 142
       51.31 -    68.42: 45
       68.42 -    85.52: 9
  Dihedral angle restraints: 8336
    sinusoidal: 4444
      harmonic: 3892
  Sorted by residual:
  dihedral pdb=" CA  HIS R 221 "
           pdb=" C   HIS R 221 "
           pdb=" N   ALA R 222 "
           pdb=" CA  ALA R 222 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.90   19.10     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.09   17.91     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  ARG E 191 "
           pdb=" C   ARG E 191 "
           pdb=" N   MET E 192 "
           pdb=" CA  MET E 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.34   15.66     0      5.00e+00 4.00e-02 9.81e+00
  ... (remaining 8333 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 995
       0.034 -    0.069: 256
       0.069 -    0.103: 75
       0.103 -    0.138: 49
       0.138 -    0.172: 2
  Chirality restraints: 1377
  Sorted by residual:
  chirality pdb=" CA  MET R  73 "
            pdb=" N   MET R  73 "
            pdb=" C   MET R  73 "
            pdb=" CB  MET R  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.41e-01
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.78e-01
  chirality pdb=" CA  VAL R 288 "
            pdb=" N   VAL R 288 "
            pdb=" C   VAL R 288 "
            pdb=" CB  VAL R 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.28e-01
  ... (remaining 1374 not shown)

  Planarity restraints: 2597
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.062 5.00e-02 4.00e+02   9.28e-02 1.38e+01
        pdb=" N   PRO B 236 "    0.161 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  38 "    0.036 5.00e-02 4.00e+02   5.40e-02 4.66e+00
        pdb=" N   PRO B  39 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO B  39 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B  39 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR R 119 "   -0.013 2.00e-02 2.50e+03   9.48e-03 2.70e+00
        pdb=" CG  TYR R 119 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR R 119 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR R 119 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR R 119 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR R 119 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR R 119 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR R 119 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD1 TYR R 119 "    0.004 2.00e-02 2.50e+03
        pdb=" HD2 TYR R 119 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE1 TYR R 119 "   -0.002 2.00e-02 2.50e+03
        pdb=" HE2 TYR R 119 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 2594 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 808
        2.18 -     2.78: 34729
        2.78 -     3.39: 48052
        3.39 -     3.99: 61642
        3.99 -     4.60: 96141
  Nonbonded interactions: 241372
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 290 "
            pdb=" HE  ARG B 314 "
     model   vdw
     1.573 2.450
  nonbonded pdb="HE21 GLN B 220 "
            pdb=" OD2 ASP B 258 "
     model   vdw
     1.576 2.450
  nonbonded pdb=" O   ALA A  41 "
            pdb=" HZ2 LYS A  46 "
     model   vdw
     1.603 2.450
  nonbonded pdb=" OD1 ASP B 153 "
            pdb=" H   GLN B 156 "
     model   vdw
     1.610 2.450
  nonbonded pdb=" HH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     1.637 2.450
  ... (remaining 241367 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.830
  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:             0.100
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     17.250
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
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   0.135   8959  Z= 0.158
  Angle     :  0.539  10.426  12135  Z= 0.307
  Chirality :  0.039   0.172   1377
  Planarity :  0.004   0.093   1523
  Dihedral  : 12.648  79.887   3207
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.64 (0.26), residues: 1097
  helix:  2.24 (0.28), residues: 381
  sheet:  1.15 (0.31), residues: 271
  loop :  0.09 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  24 
 TYR   0.027   0.001   TYR R 119 
 PHE   0.023   0.001   PHE B 235 
 TRP   0.017   0.001   TRP B 332 
 HIS   0.001   0.000   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8959)
  covalent geometry    : angle       0.53934 (12135)
  hydrogen bonds       : bond        0.18603 (  426)
  hydrogen bonds       : angle       6.68593 ( 1194)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  354 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 354
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.7741 (ttm-80) cc_final: 0.7476 (ttm-80)
REVERT: A  275 GLU cc_start: 0.7477 (tp30) cc_final: 0.7232 (tp30)
REVERT: A  309 ASP cc_start: 0.7354 (m-30) cc_final: 0.6902 (m-30)
REVERT: B  111 TYR cc_start: 0.8528 (m-80) cc_final: 0.7499 (m-80)
REVERT: B  134 ARG cc_start: 0.7374 (ptp-170) cc_final: 0.6976 (ptp-170)
REVERT: B  149 CYS cc_start: 0.7454 (m) cc_final: 0.7225 (m)
REVERT: B  170 ASP cc_start: 0.8135 (t70) cc_final: 0.7713 (t0)
REVERT: B  256 ARG cc_start: 0.8582 (mtp85) cc_final: 0.8153 (mtm180)
REVERT: B  298 ASP cc_start: 0.7563 (t70) cc_final: 0.7248 (t0)
REVERT: B  317 CYS cc_start: 0.7113 (p) cc_final: 0.6912 (p)
REVERT: B  321 THR cc_start: 0.7243 (p) cc_final: 0.6958 (p)
REVERT: B  323 ASP cc_start: 0.7115 (p0) cc_final: 0.6763 (p0)
REVERT: E   67 ARG cc_start: 0.7191 (ttm170) cc_final: 0.6858 (ttm170)
REVERT: G   14 LYS cc_start: 0.8030 (pttm) cc_final: 0.7818 (pttm)
REVERT: G   58 GLU cc_start: 0.7418 (mp0) cc_final: 0.7105 (mp0)
REVERT: R   53 LYS cc_start: 0.6841 (mmtp) cc_final: 0.6636 (mmtp)
REVERT: R   79 GLU cc_start: 0.7659 (tt0) cc_final: 0.7448 (tt0)
REVERT: R  112 CYS cc_start: 0.7292 (m) cc_final: 0.6707 (m)
REVERT: R  139 LEU cc_start: 0.7271 (tp) cc_final: 0.6972 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 354
  average time/residue: 0.2300
  time to fit residues: 106.1600
Evaluate side-chains
  319 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 319
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 244 HIS
B 295 ASN
R 221 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.131531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.112787 restraints weight = 37777.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.46
r_work: 0.3356 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   8959  Z= 0.258
  Angle     :  0.570   5.490  12135  Z= 0.316
  Chirality :  0.042   0.154   1377
  Planarity :  0.004   0.047   1523
  Dihedral  :  4.314  20.382   1207
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  9.78 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.25 (0.26), residues: 1097
  helix:  2.00 (0.27), residues: 383
  sheet:  0.78 (0.30), residues: 291
  loop : -0.16 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  87 
 TYR   0.017   0.002   TYR E  60 
 PHE   0.017   0.002   PHE B 234 
 TRP   0.018   0.002   TRP B 211 
 HIS   0.008   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 8959)
  covalent geometry    : angle       0.57030 (12135)
  hydrogen bonds       : bond        0.05020 (  426)
  hydrogen bonds       : angle       5.09798 ( 1194)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  347 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 336
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8131 (m-30) cc_final: 0.7873 (m-30)
REVERT: A   21 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7935 (ttm-80)
REVERT: A  204 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8081 (mm-40)
REVERT: A  205 ARG cc_start: 0.8206 (mmt-90) cc_final: 0.7843 (mmt-90)
REVERT: A  252 SER cc_start: 0.8607 (t) cc_final: 0.8274 (p)
REVERT: A  275 GLU cc_start: 0.7991 (tp30) cc_final: 0.7526 (tp30)
REVERT: A  309 ASP cc_start: 0.7754 (m-30) cc_final: 0.7346 (m-30)
REVERT: B   13 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8229 (tm-30)
REVERT: B   44 GLN cc_start: 0.7610 (pm20) cc_final: 0.7373 (pm20)
REVERT: B   87 THR cc_start: 0.8668 (m) cc_final: 0.8363 (p)
REVERT: B  111 TYR cc_start: 0.8842 (m-80) cc_final: 0.8488 (m-80)
REVERT: B  134 ARG cc_start: 0.8216 (ptp-170) cc_final: 0.7826 (ptp-170)
REVERT: B  149 CYS cc_start: 0.8364 (m) cc_final: 0.8130 (m)
REVERT: B  189 SER cc_start: 0.8843 (p) cc_final: 0.8579 (t)
REVERT: B  220 GLN cc_start: 0.8028 (mt0) cc_final: 0.7503 (mt0)
REVERT: B  256 ARG cc_start: 0.8723 (mtp85) cc_final: 0.8360 (mtm180)
REVERT: B  258 ASP cc_start: 0.8041 (t0) cc_final: 0.7644 (t0)
REVERT: B  321 THR cc_start: 0.7594 (p) cc_final: 0.7350 (p)
REVERT: G   14 LYS cc_start: 0.8292 (pttm) cc_final: 0.7912 (pttm)
REVERT: R   53 LYS cc_start: 0.7109 (mmtp) cc_final: 0.6809 (mmtp)
REVERT: R   72 VAL cc_start: 0.8247 (t) cc_final: 0.7962 (t)
REVERT: R  112 CYS cc_start: 0.8116 (m) cc_final: 0.7693 (m)
REVERT: R  139 LEU cc_start: 0.7242 (tp) cc_final: 0.6979 (tp)
REVERT: R  185 PHE cc_start: 0.8344 (t80) cc_final: 0.7995 (t80)
REVERT: R  301 TYR cc_start: 0.8210 (m-10) cc_final: 0.7654 (m-10)
  outliers start: 11
  outliers final: 8
  residues processed: 338
  average time/residue: 0.2734
  time to fit residues: 118.6267
Evaluate side-chains
  333 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 325
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue  183 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 109 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 94 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
E  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.129030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.110513 restraints weight = 37933.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.44
r_work: 0.3326 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.2751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052   8959  Z= 0.318
  Angle     :  0.594   5.508  12135  Z= 0.330
  Chirality :  0.043   0.159   1377
  Planarity :  0.005   0.074   1523
  Dihedral  :  4.647  21.145   1207
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.97 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.26), residues: 1097
  helix:  1.61 (0.27), residues: 382
  sheet:  0.26 (0.29), residues: 294
  loop : -0.46 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  72 
 TYR   0.018   0.002   TYR E  60 
 PHE   0.016   0.002   PHE B 199 
 TRP   0.021   0.002   TRP B 211 
 HIS   0.006   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00675 ( 8959)
  covalent geometry    : angle       0.59404 (12135)
  hydrogen bonds       : bond        0.05218 (  426)
  hydrogen bonds       : angle       5.00910 ( 1194)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  358 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 335
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7913 (ttm-80)
REVERT: A   25 GLU cc_start: 0.7854 (tt0) cc_final: 0.7607 (tt0)
REVERT: A   28 GLU cc_start: 0.8099 (tt0) cc_final: 0.7879 (tt0)
REVERT: A  190 THR cc_start: 0.8960 (m) cc_final: 0.8661 (p)
REVERT: A  204 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8163 (mm-40)
REVERT: A  252 SER cc_start: 0.8679 (t) cc_final: 0.8291 (p)
REVERT: A  275 GLU cc_start: 0.8065 (tp30) cc_final: 0.7589 (tp30)
REVERT: B   13 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8335 (tm-30)
REVERT: B   44 GLN cc_start: 0.7651 (pm20) cc_final: 0.7414 (pm20)
REVERT: B   76 ASP cc_start: 0.7681 (m-30) cc_final: 0.7368 (m-30)
REVERT: B  110 ASN cc_start: 0.8594 (m-40) cc_final: 0.8369 (m110)
REVERT: B  134 ARG cc_start: 0.8201 (ptp-170) cc_final: 0.7904 (ptp-170)
REVERT: B  149 CYS cc_start: 0.8411 (m) cc_final: 0.8174 (m)
REVERT: B  172 GLU cc_start: 0.8582 (tp30) cc_final: 0.8305 (tp30)
REVERT: B  189 SER cc_start: 0.8864 (p) cc_final: 0.8581 (t)
REVERT: B  219 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.8260 (ttm170)
REVERT: B  220 GLN cc_start: 0.8080 (mt0) cc_final: 0.7878 (mt0)
REVERT: B  321 THR cc_start: 0.7520 (p) cc_final: 0.7222 (p)
REVERT: B  323 ASP cc_start: 0.7771 (p0) cc_final: 0.7522 (p0)
REVERT: E   18 ARG cc_start: 0.7449 (tpp80) cc_final: 0.7185 (tpt-90)
REVERT: E  220 GLU cc_start: 0.7328 (pt0) cc_final: 0.6802 (pt0)
REVERT: E  234 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7689 (pp20)
REVERT: G   14 LYS cc_start: 0.8346 (pttm) cc_final: 0.8016 (pttm)
REVERT: G   58 GLU cc_start: 0.8008 (mp0) cc_final: 0.7569 (mp0)
REVERT: R   53 LYS cc_start: 0.7189 (mmtp) cc_final: 0.6878 (mmtp)
REVERT: R   72 VAL cc_start: 0.8275 (t) cc_final: 0.7842 (t)
REVERT: R  112 CYS cc_start: 0.8214 (m) cc_final: 0.7784 (m)
REVERT: R  185 PHE cc_start: 0.8430 (t80) cc_final: 0.8107 (t80)
REVERT: R  301 TYR cc_start: 0.8216 (m-10) cc_final: 0.7605 (m-10)
REVERT: R  303 ASN cc_start: 0.8282 (t0) cc_final: 0.8068 (t0)
  outliers start: 23
  outliers final: 17
  residues processed: 340
  average time/residue: 0.2694
  time to fit residues: 117.5635
Evaluate side-chains
  344 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 326
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain E residue  234 GLU
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  197 VAL
Chi-restraints excluded: chain R residue  287 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.132343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.113620 restraints weight = 37596.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.48
r_work: 0.3358 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8959  Z= 0.127
  Angle     :  0.502   5.121  12135  Z= 0.272
  Chirality :  0.040   0.136   1377
  Planarity :  0.004   0.056   1523
  Dihedral  :  4.350  20.639   1207
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.05 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.26), residues: 1097
  helix:  1.86 (0.27), residues: 386
  sheet:  0.17 (0.29), residues: 292
  loop : -0.35 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  27 
 TYR   0.012   0.001   TYR E 190 
 PHE   0.010   0.001   PHE B 234 
 TRP   0.014   0.001   TRP B 211 
 HIS   0.005   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8959)
  covalent geometry    : angle       0.50157 (12135)
  hydrogen bonds       : bond        0.04066 (  426)
  hydrogen bonds       : angle       4.75020 ( 1194)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  339 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 322
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7887 (ttm-80)
REVERT: A  204 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8137 (mm-40)
REVERT: A  252 SER cc_start: 0.8663 (t) cc_final: 0.8284 (p)
REVERT: A  275 GLU cc_start: 0.8046 (tp30) cc_final: 0.7611 (tp30)
REVERT: A  332 VAL cc_start: 0.8400 (t) cc_final: 0.8127 (m)
REVERT: B   13 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8300 (tm-30)
REVERT: B   44 GLN cc_start: 0.7634 (pm20) cc_final: 0.7388 (pm20)
REVERT: B   76 ASP cc_start: 0.7735 (m-30) cc_final: 0.7345 (m-30)
REVERT: B  134 ARG cc_start: 0.8203 (ptp-170) cc_final: 0.7914 (ptp-170)
REVERT: B  172 GLU cc_start: 0.8545 (tp30) cc_final: 0.8307 (tp30)
REVERT: B  189 SER cc_start: 0.8882 (p) cc_final: 0.8586 (t)
REVERT: B  212 ASP cc_start: 0.8394 (t0) cc_final: 0.8187 (t0)
REVERT: B  219 ARG cc_start: 0.8495 (ttm-80) cc_final: 0.8236 (ttm170)
REVERT: B  256 ARG cc_start: 0.8660 (mtp85) cc_final: 0.8320 (mtm180)
REVERT: B  321 THR cc_start: 0.7474 (p) cc_final: 0.7179 (p)
REVERT: B  323 ASP cc_start: 0.7727 (p0) cc_final: 0.7448 (p0)
REVERT: E   18 ARG cc_start: 0.7273 (tpp80) cc_final: 0.6918 (tpt-90)
REVERT: E  220 GLU cc_start: 0.7337 (pt0) cc_final: 0.6826 (pt0)
REVERT: E  234 GLU cc_start: 0.8003 (pt0) cc_final: 0.7678 (pp20)
REVERT: G   14 LYS cc_start: 0.8282 (pttm) cc_final: 0.7929 (pttm)
REVERT: G   58 GLU cc_start: 0.8041 (mp0) cc_final: 0.7628 (mp0)
REVERT: R   53 LYS cc_start: 0.7093 (mmtp) cc_final: 0.6783 (mmtp)
REVERT: R   72 VAL cc_start: 0.8259 (t) cc_final: 0.7729 (t)
REVERT: R  132 MET cc_start: 0.5500 (mmp) cc_final: 0.4675 (mmp)
REVERT: R  185 PHE cc_start: 0.8423 (t80) cc_final: 0.8076 (t80)
REVERT: R  264 MET cc_start: 0.8117 (mmm) cc_final: 0.7885 (mmm)
REVERT: R  301 TYR cc_start: 0.8102 (m-10) cc_final: 0.7449 (m-10)
  outliers start: 17
  outliers final: 16
  residues processed: 327
  average time/residue: 0.2700
  time to fit residues: 113.6944
Evaluate side-chains
  338 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 322
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  197 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 5 optimal weight:    0.2980
   chunk 107 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.131342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.112633 restraints weight = 37459.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.47
r_work: 0.3333 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8959  Z= 0.210
  Angle     :  0.523   4.616  12135  Z= 0.287
  Chirality :  0.040   0.139   1377
  Planarity :  0.004   0.066   1523
  Dihedral  :  4.360  20.744   1207
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 14.36 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.26), residues: 1097
  helix:  1.85 (0.27), residues: 386
  sheet:  0.06 (0.29), residues: 292
  loop : -0.45 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  27 
 TYR   0.012   0.001   TYR E 190 
 PHE   0.011   0.001   PHE B 151 
 TRP   0.012   0.002   TRP B 211 
 HIS   0.005   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 8959)
  covalent geometry    : angle       0.52272 (12135)
  hydrogen bonds       : bond        0.04268 (  426)
  hydrogen bonds       : angle       4.73668 ( 1194)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  351 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 331
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7906 (ttm-80)
REVERT: A   25 GLU cc_start: 0.7859 (tt0) cc_final: 0.7620 (tt0)
REVERT: A   28 GLU cc_start: 0.8090 (tt0) cc_final: 0.7882 (tt0)
REVERT: A  204 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8129 (mm-40)
REVERT: A  252 SER cc_start: 0.8636 (t) cc_final: 0.8279 (p)
REVERT: A  275 GLU cc_start: 0.8026 (tp30) cc_final: 0.7600 (tp30)
REVERT: A  297 GLU cc_start: 0.8224 (mp0) cc_final: 0.7740 (mp0)
REVERT: A  332 VAL cc_start: 0.8414 (t) cc_final: 0.8154 (m)
REVERT: B   13 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8301 (tm-30)
REVERT: B   76 ASP cc_start: 0.7785 (m-30) cc_final: 0.7378 (m-30)
REVERT: B  110 ASN cc_start: 0.8569 (m-40) cc_final: 0.8329 (m110)
REVERT: B  134 ARG cc_start: 0.8191 (ptp-170) cc_final: 0.7929 (ptp-170)
REVERT: B  170 ASP cc_start: 0.8583 (t70) cc_final: 0.8113 (t0)
REVERT: B  172 GLU cc_start: 0.8529 (tp30) cc_final: 0.8289 (tp30)
REVERT: B  189 SER cc_start: 0.8884 (p) cc_final: 0.8607 (t)
REVERT: B  219 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.8251 (ttm170)
REVERT: B  227 SER cc_start: 0.8863 (t) cc_final: 0.8622 (t)
REVERT: B  234 PHE cc_start: 0.8561 (m-80) cc_final: 0.8321 (m-80)
REVERT: B  256 ARG cc_start: 0.8696 (mtp85) cc_final: 0.8321 (mtm180)
REVERT: B  290 ASP cc_start: 0.7390 (t0) cc_final: 0.7163 (t0)
REVERT: B  298 ASP cc_start: 0.8362 (t70) cc_final: 0.8067 (t70)
REVERT: B  321 THR cc_start: 0.7496 (p) cc_final: 0.7208 (p)
REVERT: B  323 ASP cc_start: 0.7751 (p0) cc_final: 0.7462 (p0)
REVERT: E   18 ARG cc_start: 0.7293 (tpp80) cc_final: 0.6937 (tpt-90)
REVERT: E  158 SER cc_start: 0.8723 (t) cc_final: 0.8384 (p)
REVERT: E  192 MET cc_start: 0.7973 (ttt) cc_final: 0.7758 (ttt)
REVERT: E  220 GLU cc_start: 0.7298 (pt0) cc_final: 0.6803 (pt0)
REVERT: E  234 GLU cc_start: 0.7997 (pt0) cc_final: 0.7691 (pp20)
REVERT: G   14 LYS cc_start: 0.8308 (pttm) cc_final: 0.8068 (pttm)
REVERT: G   58 GLU cc_start: 0.8041 (mp0) cc_final: 0.7629 (mp0)
REVERT: R   72 VAL cc_start: 0.8299 (t) cc_final: 0.7880 (t)
REVERT: R  132 MET cc_start: 0.5462 (mmp) cc_final: 0.4704 (mmp)
REVERT: R  185 PHE cc_start: 0.8448 (t80) cc_final: 0.8123 (t80)
REVERT: R  205 LEU cc_start: 0.7911 (tp) cc_final: 0.7683 (tt)
REVERT: R  207 MET cc_start: 0.8258 (mtp) cc_final: 0.8033 (ttm)
REVERT: R  301 TYR cc_start: 0.8146 (m-10) cc_final: 0.7655 (m-10)
REVERT: R  306 LEU cc_start: 0.7905 (tp) cc_final: 0.7464 (tp)
  outliers start: 20
  outliers final: 19
  residues processed: 337
  average time/residue: 0.2582
  time to fit residues: 112.8399
Evaluate side-chains
  336 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 317
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  287 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.131363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.112613 restraints weight = 37284.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.50
r_work: 0.3360 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8959  Z= 0.146
  Angle     :  0.496   4.584  12135  Z= 0.269
  Chirality :  0.040   0.135   1377
  Planarity :  0.004   0.067   1523
  Dihedral  :  4.244  20.368   1207
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 14.98 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.26), residues: 1097
  helix:  1.94 (0.27), residues: 388
  sheet:  0.07 (0.29), residues: 290
  loop : -0.38 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G  27 
 TYR   0.011   0.001   TYR E 190 
 PHE   0.009   0.001   PHE B 151 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.003   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8959)
  covalent geometry    : angle       0.49580 (12135)
  hydrogen bonds       : bond        0.03863 (  426)
  hydrogen bonds       : angle       4.58770 ( 1194)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  338 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 318
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7869 (ttm-80)
REVERT: A   25 GLU cc_start: 0.7848 (tt0) cc_final: 0.7624 (tt0)
REVERT: A  204 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8125 (mm-40)
REVERT: A  252 SER cc_start: 0.8651 (t) cc_final: 0.8296 (p)
REVERT: A  254 CYS cc_start: 0.8344 (p) cc_final: 0.7871 (p)
REVERT: A  275 GLU cc_start: 0.8008 (tp30) cc_final: 0.7603 (tp30)
REVERT: A  297 GLU cc_start: 0.8217 (mp0) cc_final: 0.7736 (mp0)
REVERT: A  332 VAL cc_start: 0.8364 (t) cc_final: 0.8109 (m)
REVERT: B   13 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8283 (tm-30)
REVERT: B   76 ASP cc_start: 0.7773 (m-30) cc_final: 0.7334 (m-30)
REVERT: B  110 ASN cc_start: 0.8547 (m-40) cc_final: 0.8309 (m110)
REVERT: B  172 GLU cc_start: 0.8515 (tp30) cc_final: 0.8277 (tp30)
REVERT: B  189 SER cc_start: 0.8883 (p) cc_final: 0.8609 (t)
REVERT: B  219 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.8231 (ttm170)
REVERT: B  227 SER cc_start: 0.8883 (t) cc_final: 0.8388 (m)
REVERT: B  234 PHE cc_start: 0.8582 (m-80) cc_final: 0.8263 (m-80)
REVERT: B  301 LYS cc_start: 0.8652 (mmtt) cc_final: 0.8450 (mmtt)
REVERT: B  321 THR cc_start: 0.7442 (p) cc_final: 0.7145 (p)
REVERT: B  323 ASP cc_start: 0.7724 (p0) cc_final: 0.7459 (p0)
REVERT: E   18 ARG cc_start: 0.7095 (tpp80) cc_final: 0.6634 (tpt170)
REVERT: E  158 SER cc_start: 0.8734 (t) cc_final: 0.8394 (p)
REVERT: E  186 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8035 (pt0)
REVERT: E  192 MET cc_start: 0.7980 (ttt) cc_final: 0.7779 (ttt)
REVERT: E  220 GLU cc_start: 0.7350 (pt0) cc_final: 0.6865 (pt0)
REVERT: E  234 GLU cc_start: 0.8021 (pt0) cc_final: 0.7710 (pp20)
REVERT: G   14 LYS cc_start: 0.8259 (pttm) cc_final: 0.8022 (pttm)
REVERT: G   58 GLU cc_start: 0.8030 (mp0) cc_final: 0.7623 (mp0)
REVERT: R  139 LEU cc_start: 0.7185 (tp) cc_final: 0.6934 (tp)
REVERT: R  185 PHE cc_start: 0.8452 (t80) cc_final: 0.8119 (t80)
REVERT: R  205 LEU cc_start: 0.7875 (tp) cc_final: 0.7647 (tt)
REVERT: R  207 MET cc_start: 0.8209 (mtp) cc_final: 0.7995 (ttm)
REVERT: R  301 TYR cc_start: 0.8107 (m-10) cc_final: 0.7614 (m-10)
REVERT: R  306 LEU cc_start: 0.7937 (tp) cc_final: 0.7484 (tp)
  outliers start: 20
  outliers final: 18
  residues processed: 326
  average time/residue: 0.2579
  time to fit residues: 109.0112
Evaluate side-chains
  333 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 314
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   25 LEU
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  197 VAL
Chi-restraints excluded: chain R residue  287 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 24 optimal weight:    0.4980
   chunk 5 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 69 optimal weight:    0.3980
   chunk 6 optimal weight:    0.6980
   overall best weight:    1.0982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.132122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.113337 restraints weight = 37577.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.48
r_work: 0.3363 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8959  Z= 0.154
  Angle     :  0.493   4.897  12135  Z= 0.268
  Chirality :  0.040   0.134   1377
  Planarity :  0.004   0.070   1523
  Dihedral  :  4.191  20.126   1207
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.30 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.26), residues: 1097
  helix:  2.05 (0.27), residues: 387
  sheet:  0.01 (0.29), residues: 290
  loop : -0.34 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G  27 
 TYR   0.011   0.001   TYR E 190 
 PHE   0.010   0.001   PHE A 199 
 TRP   0.012   0.001   TRP R  85 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8959)
  covalent geometry    : angle       0.49333 (12135)
  hydrogen bonds       : bond        0.03812 (  426)
  hydrogen bonds       : angle       4.54171 ( 1194)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  341 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 321
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7893 (ttm-80)
REVERT: A   25 GLU cc_start: 0.7861 (tt0) cc_final: 0.7611 (tt0)
REVERT: A   28 GLU cc_start: 0.8085 (tt0) cc_final: 0.7884 (tt0)
REVERT: A  204 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8091 (mm-40)
REVERT: A  252 SER cc_start: 0.8644 (t) cc_final: 0.8289 (p)
REVERT: A  275 GLU cc_start: 0.8014 (tp30) cc_final: 0.7588 (tp30)
REVERT: A  297 GLU cc_start: 0.8205 (mp0) cc_final: 0.7740 (mp0)
REVERT: A  332 VAL cc_start: 0.8362 (t) cc_final: 0.8111 (m)
REVERT: B   13 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8278 (tm-30)
REVERT: B   51 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8182 (mp)
REVERT: B   76 ASP cc_start: 0.7765 (m-30) cc_final: 0.7331 (m-30)
REVERT: B  110 ASN cc_start: 0.8539 (m-40) cc_final: 0.8310 (m110)
REVERT: B  172 GLU cc_start: 0.8487 (tp30) cc_final: 0.8254 (tp30)
REVERT: B  189 SER cc_start: 0.8915 (p) cc_final: 0.8616 (t)
REVERT: B  205 ASP cc_start: 0.8074 (p0) cc_final: 0.7837 (p0)
REVERT: B  212 ASP cc_start: 0.8345 (t0) cc_final: 0.7667 (p0)
REVERT: B  219 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.8062 (ttm170)
REVERT: B  234 PHE cc_start: 0.8596 (m-80) cc_final: 0.8145 (m-80)
REVERT: B  301 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8459 (mmtt)
REVERT: B  321 THR cc_start: 0.7460 (p) cc_final: 0.7161 (p)
REVERT: B  323 ASP cc_start: 0.7706 (p0) cc_final: 0.7449 (p0)
REVERT: E   18 ARG cc_start: 0.7062 (tpp80) cc_final: 0.6631 (tpt170)
REVERT: E  186 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8034 (pt0)
REVERT: E  220 GLU cc_start: 0.7352 (pt0) cc_final: 0.6884 (pt0)
REVERT: E  234 GLU cc_start: 0.7998 (pt0) cc_final: 0.7691 (pp20)
REVERT: G   14 LYS cc_start: 0.8269 (pttm) cc_final: 0.8036 (pttm)
REVERT: G   58 GLU cc_start: 0.8021 (mp0) cc_final: 0.7648 (mp0)
REVERT: R  139 LEU cc_start: 0.7249 (tp) cc_final: 0.6992 (tp)
REVERT: R  185 PHE cc_start: 0.8435 (t80) cc_final: 0.8105 (t80)
REVERT: R  205 LEU cc_start: 0.7883 (tp) cc_final: 0.7654 (tt)
REVERT: R  207 MET cc_start: 0.8232 (mtp) cc_final: 0.8026 (ttm)
REVERT: R  301 TYR cc_start: 0.8137 (m-10) cc_final: 0.7641 (m-10)
REVERT: R  306 LEU cc_start: 0.7942 (tp) cc_final: 0.7505 (tp)
  outliers start: 20
  outliers final: 18
  residues processed: 331
  average time/residue: 0.2611
  time to fit residues: 111.9372
Evaluate side-chains
  335 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 315
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  197 VAL
Chi-restraints excluded: chain R residue  287 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 24 optimal weight:    0.3980
   chunk 78 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 95 optimal weight:    1.9990
   chunk 106 optimal weight:    0.3980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.133106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.114389 restraints weight = 37363.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.48
r_work: 0.3382 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8959  Z= 0.111
  Angle     :  0.475   4.689  12135  Z= 0.256
  Chirality :  0.039   0.146   1377
  Planarity :  0.004   0.076   1523
  Dihedral  :  4.071  19.616   1207
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 16.02 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.26), residues: 1097
  helix:  2.17 (0.27), residues: 387
  sheet: -0.03 (0.29), residues: 291
  loop : -0.24 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG G  27 
 TYR   0.009   0.001   TYR A 302 
 PHE   0.016   0.001   PHE E  32 
 TRP   0.012   0.001   TRP R  85 
 HIS   0.004   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8959)
  covalent geometry    : angle       0.47523 (12135)
  hydrogen bonds       : bond        0.03488 (  426)
  hydrogen bonds       : angle       4.44062 ( 1194)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  342 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 325
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7885 (ttm-80)
REVERT: A  204 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8103 (mm-40)
REVERT: A  252 SER cc_start: 0.8673 (t) cc_final: 0.8284 (p)
REVERT: A  254 CYS cc_start: 0.8336 (p) cc_final: 0.7934 (p)
REVERT: A  275 GLU cc_start: 0.8063 (tp30) cc_final: 0.7584 (tp30)
REVERT: A  297 GLU cc_start: 0.8185 (mp0) cc_final: 0.7730 (mp0)
REVERT: A  332 VAL cc_start: 0.8336 (t) cc_final: 0.8093 (m)
REVERT: B   13 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8309 (tm-30)
REVERT: B   76 ASP cc_start: 0.7753 (m-30) cc_final: 0.7304 (m-30)
REVERT: B   96 ARG cc_start: 0.8270 (ttm-80) cc_final: 0.8059 (ttm170)
REVERT: B  110 ASN cc_start: 0.8509 (m-40) cc_final: 0.8281 (m110)
REVERT: B  172 GLU cc_start: 0.8468 (tp30) cc_final: 0.8260 (tp30)
REVERT: B  189 SER cc_start: 0.8881 (p) cc_final: 0.8608 (t)
REVERT: B  205 ASP cc_start: 0.8052 (p0) cc_final: 0.7819 (p0)
REVERT: B  219 ARG cc_start: 0.8470 (ttm-80) cc_final: 0.8204 (ttm170)
REVERT: B  234 PHE cc_start: 0.8605 (m-80) cc_final: 0.8088 (m-80)
REVERT: B  321 THR cc_start: 0.7426 (p) cc_final: 0.7116 (p)
REVERT: B  323 ASP cc_start: 0.7611 (p0) cc_final: 0.7294 (p0)
REVERT: E   18 ARG cc_start: 0.6992 (tpp80) cc_final: 0.6572 (tpt170)
REVERT: E  140 MET cc_start: 0.7470 (mtp) cc_final: 0.7218 (mtp)
REVERT: E  186 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7955 (pt0)
REVERT: E  220 GLU cc_start: 0.7358 (pt0) cc_final: 0.6894 (pt0)
REVERT: E  234 GLU cc_start: 0.8000 (pt0) cc_final: 0.7663 (pp20)
REVERT: G   14 LYS cc_start: 0.8248 (pttm) cc_final: 0.8032 (pttm)
REVERT: G   58 GLU cc_start: 0.8024 (mp0) cc_final: 0.7671 (mp0)
REVERT: R   72 VAL cc_start: 0.8265 (t) cc_final: 0.7780 (t)
REVERT: R  139 LEU cc_start: 0.7225 (tp) cc_final: 0.6969 (tp)
REVERT: R  185 PHE cc_start: 0.8428 (t80) cc_final: 0.8092 (t80)
REVERT: R  205 LEU cc_start: 0.7849 (tp) cc_final: 0.7621 (tt)
REVERT: R  301 TYR cc_start: 0.8025 (m-10) cc_final: 0.7515 (m-10)
REVERT: R  306 LEU cc_start: 0.8014 (tp) cc_final: 0.7512 (tp)
REVERT: R  310 LEU cc_start: 0.8186 (mm) cc_final: 0.7930 (mm)
  outliers start: 17
  outliers final: 15
  residues processed: 330
  average time/residue: 0.2557
  time to fit residues: 109.8719
Evaluate side-chains
  328 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 312
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  287 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 14 optimal weight:    0.3980
   chunk 49 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0070
   chunk 84 optimal weight:    8.9990
   chunk 48 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.2802

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.132272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.113536 restraints weight = 37588.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.49
r_work: 0.3365 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.3256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8959  Z= 0.171
  Angle     :  0.500   4.994  12135  Z= 0.273
  Chirality :  0.040   0.148   1377
  Planarity :  0.004   0.076   1523
  Dihedral  :  4.144  19.651   1207
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.13 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.26), residues: 1097
  helix:  2.14 (0.27), residues: 387
  sheet: -0.11 (0.29), residues: 291
  loop : -0.30 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG G  27 
 TYR   0.010   0.001   TYR E  95 
 PHE   0.022   0.001   PHE E  32 
 TRP   0.017   0.001   TRP R  85 
 HIS   0.005   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 8959)
  covalent geometry    : angle       0.50041 (12135)
  hydrogen bonds       : bond        0.03766 (  426)
  hydrogen bonds       : angle       4.49657 ( 1194)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  345 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 326
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7896 (ttm-80)
REVERT: A   25 GLU cc_start: 0.7863 (tt0) cc_final: 0.7627 (tt0)
REVERT: A  204 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8130 (mm-40)
REVERT: A  252 SER cc_start: 0.8643 (t) cc_final: 0.8305 (p)
REVERT: A  275 GLU cc_start: 0.8053 (tp30) cc_final: 0.7575 (tp30)
REVERT: A  321 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8772 (p)
REVERT: A  332 VAL cc_start: 0.8355 (t) cc_final: 0.8118 (m)
REVERT: B   13 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8365 (tm-30)
REVERT: B   51 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8185 (mp)
REVERT: B   76 ASP cc_start: 0.7796 (m-30) cc_final: 0.7365 (m-30)
REVERT: B   96 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.8046 (ttm170)
REVERT: B  110 ASN cc_start: 0.8543 (m-40) cc_final: 0.8322 (m110)
REVERT: B  172 GLU cc_start: 0.8478 (tp30) cc_final: 0.8264 (tp30)
REVERT: B  189 SER cc_start: 0.8882 (p) cc_final: 0.8601 (t)
REVERT: B  205 ASP cc_start: 0.8091 (p0) cc_final: 0.7862 (p0)
REVERT: B  219 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8211 (ttm170)
REVERT: B  234 PHE cc_start: 0.8607 (m-80) cc_final: 0.8154 (m-80)
REVERT: B  256 ARG cc_start: 0.8697 (mtp85) cc_final: 0.8286 (mtm180)
REVERT: B  321 THR cc_start: 0.7446 (p) cc_final: 0.7123 (p)
REVERT: B  323 ASP cc_start: 0.7626 (p0) cc_final: 0.7305 (p0)
REVERT: E   18 ARG cc_start: 0.7018 (tpp80) cc_final: 0.6557 (tpt170)
REVERT: E  186 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7946 (pt0)
REVERT: E  220 GLU cc_start: 0.7359 (pt0) cc_final: 0.6907 (pt0)
REVERT: E  234 GLU cc_start: 0.8016 (pt0) cc_final: 0.7685 (pp20)
REVERT: G   58 GLU cc_start: 0.8023 (mp0) cc_final: 0.7661 (mp0)
REVERT: R   72 VAL cc_start: 0.8278 (t) cc_final: 0.7905 (t)
REVERT: R   79 GLU cc_start: 0.7849 (tp30) cc_final: 0.7524 (tp30)
REVERT: R  139 LEU cc_start: 0.7231 (tp) cc_final: 0.6977 (tp)
REVERT: R  185 PHE cc_start: 0.8420 (t80) cc_final: 0.8093 (t80)
REVERT: R  205 LEU cc_start: 0.7880 (tp) cc_final: 0.7646 (tt)
REVERT: R  301 TYR cc_start: 0.8115 (m-10) cc_final: 0.7678 (m-10)
REVERT: R  306 LEU cc_start: 0.8006 (tp) cc_final: 0.7560 (tp)
  outliers start: 19
  outliers final: 16
  residues processed: 333
  average time/residue: 0.2615
  time to fit residues: 113.2825
Evaluate side-chains
  343 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 324
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  287 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0370
   chunk 35 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 107 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 105 optimal weight:    0.0000
   chunk 93 optimal weight:    9.9990
   overall best weight:    0.6864

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.133354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.114677 restraints weight = 37199.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.48
r_work: 0.3383 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.3290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8959  Z= 0.115
  Angle     :  0.487   4.878  12135  Z= 0.262
  Chirality :  0.040   0.148   1377
  Planarity :  0.004   0.077   1523
  Dihedral  :  4.075  19.248   1207
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 16.65 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.27), residues: 1097
  helix:  2.22 (0.28), residues: 387
  sheet: -0.13 (0.29), residues: 291
  loop : -0.18 (0.33), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG G  27 
 TYR   0.010   0.001   TYR A 302 
 PHE   0.025   0.001   PHE E  32 
 TRP   0.016   0.001   TRP R  85 
 HIS   0.004   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8959)
  covalent geometry    : angle       0.48748 (12135)
  hydrogen bonds       : bond        0.03419 (  426)
  hydrogen bonds       : angle       4.39002 ( 1194)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ALA   11 is missing expected H atoms. Skipping.
Evaluate side-chains
  345 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 328
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8107 (ttm-80) cc_final: 0.7871 (ttm-80)
REVERT: A   25 GLU cc_start: 0.7841 (tt0) cc_final: 0.7626 (tt0)
REVERT: A  197 LYS cc_start: 0.8404 (ptpp) cc_final: 0.8180 (ptpp)
REVERT: A  204 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8112 (mm-40)
REVERT: A  252 SER cc_start: 0.8662 (t) cc_final: 0.8294 (p)
REVERT: A  254 CYS cc_start: 0.8313 (p) cc_final: 0.7950 (p)
REVERT: A  275 GLU cc_start: 0.8050 (tp30) cc_final: 0.7568 (tp30)
REVERT: A  321 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8758 (p)
REVERT: A  332 VAL cc_start: 0.8382 (t) cc_final: 0.8117 (m)
REVERT: B   13 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8328 (tm-30)
REVERT: B   76 ASP cc_start: 0.7754 (m-30) cc_final: 0.7316 (m-30)
REVERT: B   96 ARG cc_start: 0.8265 (ttm-80) cc_final: 0.8050 (ttm170)
REVERT: B  110 ASN cc_start: 0.8529 (m-40) cc_final: 0.8305 (m110)
REVERT: B  189 SER cc_start: 0.8860 (p) cc_final: 0.8581 (t)
REVERT: B  205 ASP cc_start: 0.8078 (p0) cc_final: 0.7837 (p0)
REVERT: B  219 ARG cc_start: 0.8475 (ttm-80) cc_final: 0.8218 (ttm170)
REVERT: B  234 PHE cc_start: 0.8606 (m-80) cc_final: 0.8124 (m-80)
REVERT: B  321 THR cc_start: 0.7395 (p) cc_final: 0.7145 (p)
REVERT: B  323 ASP cc_start: 0.7595 (p0) cc_final: 0.7382 (p0)
REVERT: E   18 ARG cc_start: 0.6975 (tpp80) cc_final: 0.6558 (tpt170)
REVERT: E  186 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7893 (pt0)
REVERT: E  220 GLU cc_start: 0.7347 (pt0) cc_final: 0.6964 (pt0)
REVERT: E  234 GLU cc_start: 0.8048 (pt0) cc_final: 0.7716 (pp20)
REVERT: G   58 GLU cc_start: 0.8010 (mp0) cc_final: 0.7650 (mp0)
REVERT: R   79 GLU cc_start: 0.7847 (tp30) cc_final: 0.7523 (tp30)
REVERT: R  139 LEU cc_start: 0.7234 (tp) cc_final: 0.6864 (tp)
REVERT: R  140 MET cc_start: 0.7736 (mmp) cc_final: 0.7327 (mmp)
REVERT: R  163 ILE cc_start: 0.8118 (pt) cc_final: 0.7845 (mm)
REVERT: R  185 PHE cc_start: 0.8426 (t80) cc_final: 0.8095 (t80)
REVERT: R  205 LEU cc_start: 0.7855 (tp) cc_final: 0.7621 (tt)
REVERT: R  301 TYR cc_start: 0.8030 (m-10) cc_final: 0.7568 (m-10)
REVERT: R  306 LEU cc_start: 0.8017 (tp) cc_final: 0.7558 (tp)
  outliers start: 17
  outliers final: 15
  residues processed: 334
  average time/residue: 0.2687
  time to fit residues: 115.5793
Evaluate side-chains
  341 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 324
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain E residue  159 CYS
Chi-restraints excluded: chain E residue  183 GLN
Chi-restraints excluded: chain E residue  186 GLN
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  154 LEU
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  287 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 109 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B 119 ASN
B 239 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.133228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.114506 restraints weight = 37677.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 2.51
r_work: 0.3377 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8959  Z= 0.124
  Angle     :  0.489   4.940  12135  Z= 0.263
  Chirality :  0.040   0.145   1377
  Planarity :  0.004   0.078   1523
  Dihedral  :  4.028  18.922   1207
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 17.27 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.03 (0.27), residues: 1097
  helix:  2.30 (0.28), residues: 387
  sheet: -0.11 (0.29), residues: 291
  loop : -0.18 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG G  27 
 TYR   0.010   0.001   TYR E 190 
 PHE   0.013   0.001   PHE E  32 
 TRP   0.014   0.001   TRP R  85 
 HIS   0.004   0.001   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8959)
  covalent geometry    : angle       0.48870 (12135)
  hydrogen bonds       : bond        0.03451 (  426)
  hydrogen bonds       : angle       4.37388 ( 1194)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5122.39 seconds
wall clock time: 87 minutes 21.81 seconds (5241.81 seconds total)