Starting phenix.real_space_refine
on Wed Feb  4 01:18:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kzk_62665/02_2026/9kzk_62665.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kzk_62665/02_2026/9kzk_62665.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kzk_62665/02_2026/9kzk_62665.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kzk_62665/02_2026/9kzk_62665.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kzk_62665/02_2026/9kzk_62665.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kzk_62665/02_2026/9kzk_62665.map"
  }
  resolution = 3.54
  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=   0.001 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      51      5.16       5
     C    5148      2.51       5
     N    1390      2.21       5
     O    1483      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8072
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1543
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PTRANS': 4, 'TRANS': 203}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 130
          Unresolved non-hydrogen dihedrals: 86
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 6, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 61
    Chain: "B"
      Number of atoms: 2382
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2382
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 66}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 219
          Unresolved non-hydrogen angles: 272
          Unresolved non-hydrogen dihedrals: 166
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 12, 'GLN:plan1': 4, 'ARG:plan': 8, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 126
    Chain: "D"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 97
          Classifications: {'peptide': 12}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 11}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "E"
      Number of atoms: 2062
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2062
          Classifications: {'peptide': 279}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 12, 'TRANS': 266}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 157
          Unresolved non-hydrogen angles: 190
          Unresolved non-hydrogen dihedrals: 130
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 7, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 66
    Chain: "G"
      Number of atoms: 360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 360
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 81
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "H"
      Number of atoms: 1628
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1628
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 127
          Unresolved non-hydrogen angles: 154
          Unresolved non-hydrogen dihedrals: 100
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 67
  Time building chain proxies: 1.42, per 1000 atoms: 0.18
  Number of scatterers: 8072
  At special positions: 0
  Unit cell: (87.9784, 121.617, 124.205, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      51     16.00
     O    1483      8.00
     N    1390      7.00
     C    5148      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  95 " - pdb=" SG  CYS E 172 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 227.1 milliseconds
  

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2094

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 14 sheets defined
      38.9% alpha, 21.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 31
      removed outlier: 3.597A  pdb=" N   ASN A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.911A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
      removed outlier: 4.468A  pdb=" N   ILE A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 5.655A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 256
    Processing helix  chain 'A' and resid 271 through 282
    Processing helix  chain 'A' and resid 283 through 287
      removed outlier: 3.656A  pdb=" N   CYS A 287 " --> pdb=" O   LEU A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 4.081A  pdb=" N   ALA A 302 " --> pdb=" O   GLU A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 25
    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 'D' and resid 68 through 73
    Processing helix  chain 'E' and resid 20 through 51
    Processing helix  chain 'E' and resid 57 through 85
      removed outlier: 4.295A  pdb=" N   PHE E  61 " --> pdb=" O   ASN E  57 " (cutoff:3.500A)
      Proline residue:  E  76  - end of helix
    Processing helix  chain 'E' and resid 91 through 126
      Proline residue:  E  99  - end of helix
      removed outlier: 3.701A  pdb=" N   VAL E 124 " --> pdb=" O   ARG E 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 126 through 134
      removed outlier: 3.777A  pdb=" N   ASN E 132 " --> pdb=" O   ILE E 128 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 135 through 161
      Proline residue:  E 156  - end of helix
    Processing helix  chain 'E' and resid 323 through 357
      removed outlier: 4.650A  pdb=" N   VAL E 340 " --> pdb=" O   VAL E 336 " (cutoff:3.500A)
      Proline residue:  E 341  - end of helix
      removed outlier: 3.534A  pdb=" N   ARG E 357 " --> pdb=" O   VAL E 353 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 366 through 396
      removed outlier: 3.561A  pdb=" N   ARG E 370 " --> pdb=" O   ASN E 366 " (cutoff:3.500A)
      Proline residue:  E 385  - end of helix
    Processing helix  chain 'E' and resid 400 through 428
      removed outlier: 4.348A  pdb=" N   HIS E 411 " --> pdb=" O   MET E 407 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   MET E 412 " --> pdb=" O   SER E 408 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   SER E 421 " --> pdb=" O   ALA E 417 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   CYS E 422 " --> pdb=" O   SER E 418 " (cutoff:3.500A)
      Proline residue:  E 425  - end of helix
    Processing helix  chain 'E' and resid 432 through 443
    Processing helix  chain 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.704A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 53 through 56
      removed outlier: 3.909A  pdb=" N   GLY H  56 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 53 through 56'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.790A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 220 through 224
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192
      removed outlier: 9.239A  pdb=" N   ALA A 221 " --> pdb=" O   ASP A  33 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.753A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.959A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 8.270A  pdb=" N   ASP A 227 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.691A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.576A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   CYS B 121 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.579A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.636A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 284 through 287
      removed outlier: 6.959A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 162 through 164
    Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.551A  pdb=" N   LEU H  20 " --> pdb=" O   LEU H  81 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.686A  pdb=" N   VAL H  97 " --> pdb=" O   HIS H  35 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TYR H  50 " --> pdb=" O   TYR H  59 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.542A  pdb=" N   ARG H  98 " --> pdb=" O   PHE H 110 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141
      removed outlier: 3.821A  pdb=" N   ALA H 211 " --> pdb=" O   SER H 208 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148
      removed outlier: 5.917A  pdb=" N   LEU H 178 " --> pdb=" O   LEU H 187 " (cutoff:3.500A)
      removed outlier: 5.291A  pdb=" N   LEU H 187 " --> pdb=" O   LEU H 178 " (cutoff:3.500A)

    443 hydrogen bonds defined for protein.
    1236 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.04

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2631
        1.35 -     1.47: 2130
        1.47 -     1.59: 3423
        1.59 -     1.71: 0
        1.71 -     1.83: 66
  Bond restraints: 8250
  Sorted by residual:
  bond pdb=" N   TYR E 174 "
       pdb=" CA  TYR E 174 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.02e+00
  bond pdb=" C   ARG E 173 "
       pdb=" N   TYR E 174 "
    ideal  model  delta    sigma   weight residual
    1.329  1.352 -0.023 1.40e-02 5.10e+03 2.77e+00
  bond pdb=" CA  VAL E 155 "
       pdb=" C   VAL E 155 "
    ideal  model  delta    sigma   weight residual
    1.520  1.532 -0.012 8.80e-03 1.29e+04 1.97e+00
  bond pdb=" CA  CYS E 172 "
       pdb=" CB  CYS E 172 "
    ideal  model  delta    sigma   weight residual
    1.528  1.544 -0.017 1.39e-02 5.18e+03 1.45e+00
  bond pdb=" CA  VAL E  28 "
       pdb=" CB  VAL E  28 "
    ideal  model  delta    sigma   weight residual
    1.540  1.528  0.011 1.29e-02 6.01e+03 7.69e-01
  ... (remaining 8245 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 11047
        1.34 -     2.69: 175
        2.69 -     4.03: 32
        4.03 -     5.37: 12
        5.37 -     6.71: 2
  Bond angle restraints: 11268
  Sorted by residual:
  angle pdb=" CA  ARG E 173 "
        pdb=" C   ARG E 173 "
        pdb=" N   TYR E 174 "
      ideal   model   delta    sigma   weight residual
     116.18  111.28    4.90 1.15e+00 7.56e-01 1.81e+01
  angle pdb=" C   VAL E 155 "
        pdb=" CA  VAL E 155 "
        pdb=" CB  VAL E 155 "
      ideal   model   delta    sigma   weight residual
     114.35  109.93    4.42 1.06e+00 8.90e-01 1.74e+01
  angle pdb=" C   TYR E 174 "
        pdb=" CA  TYR E 174 "
        pdb=" CB  TYR E 174 "
      ideal   model   delta    sigma   weight residual
     110.10  105.00    5.10 1.90e+00 2.77e-01 7.21e+00
  angle pdb=" O   ARG E 173 "
        pdb=" C   ARG E 173 "
        pdb=" N   TYR E 174 "
      ideal   model   delta    sigma   weight residual
     121.70  126.42   -4.72 1.84e+00 2.95e-01 6.58e+00
  angle pdb=" C   GLY E 337 "
        pdb=" N   PHE E 338 "
        pdb=" CA  PHE E 338 "
      ideal   model   delta    sigma   weight residual
     122.15  115.44    6.71 2.83e+00 1.25e-01 5.63e+00
  ... (remaining 11263 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 4445
       17.93 -    35.87: 283
       35.87 -    53.80: 36
       53.80 -    71.74: 4
       71.74 -    89.67: 6
  Dihedral angle restraints: 4774
    sinusoidal: 1535
      harmonic: 3239
  Sorted by residual:
  dihedral pdb=" CB  GLU G  42 "
           pdb=" CG  GLU G  42 "
           pdb=" CD  GLU G  42 "
           pdb=" OE1 GLU G  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.67   89.67     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU H 246 "
           pdb=" CG  GLU H 246 "
           pdb=" CD  GLU H 246 "
           pdb=" OE1 GLU H 246 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.18   87.18     1      3.00e+01 1.11e-03 1.01e+01
  dihedral pdb=" CG  ARG D  78 "
           pdb=" CD  ARG D  78 "
           pdb=" NE  ARG D  78 "
           pdb=" CZ  ARG D  78 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -133.29   43.29     2      1.50e+01 4.44e-03 1.00e+01
  ... (remaining 4771 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 998
       0.042 -    0.084: 246
       0.084 -    0.125: 81
       0.125 -    0.167: 2
       0.167 -    0.209: 1
  Chirality restraints: 1328
  Sorted by residual:
  chirality pdb=" CA  TYR E 174 "
            pdb=" N   TYR E 174 "
            pdb=" C   TYR E 174 "
            pdb=" CB  TYR E 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CA  ILE B 232 "
            pdb=" N   ILE B 232 "
            pdb=" C   ILE B 232 "
            pdb=" CB  ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.35e-01
  chirality pdb=" CA  THR E 324 "
            pdb=" N   THR E 324 "
            pdb=" C   THR E 324 "
            pdb=" CB  THR E 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.17e-01
  ... (remaining 1325 not shown)

  Planarity restraints: 1438
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "   -0.031 5.00e-02 4.00e+02   4.69e-02 3.52e+00
        pdb=" N   PRO G  49 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E 335 "    0.007 2.00e-02 2.50e+03   1.49e-02 2.21e+00
        pdb=" C   VAL E 335 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   VAL E 335 "    0.010 2.00e-02 2.50e+03
        pdb=" N   VAL E 336 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 173 "   -0.006 2.00e-02 2.50e+03   1.25e-02 1.56e+00
        pdb=" C   ARG E 173 "    0.022 2.00e-02 2.50e+03
        pdb=" O   ARG E 173 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   TYR E 174 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1435 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2522
        2.82 -     3.34: 7538
        3.34 -     3.86: 12944
        3.86 -     4.38: 14075
        4.38 -     4.90: 25592
  Nonbonded interactions: 62671
  Sorted by model distance:
  nonbonded pdb=" O   ILE H 100 "
            pdb=" OG  SER H 105 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" NH2 ARG D  78 "
            pdb=" OD2 ASP E 410 "
     model   vdw
     2.317 3.120
  nonbonded pdb=" OH  TYR A 320 "
            pdb=" OD2 ASP A 341 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" NH1 ARG B  49 "
            pdb=" O   PHE G  61 "
     model   vdw
     2.328 3.120
  ... (remaining 62666 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.380
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
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      :  0.002   0.033   8253  Z= 0.113
  Angle     :  0.469   6.713  11274  Z= 0.260
  Chirality :  0.040   0.209   1328
  Planarity :  0.003   0.047   1438
  Dihedral  : 12.267  89.672   2671
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.63 (0.27), residues: 1100
  helix:  2.31 (0.27), residues: 394
  sheet: -0.50 (0.32), residues: 282
  loop : -0.71 (0.32), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 134 
 TYR   0.008   0.001   TYR H 102 
 PHE   0.011   0.001   PHE E 140 
 TRP   0.010   0.001   TRP E 129 
 HIS   0.003   0.001   HIS E 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 8250)
  covalent geometry    : angle       0.46810 (11268)
  SS BOND              : bond        0.00191 (    3)
  SS BOND              : angle       1.05784 (    6)
  hydrogen bonds       : bond        0.18864 (  438)
  hydrogen bonds       : angle       7.31948 ( 1236)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 276
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.7714 (ttt90) cc_final: 0.7513 (ttt-90)
REVERT: A   19 ILE cc_start: 0.6895 (pt) cc_final: 0.6409 (tt)
REVERT: A   21 LYS cc_start: 0.7889 (ttmm) cc_final: 0.7637 (ttmm)
REVERT: A   38 LEU cc_start: 0.7795 (mt) cc_final: 0.7582 (mp)
REVERT: A  207 SER cc_start: 0.8020 (m) cc_final: 0.7814 (p)
REVERT: A  217 GLU cc_start: 0.7396 (tt0) cc_final: 0.7171 (tt0)
REVERT: A  247 SER cc_start: 0.8304 (m) cc_final: 0.7618 (p)
REVERT: A  256 ASN cc_start: 0.7452 (t0) cc_final: 0.6906 (t0)
REVERT: A  258 LYS cc_start: 0.8282 (tttm) cc_final: 0.7943 (tttm)
REVERT: A  263 THR cc_start: 0.8733 (p) cc_final: 0.8524 (p)
REVERT: A  311 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8048 (mmmm)
REVERT: A  330 ASN cc_start: 0.7450 (t0) cc_final: 0.6998 (t0)
REVERT: A  349 ARG cc_start: 0.8378 (ttm110) cc_final: 0.8175 (ttm110)
REVERT: B   97 SER cc_start: 0.8777 (t) cc_final: 0.8483 (p)
REVERT: B  112 VAL cc_start: 0.8187 (t) cc_final: 0.7809 (m)
REVERT: B  117 LEU cc_start: 0.8340 (mt) cc_final: 0.8092 (mm)
REVERT: B  168 LEU cc_start: 0.7637 (tp) cc_final: 0.7426 (tt)
REVERT: B  220 GLN cc_start: 0.7606 (mt0) cc_final: 0.7177 (mp-120)
REVERT: B  259 GLN cc_start: 0.8213 (pt0) cc_final: 0.7911 (pt0)
REVERT: B  270 ILE cc_start: 0.8664 (pt) cc_final: 0.8235 (mm)
REVERT: B  325 MET cc_start: 0.7613 (tpp) cc_final: 0.7411 (tpp)
REVERT: B  327 VAL cc_start: 0.8109 (t) cc_final: 0.7789 (p)
REVERT: E   30 LEU cc_start: 0.7926 (mt) cc_final: 0.7692 (mt)
REVERT: E   66 LEU cc_start: 0.8172 (tp) cc_final: 0.7538 (tp)
REVERT: E   69 PHE cc_start: 0.8065 (t80) cc_final: 0.7569 (t80)
REVERT: E  110 VAL cc_start: 0.8094 (t) cc_final: 0.7875 (m)
REVERT: E  134 ARG cc_start: 0.8231 (ttt-90) cc_final: 0.7821 (ttt-90)
REVERT: E  143 CYS cc_start: 0.7622 (m) cc_final: 0.7066 (p)
REVERT: E  377 THR cc_start: 0.7369 (m) cc_final: 0.7163 (t)
REVERT: E  407 MET cc_start: 0.7331 (mmt) cc_final: 0.6856 (mmt)
REVERT: E  414 ILE cc_start: 0.8149 (mm) cc_final: 0.7799 (mm)
REVERT: E  422 CYS cc_start: 0.7769 (t) cc_final: 0.7515 (p)
REVERT: E  428 TYR cc_start: 0.7922 (m-80) cc_final: 0.7698 (m-10)
REVERT: H    4 LEU cc_start: 0.7737 (mt) cc_final: 0.7279 (mm)
REVERT: H   30 SER cc_start: 0.8240 (m) cc_final: 0.7899 (p)
REVERT: H   94 TYR cc_start: 0.7364 (m-80) cc_final: 0.7118 (m-80)
REVERT: H  106 SER cc_start: 0.8308 (t) cc_final: 0.7429 (p)
REVERT: H  109 ASP cc_start: 0.6280 (p0) cc_final: 0.6043 (p0)
REVERT: H  140 MET cc_start: 0.6294 (mmt) cc_final: 0.5973 (mmt)
REVERT: H  191 ARG cc_start: 0.8482 (mtm-85) cc_final: 0.7687 (mtt-85)
REVERT: H  195 LEU cc_start: 0.8277 (tt) cc_final: 0.7937 (tt)
REVERT: H  219 LEU cc_start: 0.8407 (tp) cc_final: 0.8095 (tp)
REVERT: H  226 VAL cc_start: 0.7362 (p) cc_final: 0.7114 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 276
  average time/residue: 0.0749
  time to fit residues: 28.2551
Evaluate side-chains
  242 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    7.9990
   chunk 106 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 333 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 105 ASN
** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.125878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.107650 restraints weight = 14192.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.111249 restraints weight = 7031.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.113597 restraints weight = 4157.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.115011 restraints weight = 2786.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.116139 restraints weight = 2092.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8253  Z= 0.254
  Angle     :  0.624   7.381  11274  Z= 0.336
  Chirality :  0.046   0.152   1328
  Planarity :  0.004   0.041   1438
  Dihedral  :  4.292  28.000   1184
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 13.39 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.18 (0.26), residues: 1100
  helix:  1.91 (0.26), residues: 397
  sheet: -0.65 (0.30), residues: 294
  loop : -1.02 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 191 
 TYR   0.017   0.003   TYR H  59 
 PHE   0.019   0.002   PHE B 235 
 TRP   0.018   0.003   TRP E  88 
 HIS   0.008   0.002   HIS E 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 ( 8250)
  covalent geometry    : angle       0.62376 (11268)
  SS BOND              : bond        0.00408 (    3)
  SS BOND              : angle       1.14512 (    6)
  hydrogen bonds       : bond        0.05068 (  438)
  hydrogen bonds       : angle       5.55445 ( 1236)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 248
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.7686 (ttt90) cc_final: 0.7430 (ttt-90)
REVERT: A   21 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7665 (ttmm)
REVERT: A  218 ASP cc_start: 0.7321 (p0) cc_final: 0.6975 (p0)
REVERT: A  247 SER cc_start: 0.8408 (m) cc_final: 0.7953 (p)
REVERT: A  256 ASN cc_start: 0.7186 (t0) cc_final: 0.6711 (t0)
REVERT: A  258 LYS cc_start: 0.8242 (tttm) cc_final: 0.7977 (tttm)
REVERT: A  313 ARG cc_start: 0.7792 (mpt-90) cc_final: 0.7332 (mpt-90)
REVERT: A  330 ASN cc_start: 0.6994 (t0) cc_final: 0.6644 (t0)
REVERT: A  349 ARG cc_start: 0.8279 (ttm110) cc_final: 0.8070 (ttm110)
REVERT: B   97 SER cc_start: 0.8782 (t) cc_final: 0.8552 (p)
REVERT: B  117 LEU cc_start: 0.8485 (mt) cc_final: 0.8093 (mm)
REVERT: B  126 LEU cc_start: 0.8338 (mt) cc_final: 0.8086 (mp)
REVERT: B  270 ILE cc_start: 0.8801 (pt) cc_final: 0.8445 (mm)
REVERT: B  280 LYS cc_start: 0.8093 (tttm) cc_final: 0.7712 (ttmt)
REVERT: E   20 GLN cc_start: 0.6382 (OUTLIER) cc_final: 0.5587 (tm-30)
REVERT: E   30 LEU cc_start: 0.7906 (mt) cc_final: 0.7652 (mt)
REVERT: E   66 LEU cc_start: 0.8336 (tp) cc_final: 0.7960 (tp)
REVERT: E   69 PHE cc_start: 0.7663 (t80) cc_final: 0.7442 (t80)
REVERT: E   70 LEU cc_start: 0.7786 (mp) cc_final: 0.7258 (mp)
REVERT: E  118 LEU cc_start: 0.7767 (mt) cc_final: 0.7511 (mt)
REVERT: E  382 CYS cc_start: 0.7532 (m) cc_final: 0.7284 (m)
REVERT: E  393 LEU cc_start: 0.8171 (tp) cc_final: 0.7940 (tp)
REVERT: E  407 MET cc_start: 0.6740 (mmt) cc_final: 0.6413 (mmt)
REVERT: E  422 CYS cc_start: 0.7810 (t) cc_final: 0.7492 (p)
REVERT: H   18 ARG cc_start: 0.7918 (mmm-85) cc_final: 0.7183 (tpt-90)
REVERT: H   30 SER cc_start: 0.8313 (m) cc_final: 0.8057 (p)
REVERT: H  106 SER cc_start: 0.8185 (t) cc_final: 0.7439 (p)
REVERT: H  140 MET cc_start: 0.6703 (mmt) cc_final: 0.6328 (mmt)
REVERT: H  141 THR cc_start: 0.7961 (t) cc_final: 0.7626 (p)
REVERT: H  191 ARG cc_start: 0.8578 (mtm-85) cc_final: 0.7838 (mtt-85)
REVERT: H  226 VAL cc_start: 0.7397 (p) cc_final: 0.7170 (m)
  outliers start: 21
  outliers final: 15
  residues processed: 260
  average time/residue: 0.0741
  time to fit residues: 26.2678
Evaluate side-chains
  253 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 237
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain E residue   20 GLN
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  353 VAL
Chi-restraints excluded: chain E residue  427 LEU
Chi-restraints excluded: chain H residue   51 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0370
   chunk 39 optimal weight:    0.6980
   chunk 75 optimal weight:    0.5980
   chunk 96 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 106 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 387 HIS ** 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 = 0.3677 r_free = 0.3677 target = 0.127575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.109338 restraints weight = 14042.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.112936 restraints weight = 6942.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.115292 restraints weight = 4104.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.116854 restraints weight = 2745.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.117746 restraints weight = 2024.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8253  Z= 0.150
  Angle     :  0.564  10.103  11274  Z= 0.294
  Chirality :  0.043   0.163   1328
  Planarity :  0.004   0.045   1438
  Dihedral  :  4.101  29.457   1184
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 16.67 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.26 (0.26), residues: 1100
  helix:  1.97 (0.27), residues: 397
  sheet: -0.47 (0.30), residues: 292
  loop : -1.09 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 134 
 TYR   0.015   0.002   TYR A 291 
 PHE   0.023   0.002   PHE E 338 
 TRP   0.011   0.002   TRP H  47 
 HIS   0.008   0.001   HIS E 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8250)
  covalent geometry    : angle       0.56326 (11268)
  SS BOND              : bond        0.00709 (    3)
  SS BOND              : angle       1.23099 (    6)
  hydrogen bonds       : bond        0.04164 (  438)
  hydrogen bonds       : angle       5.14296 ( 1236)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 244
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.7823 (ttt90) cc_final: 0.7590 (ttt-90)
REVERT: A   21 LYS cc_start: 0.7901 (ttmm) cc_final: 0.7612 (ttmm)
REVERT: A  218 ASP cc_start: 0.7212 (p0) cc_final: 0.6964 (p0)
REVERT: A  247 SER cc_start: 0.8327 (m) cc_final: 0.7780 (p)
REVERT: A  256 ASN cc_start: 0.7147 (t0) cc_final: 0.6676 (t0)
REVERT: A  257 ASN cc_start: 0.7838 (t0) cc_final: 0.7581 (t0)
REVERT: A  290 GLU cc_start: 0.6328 (tp30) cc_final: 0.5969 (tp30)
REVERT: A  313 ARG cc_start: 0.7763 (mpt-90) cc_final: 0.7346 (mpt-90)
REVERT: A  330 ASN cc_start: 0.6856 (t0) cc_final: 0.6517 (t0)
REVERT: A  349 ARG cc_start: 0.8318 (ttm110) cc_final: 0.8091 (ttm110)
REVERT: B   97 SER cc_start: 0.8822 (t) cc_final: 0.8526 (p)
REVERT: B  117 LEU cc_start: 0.8427 (mt) cc_final: 0.8038 (mm)
REVERT: B  168 LEU cc_start: 0.7823 (tp) cc_final: 0.7497 (tt)
REVERT: B  205 ASP cc_start: 0.6789 (p0) cc_final: 0.6529 (p0)
REVERT: B  239 ASN cc_start: 0.8250 (t0) cc_final: 0.8020 (t0)
REVERT: B  270 ILE cc_start: 0.8773 (pt) cc_final: 0.8411 (mm)
REVERT: B  280 LYS cc_start: 0.8167 (tttm) cc_final: 0.7760 (ttmt)
REVERT: B  333 ASP cc_start: 0.7723 (p0) cc_final: 0.7407 (p0)
REVERT: E   20 GLN cc_start: 0.6407 (mm-40) cc_final: 0.5884 (tm-30)
REVERT: E   30 LEU cc_start: 0.7869 (mt) cc_final: 0.7622 (mt)
REVERT: E   64 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7599 (tt)
REVERT: E   66 LEU cc_start: 0.8261 (tp) cc_final: 0.7877 (tp)
REVERT: E   70 LEU cc_start: 0.7881 (mp) cc_final: 0.7623 (mp)
REVERT: E  118 LEU cc_start: 0.7769 (mt) cc_final: 0.7357 (mt)
REVERT: E  382 CYS cc_start: 0.7540 (m) cc_final: 0.7327 (m)
REVERT: E  393 LEU cc_start: 0.8143 (tp) cc_final: 0.7931 (tp)
REVERT: E  407 MET cc_start: 0.6747 (mmt) cc_final: 0.6435 (mmt)
REVERT: E  422 CYS cc_start: 0.7721 (t) cc_final: 0.7364 (p)
REVERT: H    4 LEU cc_start: 0.7845 (mt) cc_final: 0.7588 (mp)
REVERT: H   18 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7091 (tpt-90)
REVERT: H   30 SER cc_start: 0.8326 (m) cc_final: 0.8053 (p)
REVERT: H  106 SER cc_start: 0.8093 (t) cc_final: 0.7649 (p)
REVERT: H  140 MET cc_start: 0.6722 (mmt) cc_final: 0.6385 (mmt)
REVERT: H  141 THR cc_start: 0.7982 (t) cc_final: 0.7673 (p)
REVERT: H  226 VAL cc_start: 0.7347 (p) cc_final: 0.7125 (m)
  outliers start: 27
  outliers final: 19
  residues processed: 255
  average time/residue: 0.0793
  time to fit residues: 27.9331
Evaluate side-chains
  254 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 234
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain E residue   71 CYS
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   83 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0270
   chunk 80 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0870
   chunk 41 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.4816

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 175 GLN
** E  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.128181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.111023 restraints weight = 14142.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.114429 restraints weight = 7100.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.116625 restraints weight = 4209.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.118084 restraints weight = 2818.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.118927 restraints weight = 2086.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8253  Z= 0.138
  Angle     :  0.541   8.026  11274  Z= 0.283
  Chirality :  0.043   0.182   1328
  Planarity :  0.004   0.044   1438
  Dihedral  :  4.004  26.404   1184
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 17.85 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.26), residues: 1100
  helix:  2.00 (0.27), residues: 398
  sheet: -0.56 (0.29), residues: 294
  loop : -1.05 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 134 
 TYR   0.014   0.001   TYR E  90 
 PHE   0.024   0.001   PHE H 239 
 TRP   0.012   0.002   TRP H  47 
 HIS   0.004   0.001   HIS E 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8250)
  covalent geometry    : angle       0.54042 (11268)
  SS BOND              : bond        0.00425 (    3)
  SS BOND              : angle       1.20479 (    6)
  hydrogen bonds       : bond        0.03836 (  438)
  hydrogen bonds       : angle       4.89878 ( 1236)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 245
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.7789 (ttt90) cc_final: 0.7542 (ttt-90)
REVERT: A   21 LYS cc_start: 0.7893 (ttmm) cc_final: 0.7609 (ttmm)
REVERT: A  200 PHE cc_start: 0.8249 (m-80) cc_final: 0.7881 (m-80)
REVERT: A  218 ASP cc_start: 0.7188 (p0) cc_final: 0.6919 (p0)
REVERT: A  247 SER cc_start: 0.8280 (m) cc_final: 0.7755 (p)
REVERT: A  264 SER cc_start: 0.8439 (OUTLIER) cc_final: 0.8096 (p)
REVERT: A  290 GLU cc_start: 0.6427 (tp30) cc_final: 0.6108 (tp30)
REVERT: A  313 ARG cc_start: 0.7683 (mpt-90) cc_final: 0.7250 (mpt-90)
REVERT: A  341 ASP cc_start: 0.7400 (t0) cc_final: 0.7184 (m-30)
REVERT: A  349 ARG cc_start: 0.8272 (ttm110) cc_final: 0.8028 (ttm110)
REVERT: B  117 LEU cc_start: 0.8481 (mt) cc_final: 0.8097 (mm)
REVERT: B  205 ASP cc_start: 0.6839 (p0) cc_final: 0.6522 (p0)
REVERT: B  239 ASN cc_start: 0.8235 (t0) cc_final: 0.7986 (t0)
REVERT: B  270 ILE cc_start: 0.8779 (pt) cc_final: 0.8416 (mm)
REVERT: B  280 LYS cc_start: 0.8131 (tttm) cc_final: 0.7743 (ttmt)
REVERT: B  333 ASP cc_start: 0.7703 (p0) cc_final: 0.7444 (p0)
REVERT: E   20 GLN cc_start: 0.6209 (OUTLIER) cc_final: 0.5604 (tm-30)
REVERT: E   64 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7523 (tt)
REVERT: E   66 LEU cc_start: 0.8241 (tp) cc_final: 0.8035 (tp)
REVERT: E  393 LEU cc_start: 0.8094 (tp) cc_final: 0.7810 (tp)
REVERT: E  407 MET cc_start: 0.6700 (mmt) cc_final: 0.6442 (mmt)
REVERT: H    4 LEU cc_start: 0.7818 (mt) cc_final: 0.7591 (mp)
REVERT: H   18 ARG cc_start: 0.7802 (mmm-85) cc_final: 0.7061 (tpt-90)
REVERT: H   30 SER cc_start: 0.8322 (m) cc_final: 0.8041 (p)
REVERT: H  106 SER cc_start: 0.8241 (t) cc_final: 0.7964 (p)
REVERT: H  140 MET cc_start: 0.6760 (mmt) cc_final: 0.6417 (mmt)
REVERT: H  141 THR cc_start: 0.8020 (t) cc_final: 0.7733 (p)
REVERT: H  173 TYR cc_start: 0.8080 (m-80) cc_final: 0.7744 (m-80)
REVERT: H  226 VAL cc_start: 0.7318 (p) cc_final: 0.7075 (m)
  outliers start: 25
  outliers final: 18
  residues processed: 256
  average time/residue: 0.0727
  time to fit residues: 25.3136
Evaluate side-chains
  263 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 242
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain E residue   20 GLN
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain E residue   71 CYS
Chi-restraints excluded: chain E residue   79 LEU
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   83 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 22 optimal weight:    0.4980
   chunk 72 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 106 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
** E  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 387 HIS ** 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 = 0.3677 r_free = 0.3677 target = 0.127649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.110330 restraints weight = 14113.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.113732 restraints weight = 7097.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.115951 restraints weight = 4212.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.117394 restraints weight = 2820.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.118294 restraints weight = 2089.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.2779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8253  Z= 0.162
  Angle     :  0.572  10.316  11274  Z= 0.294
  Chirality :  0.043   0.188   1328
  Planarity :  0.003   0.041   1438
  Dihedral  :  4.066  25.342   1184
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 21.52 %
    Favored  : 74.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.21 (0.26), residues: 1100
  helix:  1.93 (0.26), residues: 398
  sheet: -0.54 (0.30), residues: 293
  loop : -1.09 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  18 
 TYR   0.014   0.002   TYR A 303 
 PHE   0.020   0.001   PHE H 239 
 TRP   0.012   0.002   TRP H  36 
 HIS   0.005   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 8250)
  covalent geometry    : angle       0.57147 (11268)
  SS BOND              : bond        0.00417 (    3)
  SS BOND              : angle       1.38753 (    6)
  hydrogen bonds       : bond        0.03988 (  438)
  hydrogen bonds       : angle       4.84375 ( 1236)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 254
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.7792 (ttt90) cc_final: 0.7548 (ttt-90)
REVERT: A   19 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6226 (pt)
REVERT: A   21 LYS cc_start: 0.7902 (ttmm) cc_final: 0.7613 (ttmm)
REVERT: A  247 SER cc_start: 0.8315 (m) cc_final: 0.7777 (p)
REVERT: A  264 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8026 (p)
REVERT: A  290 GLU cc_start: 0.6527 (tp30) cc_final: 0.6174 (tp30)
REVERT: A  341 ASP cc_start: 0.7442 (t0) cc_final: 0.7232 (m-30)
REVERT: A  349 ARG cc_start: 0.8280 (ttm110) cc_final: 0.8040 (ttm110)
REVERT: B  168 LEU cc_start: 0.7781 (tp) cc_final: 0.7475 (tt)
REVERT: B  170 ASP cc_start: 0.8006 (t0) cc_final: 0.7799 (t70)
REVERT: B  205 ASP cc_start: 0.6859 (p0) cc_final: 0.6593 (p0)
REVERT: B  270 ILE cc_start: 0.8781 (pt) cc_final: 0.8414 (mm)
REVERT: B  280 LYS cc_start: 0.8164 (tttm) cc_final: 0.7762 (ttmt)
REVERT: B  325 MET cc_start: 0.7157 (tpp) cc_final: 0.6845 (tpp)
REVERT: B  333 ASP cc_start: 0.7699 (p0) cc_final: 0.7459 (p0)
REVERT: E   58 THR cc_start: 0.7653 (p) cc_final: 0.7304 (t)
REVERT: E   64 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7511 (tt)
REVERT: E  111 PHE cc_start: 0.7823 (m-10) cc_final: 0.7086 (m-80)
REVERT: E  327 MET cc_start: 0.6434 (ptt) cc_final: 0.6192 (ptt)
REVERT: E  382 CYS cc_start: 0.7418 (m) cc_final: 0.7129 (p)
REVERT: E  393 LEU cc_start: 0.8114 (tp) cc_final: 0.7892 (tp)
REVERT: E  407 MET cc_start: 0.6713 (mmt) cc_final: 0.6471 (mmt)
REVERT: H   18 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.7150 (tpt-90)
REVERT: H   30 SER cc_start: 0.8348 (m) cc_final: 0.8075 (p)
REVERT: H  106 SER cc_start: 0.8306 (t) cc_final: 0.8023 (p)
REVERT: H  140 MET cc_start: 0.6795 (mmt) cc_final: 0.6470 (mmt)
REVERT: H  141 THR cc_start: 0.8048 (t) cc_final: 0.7769 (p)
REVERT: H  173 TYR cc_start: 0.8043 (m-80) cc_final: 0.7764 (m-80)
REVERT: H  226 VAL cc_start: 0.7293 (p) cc_final: 0.7076 (m)
  outliers start: 30
  outliers final: 20
  residues processed: 269
  average time/residue: 0.0750
  time to fit residues: 27.8733
Evaluate side-chains
  273 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 250
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain E residue   71 CYS
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  165 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
B 239 ASN
** E  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 133 HIS
** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 194 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.126693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.109546 restraints weight = 14036.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.112952 restraints weight = 7028.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.115090 restraints weight = 4153.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.116556 restraints weight = 2795.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.117509 restraints weight = 2055.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8253  Z= 0.201
  Angle     :  0.607   9.940  11274  Z= 0.314
  Chirality :  0.044   0.202   1328
  Planarity :  0.004   0.050   1438
  Dihedral  :  4.338  41.857   1184
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 22.31 %
    Favored  : 73.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.09 (0.26), residues: 1100
  helix:  1.80 (0.26), residues: 398
  sheet: -0.56 (0.30), residues: 292
  loop : -1.17 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  78 
 TYR   0.019   0.002   TYR A 303 
 PHE   0.025   0.002   PHE E 338 
 TRP   0.016   0.002   TRP H  36 
 HIS   0.008   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 8250)
  covalent geometry    : angle       0.60614 (11268)
  SS BOND              : bond        0.00444 (    3)
  SS BOND              : angle       1.28580 (    6)
  hydrogen bonds       : bond        0.04202 (  438)
  hydrogen bonds       : angle       4.90864 ( 1236)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 252
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.7768 (ttt90) cc_final: 0.7511 (ttt-90)
REVERT: A   19 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.5824 (pt)
REVERT: A   21 LYS cc_start: 0.7931 (ttmm) cc_final: 0.7629 (ttmm)
REVERT: A  200 PHE cc_start: 0.8195 (m-80) cc_final: 0.7872 (m-80)
REVERT: A  247 SER cc_start: 0.8362 (m) cc_final: 0.7790 (p)
REVERT: A  257 ASN cc_start: 0.7864 (t0) cc_final: 0.7415 (t0)
REVERT: A  290 GLU cc_start: 0.6359 (tp30) cc_final: 0.6026 (tp30)
REVERT: A  341 ASP cc_start: 0.7475 (t0) cc_final: 0.7266 (m-30)
REVERT: A  349 ARG cc_start: 0.8293 (ttm110) cc_final: 0.8061 (ttm110)
REVERT: B  168 LEU cc_start: 0.7799 (tp) cc_final: 0.7509 (tt)
REVERT: B  205 ASP cc_start: 0.7079 (p0) cc_final: 0.6664 (p0)
REVERT: B  270 ILE cc_start: 0.8799 (pt) cc_final: 0.8392 (mm)
REVERT: B  325 MET cc_start: 0.7107 (tpp) cc_final: 0.6769 (tpp)
REVERT: B  333 ASP cc_start: 0.7699 (p0) cc_final: 0.7471 (p0)
REVERT: E   58 THR cc_start: 0.7665 (p) cc_final: 0.7345 (t)
REVERT: E   64 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7571 (tt)
REVERT: E  342 PHE cc_start: 0.7164 (t80) cc_final: 0.6963 (t80)
REVERT: E  356 MET cc_start: 0.7285 (mmm) cc_final: 0.7024 (mmm)
REVERT: E  382 CYS cc_start: 0.7432 (m) cc_final: 0.7155 (m)
REVERT: E  407 MET cc_start: 0.6778 (mmt) cc_final: 0.6546 (mmt)
REVERT: H    4 LEU cc_start: 0.7635 (mp) cc_final: 0.7425 (mm)
REVERT: H   18 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7107 (tpt-90)
REVERT: H   30 SER cc_start: 0.8272 (m) cc_final: 0.8021 (p)
REVERT: H  106 SER cc_start: 0.8320 (t) cc_final: 0.8097 (p)
REVERT: H  140 MET cc_start: 0.6805 (mmt) cc_final: 0.6458 (mmt)
REVERT: H  141 THR cc_start: 0.8069 (t) cc_final: 0.7790 (p)
REVERT: H  173 TYR cc_start: 0.8055 (m-80) cc_final: 0.7743 (m-80)
REVERT: H  226 VAL cc_start: 0.7304 (p) cc_final: 0.7099 (m)
  outliers start: 35
  outliers final: 26
  residues processed: 270
  average time/residue: 0.0820
  time to fit residues: 30.4743
Evaluate side-chains
  276 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 248
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain E residue   71 CYS
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain E residue  422 CYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  165 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 104 optimal weight:    0.0060
   chunk 55 optimal weight:    0.7980
   chunk 100 optimal weight:    0.0770
   chunk 44 optimal weight:    0.8980
   chunk 88 optimal weight:    0.5980
   overall best weight:    0.4154

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

Flipped N/Q/H residues before XYZ refinement:
E  87 HIS
** E 387 HIS ** 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 = 0.3688 r_free = 0.3688 target = 0.128617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.111390 restraints weight = 14033.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.114785 restraints weight = 7003.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.116969 restraints weight = 4130.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.118274 restraints weight = 2768.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.119345 restraints weight = 2079.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7092
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8253  Z= 0.129
  Angle     :  0.583  11.135  11274  Z= 0.292
  Chirality :  0.043   0.214   1328
  Planarity :  0.003   0.052   1438
  Dihedral  :  4.172  42.886   1184
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 24.15 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.24 (0.26), residues: 1100
  helix:  1.96 (0.26), residues: 400
  sheet: -0.55 (0.30), residues: 293
  loop : -1.07 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 333 
 TYR   0.023   0.001   TYR A 303 
 PHE   0.024   0.001   PHE E 338 
 TRP   0.011   0.002   TRP H  47 
 HIS   0.005   0.001   HIS E  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8250)
  covalent geometry    : angle       0.58216 (11268)
  SS BOND              : bond        0.00428 (    3)
  SS BOND              : angle       1.31273 (    6)
  hydrogen bonds       : bond        0.03705 (  438)
  hydrogen bonds       : angle       4.66843 ( 1236)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 260
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.7757 (ttt90) cc_final: 0.7509 (ttt-90)
REVERT: A   21 LYS cc_start: 0.7856 (ttmm) cc_final: 0.7534 (ttmm)
REVERT: A  247 SER cc_start: 0.8237 (m) cc_final: 0.7666 (p)
REVERT: A  257 ASN cc_start: 0.7825 (t0) cc_final: 0.7432 (t0)
REVERT: A  264 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.8060 (p)
REVERT: A  290 GLU cc_start: 0.6295 (tp30) cc_final: 0.5942 (tp30)
REVERT: A  349 ARG cc_start: 0.8267 (ttm110) cc_final: 0.8022 (ttm110)
REVERT: B  168 LEU cc_start: 0.7739 (tp) cc_final: 0.7466 (tt)
REVERT: B  270 ILE cc_start: 0.8754 (pt) cc_final: 0.8367 (mm)
REVERT: B  280 LYS cc_start: 0.8123 (tttm) cc_final: 0.7741 (ttmt)
REVERT: B  297 TRP cc_start: 0.8437 (m100) cc_final: 0.8145 (m100)
REVERT: B  325 MET cc_start: 0.7109 (tpp) cc_final: 0.6813 (tpp)
REVERT: B  333 ASP cc_start: 0.7702 (p0) cc_final: 0.7455 (p0)
REVERT: E   58 THR cc_start: 0.7624 (p) cc_final: 0.7287 (t)
REVERT: E   64 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7525 (tt)
REVERT: E  134 ARG cc_start: 0.8571 (ttt-90) cc_final: 0.8166 (ttt-90)
REVERT: E  356 MET cc_start: 0.7298 (mmm) cc_final: 0.7000 (mmm)
REVERT: E  382 CYS cc_start: 0.7414 (m) cc_final: 0.7076 (m)
REVERT: E  407 MET cc_start: 0.6736 (mmt) cc_final: 0.6506 (mmt)
REVERT: H    4 LEU cc_start: 0.7615 (mp) cc_final: 0.7391 (mm)
REVERT: H   18 ARG cc_start: 0.7803 (mmm-85) cc_final: 0.7089 (tpt-90)
REVERT: H   30 SER cc_start: 0.8331 (m) cc_final: 0.8051 (p)
REVERT: H  140 MET cc_start: 0.6665 (mmt) cc_final: 0.6363 (mmt)
REVERT: H  141 THR cc_start: 0.8072 (t) cc_final: 0.7765 (p)
  outliers start: 27
  outliers final: 21
  residues processed: 274
  average time/residue: 0.0891
  time to fit residues: 33.2459
Evaluate side-chains
  277 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 254
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LYS
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain E residue   71 CYS
Chi-restraints excluded: chain E residue   87 HIS
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  119 ASP
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  165 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 90 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0060
   overall best weight:    0.7200

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
E  87 HIS
** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 194 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.127232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.110102 restraints weight = 13853.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.113476 restraints weight = 6919.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.115652 restraints weight = 4091.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.117092 restraints weight = 2736.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.117914 restraints weight = 2016.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.3332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8253  Z= 0.183
  Angle     :  0.599   9.001  11274  Z= 0.309
  Chirality :  0.044   0.227   1328
  Planarity :  0.004   0.052   1438
  Dihedral  :  4.305  43.656   1184
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 25.59 %
    Favored  : 70.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.18 (0.26), residues: 1100
  helix:  1.92 (0.26), residues: 398
  sheet: -0.62 (0.30), residues: 297
  loop : -1.07 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  49 
 TYR   0.020   0.002   TYR A 291 
 PHE   0.027   0.002   PHE E 342 
 TRP   0.014   0.002   TRP H  36 
 HIS   0.011   0.001   HIS E  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 8250)
  covalent geometry    : angle       0.59860 (11268)
  SS BOND              : bond        0.00454 (    3)
  SS BOND              : angle       1.29169 (    6)
  hydrogen bonds       : bond        0.04000 (  438)
  hydrogen bonds       : angle       4.75235 ( 1236)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 250
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.7764 (ttt90) cc_final: 0.7502 (ttt-90)
REVERT: A   19 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.5875 (pt)
REVERT: A   21 LYS cc_start: 0.7906 (ttmm) cc_final: 0.7589 (ttmm)
REVERT: A  217 GLU cc_start: 0.7029 (tt0) cc_final: 0.6807 (tt0)
REVERT: A  247 SER cc_start: 0.8332 (m) cc_final: 0.7759 (p)
REVERT: A  257 ASN cc_start: 0.7829 (t0) cc_final: 0.7420 (t0)
REVERT: A  290 GLU cc_start: 0.6463 (tp30) cc_final: 0.6135 (tp30)
REVERT: A  349 ARG cc_start: 0.8275 (ttm110) cc_final: 0.8027 (ttm110)
REVERT: B  168 LEU cc_start: 0.7768 (tp) cc_final: 0.7492 (tt)
REVERT: B  220 GLN cc_start: 0.7618 (mp10) cc_final: 0.7259 (mp10)
REVERT: B  270 ILE cc_start: 0.8800 (pt) cc_final: 0.8381 (mm)
REVERT: B  325 MET cc_start: 0.7096 (tpp) cc_final: 0.6771 (tpp)
REVERT: E   58 THR cc_start: 0.7661 (p) cc_final: 0.7341 (t)
REVERT: E   64 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7546 (tt)
REVERT: E  134 ARG cc_start: 0.8594 (ttt-90) cc_final: 0.8218 (ttt-90)
REVERT: E  382 CYS cc_start: 0.7416 (m) cc_final: 0.7103 (m)
REVERT: E  407 MET cc_start: 0.6754 (mmt) cc_final: 0.6531 (mmt)
REVERT: E  426 PHE cc_start: 0.7485 (m-80) cc_final: 0.7161 (m-80)
REVERT: H    4 LEU cc_start: 0.7654 (mp) cc_final: 0.7412 (mm)
REVERT: H   18 ARG cc_start: 0.7846 (mmm-85) cc_final: 0.7084 (tpt-90)
REVERT: H   30 SER cc_start: 0.8256 (m) cc_final: 0.7993 (p)
REVERT: H  140 MET cc_start: 0.6798 (mmt) cc_final: 0.6459 (mmt)
REVERT: H  141 THR cc_start: 0.8076 (t) cc_final: 0.7777 (p)
  outliers start: 27
  outliers final: 24
  residues processed: 263
  average time/residue: 0.0882
  time to fit residues: 31.6961
Evaluate side-chains
  272 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 246
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain E residue   71 CYS
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  119 ASP
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  165 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0370
   chunk 58 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 71 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
E  87 HIS
** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.128004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.110551 restraints weight = 13963.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.113963 restraints weight = 6973.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.116199 restraints weight = 4128.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.117670 restraints weight = 2758.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.118589 restraints weight = 2032.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8253  Z= 0.155
  Angle     :  0.609   9.667  11274  Z= 0.306
  Chirality :  0.043   0.244   1328
  Planarity :  0.004   0.052   1438
  Dihedral  :  4.293  43.765   1184
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 26.12 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.19 (0.26), residues: 1100
  helix:  1.97 (0.26), residues: 396
  sheet: -0.61 (0.30), residues: 292
  loop : -1.12 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 333 
 TYR   0.020   0.002   TYR A 303 
 PHE   0.030   0.002   PHE E 342 
 TRP   0.010   0.002   TRP H  36 
 HIS   0.007   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8250)
  covalent geometry    : angle       0.60885 (11268)
  SS BOND              : bond        0.00435 (    3)
  SS BOND              : angle       1.24208 (    6)
  hydrogen bonds       : bond        0.03838 (  438)
  hydrogen bonds       : angle       4.69452 ( 1236)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 252
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.7736 (ttt90) cc_final: 0.7482 (ttt-90)
REVERT: A   21 LYS cc_start: 0.7904 (ttmm) cc_final: 0.7583 (ttmm)
REVERT: A  217 GLU cc_start: 0.7046 (tt0) cc_final: 0.6789 (tt0)
REVERT: A  247 SER cc_start: 0.8291 (m) cc_final: 0.7717 (p)
REVERT: A  257 ASN cc_start: 0.7816 (t0) cc_final: 0.7419 (t0)
REVERT: A  290 GLU cc_start: 0.6483 (tp30) cc_final: 0.6148 (tp30)
REVERT: A  349 ARG cc_start: 0.8272 (ttm110) cc_final: 0.8028 (ttm110)
REVERT: B   96 ARG cc_start: 0.7298 (mtp-110) cc_final: 0.6995 (mtp-110)
REVERT: B  160 SER cc_start: 0.7848 (t) cc_final: 0.6970 (p)
REVERT: B  168 LEU cc_start: 0.7741 (tp) cc_final: 0.7476 (tt)
REVERT: B  220 GLN cc_start: 0.7615 (mp10) cc_final: 0.7259 (mp10)
REVERT: B  270 ILE cc_start: 0.8772 (pt) cc_final: 0.8369 (mm)
REVERT: B  297 TRP cc_start: 0.8389 (m100) cc_final: 0.8085 (m100)
REVERT: B  325 MET cc_start: 0.7115 (tpp) cc_final: 0.6794 (tpp)
REVERT: E   58 THR cc_start: 0.7633 (p) cc_final: 0.7324 (t)
REVERT: E   64 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7521 (tt)
REVERT: E  382 CYS cc_start: 0.7425 (m) cc_final: 0.7106 (m)
REVERT: E  407 MET cc_start: 0.6794 (mmt) cc_final: 0.6587 (mmt)
REVERT: E  426 PHE cc_start: 0.7505 (m-80) cc_final: 0.7181 (m-80)
REVERT: H    4 LEU cc_start: 0.7639 (mp) cc_final: 0.7398 (mm)
REVERT: H   18 ARG cc_start: 0.7861 (mmm-85) cc_final: 0.7078 (tpt-90)
REVERT: H   30 SER cc_start: 0.8259 (m) cc_final: 0.7998 (p)
REVERT: H  140 MET cc_start: 0.6653 (mmt) cc_final: 0.6361 (mmt)
REVERT: H  141 THR cc_start: 0.8080 (t) cc_final: 0.7779 (p)
REVERT: H  195 LEU cc_start: 0.8482 (tt) cc_final: 0.8025 (tp)
  outliers start: 24
  outliers final: 21
  residues processed: 263
  average time/residue: 0.0759
  time to fit residues: 27.6046
Evaluate side-chains
  268 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 246
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  119 ASP
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  165 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0870
   chunk 95 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 105 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
E  87 HIS
** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.127961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.110698 restraints weight = 13899.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.114054 restraints weight = 6928.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.116267 restraints weight = 4109.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.117686 restraints weight = 2737.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.118665 restraints weight = 2032.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.3494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8253  Z= 0.155
  Angle     :  0.600   9.231  11274  Z= 0.307
  Chirality :  0.044   0.255   1328
  Planarity :  0.004   0.052   1438
  Dihedral  :  4.284  43.424   1184
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 26.25 %
    Favored  : 70.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.18 (0.26), residues: 1100
  helix:  1.96 (0.26), residues: 397
  sheet: -0.62 (0.30), residues: 294
  loop : -1.12 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 333 
 TYR   0.029   0.002   TYR H  60 
 PHE   0.030   0.002   PHE E 342 
 TRP   0.011   0.002   TRP B 332 
 HIS   0.006   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 8250)
  covalent geometry    : angle       0.59912 (11268)
  SS BOND              : bond        0.00438 (    3)
  SS BOND              : angle       1.26467 (    6)
  hydrogen bonds       : bond        0.03865 (  438)
  hydrogen bonds       : angle       4.69896 ( 1236)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 246
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.7728 (ttt90) cc_final: 0.7479 (ttt-90)
REVERT: A   21 LYS cc_start: 0.7912 (ttmm) cc_final: 0.7576 (ttmm)
REVERT: A  217 GLU cc_start: 0.7048 (tt0) cc_final: 0.6775 (tt0)
REVERT: A  247 SER cc_start: 0.8286 (m) cc_final: 0.7720 (p)
REVERT: A  257 ASN cc_start: 0.7829 (t0) cc_final: 0.7413 (t0)
REVERT: A  290 GLU cc_start: 0.6466 (tp30) cc_final: 0.6111 (tp30)
REVERT: A  349 ARG cc_start: 0.8269 (ttm110) cc_final: 0.8022 (ttm110)
REVERT: B   96 ARG cc_start: 0.7299 (mtp-110) cc_final: 0.6997 (mtp-110)
REVERT: B  160 SER cc_start: 0.7843 (t) cc_final: 0.6995 (p)
REVERT: B  168 LEU cc_start: 0.7714 (tp) cc_final: 0.7464 (tt)
REVERT: B  220 GLN cc_start: 0.7579 (mp10) cc_final: 0.7212 (mp10)
REVERT: B  270 ILE cc_start: 0.8784 (pt) cc_final: 0.8348 (mm)
REVERT: B  297 TRP cc_start: 0.8377 (m100) cc_final: 0.8083 (m100)
REVERT: B  322 ASP cc_start: 0.7746 (m-30) cc_final: 0.7529 (m-30)
REVERT: B  325 MET cc_start: 0.7093 (tpp) cc_final: 0.6731 (tpp)
REVERT: E   58 THR cc_start: 0.7645 (p) cc_final: 0.7327 (t)
REVERT: E  382 CYS cc_start: 0.7376 (m) cc_final: 0.7080 (m)
REVERT: E  407 MET cc_start: 0.6807 (mmt) cc_final: 0.6592 (mmt)
REVERT: E  426 PHE cc_start: 0.7500 (m-80) cc_final: 0.7164 (m-80)
REVERT: G   61 PHE cc_start: 0.7290 (m-80) cc_final: 0.7075 (m-80)
REVERT: H    4 LEU cc_start: 0.7623 (mp) cc_final: 0.7386 (mm)
REVERT: H   18 ARG cc_start: 0.7827 (mmm-85) cc_final: 0.7067 (tpt-90)
REVERT: H   30 SER cc_start: 0.8260 (m) cc_final: 0.7993 (p)
REVERT: H  140 MET cc_start: 0.6584 (mmt) cc_final: 0.6307 (mmt)
REVERT: H  141 THR cc_start: 0.8081 (t) cc_final: 0.7785 (p)
  outliers start: 24
  outliers final: 20
  residues processed: 257
  average time/residue: 0.0831
  time to fit residues: 29.5066
Evaluate side-chains
  270 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 250
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  165 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 102 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0040
   chunk 94 optimal weight:    0.9980
   chunk 51 optimal weight:    0.2980
   chunk 31 optimal weight:    0.0000
   chunk 49 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 107 optimal weight:    0.5980
   overall best weight:    0.2996

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

Flipped N/Q/H residues before XYZ refinement:
E  87 HIS
** E 387 HIS ** 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 = 0.3703 r_free = 0.3703 target = 0.129462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.111510 restraints weight = 13867.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.114973 restraints weight = 6957.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.117189 restraints weight = 4173.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.118708 restraints weight = 2819.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.119556 restraints weight = 2100.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.3529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8253  Z= 0.120
  Angle     :  0.608  10.840  11274  Z= 0.300
  Chirality :  0.043   0.261   1328
  Planarity :  0.003   0.052   1438
  Dihedral  :  4.148  42.704   1184
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 26.51 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.28 (0.26), residues: 1100
  helix:  2.11 (0.26), residues: 399
  sheet: -0.61 (0.30), residues: 297
  loop : -1.11 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  49 
 TYR   0.015   0.001   TYR A 303 
 PHE   0.028   0.001   PHE E 342 
 TRP   0.016   0.002   TRP B 339 
 HIS   0.005   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8250)
  covalent geometry    : angle       0.60746 (11268)
  SS BOND              : bond        0.00402 (    3)
  SS BOND              : angle       1.25873 (    6)
  hydrogen bonds       : bond        0.03521 (  438)
  hydrogen bonds       : angle       4.53579 ( 1236)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1461.55 seconds
wall clock time: 25 minutes 52.17 seconds (1552.17 seconds total)