Starting phenix.real_space_refine
on Wed Feb  4 01:45:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kv6_62586/02_2026/9kv6_62586.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kv6_62586/02_2026/9kv6_62586.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kv6_62586/02_2026/9kv6_62586.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kv6_62586/02_2026/9kv6_62586.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kv6_62586/02_2026/9kv6_62586.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kv6_62586/02_2026/9kv6_62586.map"
  }
  resolution = 2.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    5221      2.51       5
     N    1406      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 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8163
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "D"
      Number of atoms: 100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 100
          Classifications: {'peptide': 13}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 2, 'TRANS': 10}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
    Chain: "E"
      Number of atoms: 2145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2145
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 12, 'TRANS': 268}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 85
          Unresolved non-hydrogen angles: 101
          Unresolved non-hydrogen dihedrals: 71
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 38
    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: "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: 1633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1633
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 131
          Unresolved non-hydrogen angles: 158
          Unresolved non-hydrogen dihedrals: 104
          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: 1.84, per 1000 atoms: 0.23
  Number of scatterers: 8163
  At special positions: 0
  Unit cell: (84.11, 121.636, 120.342, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    1483      8.00
     N    1406      7.00
     C    5221      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=2.07
    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: 0.77
  Conformation dependent library (CDL) restraints added in 330.2 milliseconds
  

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2102

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 13 sheets defined
      37.6% alpha, 23.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'D' and resid 9 through 16
    Processing helix  chain 'E' and resid 20 through 51
      removed outlier: 3.568A  pdb=" N   LEU E  39 " --> pdb=" O   LEU E  35 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 85
      removed outlier: 4.596A  pdb=" N   TRP E  60 " --> pdb=" O   VAL E  56 " (cutoff:3.500A)
      removed outlier: 4.243A  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 93 through 126
      Proline residue:  E  99  - end of helix
      removed outlier: 3.767A  pdb=" N   VAL E 124 " --> pdb=" O   ARG E 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 128 through 133
    Processing helix  chain 'E' and resid 135 through 160
      Proline residue:  E 156  - end of helix
    Processing helix  chain 'E' and resid 323 through 338
    Processing helix  chain 'E' and resid 338 through 357
    Processing helix  chain 'E' and resid 366 through 396
      Proline residue:  E 385  - end of helix
      removed outlier: 3.788A  pdb=" N   LEU E 394 " --> pdb=" O   GLY E 390 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 400 through 428
      removed outlier: 4.596A  pdb=" N   VAL E 406 " --> pdb=" O   LEU E 402 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   HIS E 411 " --> pdb=" O   MET E 407 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   MET E 412 " --> pdb=" O   SER E 408 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER E 421 " --> pdb=" O   ALA E 417 " (cutoff:3.500A)
      removed outlier: 3.674A  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 'A' and resid 8 through 32
      removed outlier: 3.723A  pdb=" N   LYS A  32 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 208 through 217
      removed outlier: 4.615A  pdb=" N   ILE A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLU A 217 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 256
      removed outlier: 4.124A  pdb=" N   LEU A 250 " --> pdb=" O   GLU A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 282
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 3.698A  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 'G' and resid 8 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    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 sheet with id=AA1, first strand: chain 'A' and resid 186 through 192
      removed outlier: 6.925A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.941A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 8.377A  pdb=" N   ASP A 227 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.427A  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
      removed outlier: 3.501A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.037A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.551A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.313A  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: 3.645A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.448A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.816A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.727A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 5.646A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.071A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.295A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.273A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 155 through 159
      removed outlier: 3.521A  pdb=" N   ALA H 211 " --> pdb=" O   SER H 208 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 194 through 195
      removed outlier: 5.553A  pdb=" N   LEU H 187 " --> pdb=" O   LEU H 178 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   LEU H 178 " --> pdb=" O   LEU H 187 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLY H 225 " --> pdb=" O   LEU H 245 " (cutoff:3.500A)

    454 hydrogen bonds defined for protein.
    1287 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: 1.46

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2641
        1.34 -     1.46: 2128
        1.46 -     1.58: 3508
        1.58 -     1.70: 0
        1.70 -     1.82: 70
  Bond restraints: 8347
  Sorted by residual:
  bond pdb=" N   CYS E 172 "
       pdb=" CA  CYS E 172 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.041 1.29e-02 6.01e+03 1.02e+01
  bond pdb=" N   ARG E 173 "
       pdb=" CA  ARG E 173 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.68e+00
  bond pdb=" N   CYS E  95 "
       pdb=" CA  CYS E  95 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.35e-02 5.49e+03 1.64e+00
  bond pdb=" CG  LEU B 210 "
       pdb=" CD1 LEU B 210 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 1.03e+00
  bond pdb=" N   TYR E 174 "
       pdb=" CA  TYR E 174 "
    ideal  model  delta    sigma   weight residual
    1.458  1.477 -0.019 1.90e-02 2.77e+03 9.90e-01
  ... (remaining 8342 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 11138
        1.44 -     2.89: 206
        2.89 -     4.33: 36
        4.33 -     5.78: 8
        5.78 -     7.22: 5
  Bond angle restraints: 11393
  Sorted by residual:
  angle pdb=" N   CYS E  95 "
        pdb=" CA  CYS E  95 "
        pdb=" C   CYS E  95 "
      ideal   model   delta    sigma   weight residual
     113.01  107.18    5.83 1.20e+00 6.94e-01 2.36e+01
  angle pdb=" O   CYS E 172 "
        pdb=" C   CYS E 172 "
        pdb=" N   ARG E 173 "
      ideal   model   delta    sigma   weight residual
     122.59  128.24   -5.65 1.33e+00 5.65e-01 1.81e+01
  angle pdb=" N   GLY E 403 "
        pdb=" CA  GLY E 403 "
        pdb=" C   GLY E 403 "
      ideal   model   delta    sigma   weight residual
     113.18  106.65    6.53 2.37e+00 1.78e-01 7.59e+00
  angle pdb=" N   GLY H   8 "
        pdb=" CA  GLY H   8 "
        pdb=" C   GLY H   8 "
      ideal   model   delta    sigma   weight residual
     116.01  112.09    3.92 1.64e+00 3.72e-01 5.70e+00
  angle pdb=" N   VAL E 155 "
        pdb=" CA  VAL E 155 "
        pdb=" C   VAL E 155 "
      ideal   model   delta    sigma   weight residual
     108.88  113.32   -4.44 2.16e+00 2.14e-01 4.22e+00
  ... (remaining 11388 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.90: 4451
       16.90 -    33.79: 334
       33.79 -    50.69: 42
       50.69 -    67.59: 6
       67.59 -    84.48: 3
  Dihedral angle restraints: 4836
    sinusoidal: 1585
      harmonic: 3251
  Sorted by residual:
  dihedral pdb=" CA  LEU E 402 "
           pdb=" C   LEU E 402 "
           pdb=" N   GLY E 403 "
           pdb=" CA  GLY E 403 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.67   23.33     0      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" CA  THR B 249 "
           pdb=" C   THR B 249 "
           pdb=" N   CYS B 250 "
           pdb=" CA  CYS B 250 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.18   17.82     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.39   16.61     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 4833 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1028
       0.045 -    0.090: 237
       0.090 -    0.135: 71
       0.135 -    0.180: 3
       0.180 -    0.226: 1
  Chirality restraints: 1340
  Sorted by residual:
  chirality pdb=" CA  ARG E 173 "
            pdb=" N   ARG E 173 "
            pdb=" C   ARG E 173 "
            pdb=" CB  ARG E 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CB  ILE E 171 "
            pdb=" CA  ILE E 171 "
            pdb=" CG1 ILE E 171 "
            pdb=" CG2 ILE E 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.18e-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    2.38    0.15 2.00e-01 2.50e+01 5.27e-01
  ... (remaining 1337 not shown)

  Planarity restraints: 1448
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 173 "   -0.028 2.00e-02 2.50e+03   5.62e-02 3.16e+01
        pdb=" C   ARG E 173 "    0.097 2.00e-02 2.50e+03
        pdb=" O   ARG E 173 "   -0.037 2.00e-02 2.50e+03
        pdb=" N   TYR E 174 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E  94 "    0.016 2.00e-02 2.50e+03   3.22e-02 1.04e+01
        pdb=" C   LEU E  94 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   LEU E  94 "    0.021 2.00e-02 2.50e+03
        pdb=" N   CYS E  95 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE E 171 "    0.015 2.00e-02 2.50e+03   3.11e-02 9.69e+00
        pdb=" C   ILE E 171 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   ILE E 171 "    0.021 2.00e-02 2.50e+03
        pdb=" N   CYS E 172 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1445 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1978
        2.79 -     3.32: 7642
        3.32 -     3.84: 13806
        3.84 -     4.37: 15651
        4.37 -     4.90: 28326
  Nonbonded interactions: 67403
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   ASP E 410 "
            pdb=" OG  SER E 413 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" NE2 GLN B 220 "
            pdb=" OD1 ASP B 258 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" NH2 ARG E 333 "
            pdb=" OH  TYR E 386 "
     model   vdw
     2.278 3.120
  ... (remaining 67398 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.410
  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:                    0.010
  Process input model:                     9.190
  Find NCS groups from input model:        0.040
  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:8.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
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      :  0.004   0.041   8350  Z= 0.166
  Angle     :  0.530   7.219  11399  Z= 0.289
  Chirality :  0.042   0.226   1340
  Planarity :  0.004   0.056   1448
  Dihedral  : 12.101  84.482   2725
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  0.38 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.68 (0.26), residues: 1104
  helix:  1.77 (0.26), residues: 404
  sheet: -0.24 (0.31), residues: 276
  loop : -0.25 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 173 
 TYR   0.012   0.001   TYR B 105 
 PHE   0.015   0.001   PHE H 110 
 TRP   0.009   0.001   TRP B 211 
 HIS   0.008   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8347)
  covalent geometry    : angle       0.52666 (11393)
  SS BOND              : bond        0.02220 (    3)
  SS BOND              : angle       2.76245 (    6)
  hydrogen bonds       : bond        0.15764 (  449)
  hydrogen bonds       : angle       6.78083 ( 1287)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 251
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: E   52 MET cc_start: 0.4968 (mtt) cc_final: 0.4699 (mtt)
REVERT: E   97 LEU cc_start: 0.6891 (tp) cc_final: 0.6557 (tm)
REVERT: E  120 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7950 (mtt-85)
REVERT: E  130 CYS cc_start: 0.7350 (m) cc_final: 0.7147 (m)
REVERT: E  147 TRP cc_start: 0.7700 (m100) cc_final: 0.7317 (m100)
REVERT: E  174 TYR cc_start: 0.5690 (OUTLIER) cc_final: 0.4410 (m-80)
REVERT: E  391 VAL cc_start: 0.8411 (m) cc_final: 0.8161 (p)
REVERT: E  392 LEU cc_start: 0.7780 (tt) cc_final: 0.7564 (tm)
REVERT: A   26 ASP cc_start: 0.7359 (m-30) cc_final: 0.7024 (m-30)
REVERT: A  197 PHE cc_start: 0.8565 (m-80) cc_final: 0.8146 (m-80)
REVERT: A  209 ARG cc_start: 0.7467 (mtm110) cc_final: 0.6953 (mtm110)
REVERT: A  213 ILE cc_start: 0.8396 (tp) cc_final: 0.8105 (tt)
REVERT: A  250 LEU cc_start: 0.8097 (tt) cc_final: 0.7623 (tt)
REVERT: A  253 SER cc_start: 0.8253 (t) cc_final: 0.7819 (p)
REVERT: A  271 LYS cc_start: 0.7040 (mmtm) cc_final: 0.6520 (mtpt)
REVERT: A  299 ASP cc_start: 0.7098 (t0) cc_final: 0.6858 (t0)
REVERT: A  303 TYR cc_start: 0.6544 (t80) cc_final: 0.6343 (t80)
REVERT: A  307 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7755 (mm110)
REVERT: A  309 GLU cc_start: 0.6860 (tm-30) cc_final: 0.5882 (tm-30)
REVERT: A  323 MET cc_start: 0.7655 (mmm) cc_final: 0.7069 (mmm)
REVERT: B   46 ARG cc_start: 0.6867 (mtt-85) cc_final: 0.6630 (mtt-85)
REVERT: B  129 ARG cc_start: 0.7476 (ttt90) cc_final: 0.7264 (tpt90)
REVERT: B  133 VAL cc_start: 0.8319 (t) cc_final: 0.7989 (p)
REVERT: B  135 VAL cc_start: 0.8709 (t) cc_final: 0.8415 (p)
REVERT: B  155 ASN cc_start: 0.7993 (t0) cc_final: 0.7712 (t0)
REVERT: B  209 LYS cc_start: 0.8433 (mttp) cc_final: 0.8063 (mttp)
REVERT: B  219 ARG cc_start: 0.6887 (mtp-110) cc_final: 0.6585 (mtp-110)
REVERT: B  221 THR cc_start: 0.8475 (m) cc_final: 0.8188 (t)
REVERT: B  227 SER cc_start: 0.8377 (t) cc_final: 0.8132 (p)
REVERT: B  280 LYS cc_start: 0.8363 (tttm) cc_final: 0.8061 (tttm)
REVERT: H   21 SER cc_start: 0.8318 (m) cc_final: 0.7800 (p)
REVERT: H   53 SER cc_start: 0.8373 (m) cc_final: 0.7851 (p)
REVERT: H  140 MET cc_start: 0.8026 (mmm) cc_final: 0.6826 (mmm)
REVERT: H  215 THR cc_start: 0.8468 (m) cc_final: 0.8232 (t)
  outliers start: 3
  outliers final: 2
  residues processed: 253
  average time/residue: 0.3827
  time to fit residues: 104.7241
Evaluate side-chains
  203 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 200
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   95 CYS
Chi-restraints excluded: chain E residue  174 TYR
Chi-restraints excluded: chain E residue  344 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.0980
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   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 196 HIS
B 239 ASN
H  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.135823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.116590 restraints weight = 12152.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.80
r_work: 0.3451 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   8350  Z= 0.288
  Angle     :  0.654   7.982  11399  Z= 0.347
  Chirality :  0.047   0.184   1340
  Planarity :  0.004   0.043   1448
  Dihedral  :  4.930  47.883   1196
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 13.19 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.39 (0.25), residues: 1104
  helix:  1.46 (0.25), residues: 403
  sheet: -0.37 (0.30), residues: 269
  loop : -0.35 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 134 
 TYR   0.018   0.002   TYR H  95 
 PHE   0.024   0.002   PHE H 110 
 TRP   0.011   0.002   TRP B  63 
 HIS   0.010   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00637 ( 8347)
  covalent geometry    : angle       0.65303 (11393)
  SS BOND              : bond        0.00694 (    3)
  SS BOND              : angle       1.52511 (    6)
  hydrogen bonds       : bond        0.04702 (  449)
  hydrogen bonds       : angle       5.32865 ( 1287)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 206
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: E   45 LEU cc_start: 0.8026 (tp) cc_final: 0.7781 (tm)
REVERT: E   52 MET cc_start: 0.5610 (mtt) cc_final: 0.5320 (mtt)
REVERT: E   61 PHE cc_start: 0.7711 (m-80) cc_final: 0.7428 (m-80)
REVERT: E   78 SER cc_start: 0.7979 (OUTLIER) cc_final: 0.7761 (p)
REVERT: E   97 LEU cc_start: 0.7692 (tp) cc_final: 0.7309 (tm)
REVERT: E  160 TYR cc_start: 0.5125 (t80) cc_final: 0.4729 (t80)
REVERT: E  173 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.7118 (ptt180)
REVERT: E  174 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.5772 (m-80)
REVERT: A   26 ASP cc_start: 0.7716 (m-30) cc_final: 0.7495 (m-30)
REVERT: A  213 ILE cc_start: 0.8565 (tp) cc_final: 0.8362 (tt)
REVERT: A  252 ASP cc_start: 0.8218 (t0) cc_final: 0.7582 (t0)
REVERT: A  253 SER cc_start: 0.8748 (t) cc_final: 0.8435 (p)
REVERT: A  254 ILE cc_start: 0.8737 (tp) cc_final: 0.8384 (tp)
REVERT: A  309 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6701 (tm-30)
REVERT: A  323 MET cc_start: 0.7839 (mmm) cc_final: 0.7546 (mmm)
REVERT: B  133 VAL cc_start: 0.8447 (t) cc_final: 0.8169 (p)
REVERT: B  135 VAL cc_start: 0.8800 (t) cc_final: 0.8531 (p)
REVERT: B  219 ARG cc_start: 0.7723 (mtp-110) cc_final: 0.7455 (mtp-110)
REVERT: B  220 GLN cc_start: 0.8908 (mt0) cc_final: 0.8541 (mt0)
REVERT: B  221 THR cc_start: 0.8569 (m) cc_final: 0.8288 (t)
REVERT: B  251 ARG cc_start: 0.8474 (mtt90) cc_final: 0.8111 (mtp85)
REVERT: B  261 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7926 (mp)
REVERT: B  280 LYS cc_start: 0.8527 (tttm) cc_final: 0.8321 (tttm)
REVERT: B  335 PHE cc_start: 0.8629 (m-80) cc_final: 0.8254 (m-10)
REVERT: G   31 SER cc_start: 0.8478 (m) cc_final: 0.8106 (p)
REVERT: G   47 GLU cc_start: 0.7583 (mp0) cc_final: 0.7344 (mp0)
REVERT: G   50 LEU cc_start: 0.8111 (mt) cc_final: 0.7833 (mt)
REVERT: H   21 SER cc_start: 0.8486 (m) cc_final: 0.8085 (p)
REVERT: H   53 SER cc_start: 0.8326 (m) cc_final: 0.7935 (p)
REVERT: H   86 LEU cc_start: 0.8596 (mt) cc_final: 0.8379 (mm)
REVERT: H  100 ILE cc_start: 0.8163 (tp) cc_final: 0.7865 (tp)
REVERT: H  140 MET cc_start: 0.8325 (mmm) cc_final: 0.8038 (mtp)
REVERT: H  156 SER cc_start: 0.8507 (t) cc_final: 0.8301 (m)
REVERT: H  215 THR cc_start: 0.8590 (m) cc_final: 0.8336 (t)
  outliers start: 25
  outliers final: 13
  residues processed: 216
  average time/residue: 0.3885
  time to fit residues: 90.6296
Evaluate side-chains
  215 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 198
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   78 SER
Chi-restraints excluded: chain E residue   95 CYS
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain E residue  138 THR
Chi-restraints excluded: chain E residue  145 CYS
Chi-restraints excluded: chain E residue  173 ARG
Chi-restraints excluded: chain E residue  174 TYR
Chi-restraints excluded: chain E residue  422 CYS
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  154 SER
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  189 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   chunk 103 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** E  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 196 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.136731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.117548 restraints weight = 11923.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 1.82
r_work: 0.3461 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3327 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8350  Z= 0.196
  Angle     :  0.589   7.190  11399  Z= 0.308
  Chirality :  0.044   0.198   1340
  Planarity :  0.004   0.033   1448
  Dihedral  :  4.716  47.079   1194
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 15.75 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.41 (0.25), residues: 1104
  helix:  1.43 (0.25), residues: 411
  sheet: -0.37 (0.29), residues: 279
  loop : -0.30 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  49 
 TYR   0.016   0.002   TYR H 103 
 PHE   0.017   0.002   PHE H 110 
 TRP   0.010   0.001   TRP B  63 
 HIS   0.007   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 8347)
  covalent geometry    : angle       0.58789 (11393)
  SS BOND              : bond        0.00589 (    3)
  SS BOND              : angle       1.32679 (    6)
  hydrogen bonds       : bond        0.04078 (  449)
  hydrogen bonds       : angle       5.06975 ( 1287)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 210
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: E   45 LEU cc_start: 0.8013 (tp) cc_final: 0.7804 (tm)
REVERT: E   52 MET cc_start: 0.5605 (mtt) cc_final: 0.5330 (mtt)
REVERT: E   61 PHE cc_start: 0.7791 (m-80) cc_final: 0.7564 (m-80)
REVERT: E   78 SER cc_start: 0.7968 (OUTLIER) cc_final: 0.7746 (p)
REVERT: E   97 LEU cc_start: 0.7706 (tp) cc_final: 0.7361 (tm)
REVERT: E  160 TYR cc_start: 0.5029 (t80) cc_final: 0.4694 (t80)
REVERT: E  174 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.5529 (m-80)
REVERT: E  327 MET cc_start: 0.7179 (tmm) cc_final: 0.6823 (tmm)
REVERT: E  373 VAL cc_start: 0.8065 (p) cc_final: 0.7853 (p)
REVERT: A    8 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7565 (pm20)
REVERT: A   26 ASP cc_start: 0.7692 (m-30) cc_final: 0.7468 (m-30)
REVERT: A  253 SER cc_start: 0.8712 (t) cc_final: 0.8500 (p)
REVERT: A  271 LYS cc_start: 0.7407 (mmtm) cc_final: 0.6929 (mtpt)
REVERT: A  309 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6720 (tm-30)
REVERT: A  323 MET cc_start: 0.7805 (mmm) cc_final: 0.7538 (mmm)
REVERT: B   49 ARG cc_start: 0.8486 (mmt90) cc_final: 0.8248 (mmt-90)
REVERT: B  133 VAL cc_start: 0.8443 (t) cc_final: 0.8126 (p)
REVERT: B  135 VAL cc_start: 0.8775 (t) cc_final: 0.8526 (p)
REVERT: B  163 ASP cc_start: 0.7665 (p0) cc_final: 0.7442 (p0)
REVERT: B  221 THR cc_start: 0.8572 (m) cc_final: 0.8284 (t)
REVERT: B  251 ARG cc_start: 0.8460 (mtt90) cc_final: 0.8089 (mtp85)
REVERT: B  261 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7908 (mp)
REVERT: B  335 PHE cc_start: 0.8562 (m-80) cc_final: 0.8216 (m-10)
REVERT: G   47 GLU cc_start: 0.7623 (mp0) cc_final: 0.7236 (mp0)
REVERT: G   50 LEU cc_start: 0.7990 (mt) cc_final: 0.7698 (mt)
REVERT: H    6 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7525 (pt0)
REVERT: H   21 SER cc_start: 0.8519 (m) cc_final: 0.8135 (p)
REVERT: H   53 SER cc_start: 0.8302 (m) cc_final: 0.7976 (p)
REVERT: H  215 THR cc_start: 0.8572 (m) cc_final: 0.8287 (t)
  outliers start: 33
  outliers final: 18
  residues processed: 225
  average time/residue: 0.3579
  time to fit residues: 87.6011
Evaluate side-chains
  211 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 188
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   78 SER
Chi-restraints excluded: chain E residue   95 CYS
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain E residue  138 THR
Chi-restraints excluded: chain E residue  145 CYS
Chi-restraints excluded: chain E residue  174 TYR
Chi-restraints excluded: chain E residue  332 THR
Chi-restraints excluded: chain E residue  381 ILE
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  189 ILE
Chi-restraints excluded: chain H residue  243 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 58 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 25 optimal weight:    0.3980
   chunk 59 optimal weight:    0.0980
   chunk 3 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** E  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 196 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.137367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.118180 restraints weight = 12113.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 1.83
r_work: 0.3472 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3339 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8350  Z= 0.168
  Angle     :  0.568   7.366  11399  Z= 0.297
  Chirality :  0.043   0.225   1340
  Planarity :  0.003   0.032   1448
  Dihedral  :  4.655  46.891   1194
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 17.03 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.43 (0.25), residues: 1104
  helix:  1.55 (0.26), residues: 412
  sheet: -0.49 (0.29), residues: 278
  loop : -0.31 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  49 
 TYR   0.015   0.001   TYR H 103 
 PHE   0.025   0.002   PHE E  69 
 TRP   0.009   0.001   TRP E 147 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 8347)
  covalent geometry    : angle       0.56747 (11393)
  SS BOND              : bond        0.00597 (    3)
  SS BOND              : angle       1.25682 (    6)
  hydrogen bonds       : bond        0.03774 (  449)
  hydrogen bonds       : angle       4.91218 ( 1287)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 199
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: E   52 MET cc_start: 0.5629 (mtt) cc_final: 0.5347 (mtp)
REVERT: E   61 PHE cc_start: 0.7878 (m-80) cc_final: 0.7535 (m-80)
REVERT: E   78 SER cc_start: 0.7976 (OUTLIER) cc_final: 0.7749 (p)
REVERT: E   97 LEU cc_start: 0.7359 (tp) cc_final: 0.7091 (tm)
REVERT: E  146 VAL cc_start: 0.8057 (t) cc_final: 0.7849 (t)
REVERT: E  160 TYR cc_start: 0.4928 (t80) cc_final: 0.4679 (t80)
REVERT: E  174 TYR cc_start: 0.6484 (OUTLIER) cc_final: 0.5539 (m-80)
REVERT: A    8 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7542 (pm20)
REVERT: A   21 LYS cc_start: 0.8603 (ttmm) cc_final: 0.8389 (mtpp)
REVERT: A   26 ASP cc_start: 0.7683 (m-30) cc_final: 0.7462 (m-30)
REVERT: A  213 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8343 (tp)
REVERT: A  252 ASP cc_start: 0.8132 (t0) cc_final: 0.7925 (t70)
REVERT: A  271 LYS cc_start: 0.7380 (mmtm) cc_final: 0.6929 (mtpt)
REVERT: A  309 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6594 (tm-30)
REVERT: A  311 LYS cc_start: 0.7618 (mmmt) cc_final: 0.7381 (mmtm)
REVERT: A  323 MET cc_start: 0.7781 (mmm) cc_final: 0.7540 (mmm)
REVERT: B  101 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8243 (mtm)
REVERT: B  133 VAL cc_start: 0.8442 (t) cc_final: 0.8129 (p)
REVERT: B  135 VAL cc_start: 0.8728 (t) cc_final: 0.8497 (p)
REVERT: B  220 GLN cc_start: 0.8766 (mt0) cc_final: 0.8435 (mt0)
REVERT: B  221 THR cc_start: 0.8585 (m) cc_final: 0.8246 (t)
REVERT: B  251 ARG cc_start: 0.8396 (mtt90) cc_final: 0.8042 (mtp85)
REVERT: B  261 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7892 (mp)
REVERT: B  335 PHE cc_start: 0.8495 (m-80) cc_final: 0.8153 (m-10)
REVERT: G   47 GLU cc_start: 0.7661 (mp0) cc_final: 0.7252 (mp0)
REVERT: G   50 LEU cc_start: 0.7967 (mt) cc_final: 0.7641 (mt)
REVERT: H    6 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7497 (pt0)
REVERT: H   21 SER cc_start: 0.8493 (m) cc_final: 0.8115 (p)
REVERT: H   52 SER cc_start: 0.8479 (t) cc_final: 0.8197 (p)
REVERT: H   53 SER cc_start: 0.8328 (m) cc_final: 0.8079 (p)
REVERT: H   59 TYR cc_start: 0.8194 (m-10) cc_final: 0.7971 (m-80)
REVERT: H  100 ILE cc_start: 0.8070 (tp) cc_final: 0.7702 (tp)
REVERT: H  162 SER cc_start: 0.8647 (OUTLIER) cc_final: 0.8419 (p)
REVERT: H  215 THR cc_start: 0.8566 (m) cc_final: 0.8269 (t)
  outliers start: 43
  outliers final: 21
  residues processed: 220
  average time/residue: 0.3478
  time to fit residues: 82.9338
Evaluate side-chains
  220 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 191
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   78 SER
Chi-restraints excluded: chain E residue   95 CYS
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain E residue  138 THR
Chi-restraints excluded: chain E residue  140 PHE
Chi-restraints excluded: chain E residue  145 CYS
Chi-restraints excluded: chain E residue  174 TYR
Chi-restraints excluded: chain E residue  332 THR
Chi-restraints excluded: chain E residue  392 LEU
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  154 SER
Chi-restraints excluded: chain H residue  162 SER
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  189 ILE
Chi-restraints excluded: chain H residue  243 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 107 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0770
   chunk 13 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
** E  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 196 HIS
A 307 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.136295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.117252 restraints weight = 12174.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 1.82
r_work: 0.3453 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3320 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8350  Z= 0.197
  Angle     :  0.578   7.500  11399  Z= 0.301
  Chirality :  0.044   0.197   1340
  Planarity :  0.004   0.043   1448
  Dihedral  :  4.716  46.549   1194
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 18.05 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.33 (0.25), residues: 1104
  helix:  1.45 (0.26), residues: 408
  sheet: -0.62 (0.28), residues: 274
  loop : -0.27 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 283 
 TYR   0.013   0.002   TYR H 103 
 PHE   0.013   0.002   PHE E 164 
 TRP   0.009   0.001   TRP E 147 
 HIS   0.007   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 8347)
  covalent geometry    : angle       0.57715 (11393)
  SS BOND              : bond        0.00598 (    3)
  SS BOND              : angle       1.24164 (    6)
  hydrogen bonds       : bond        0.03826 (  449)
  hydrogen bonds       : angle       4.94118 ( 1287)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 200
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: E   45 LEU cc_start: 0.8039 (tp) cc_final: 0.7834 (tm)
REVERT: E   52 MET cc_start: 0.5573 (mtt) cc_final: 0.5301 (mtt)
REVERT: E   61 PHE cc_start: 0.7883 (m-80) cc_final: 0.7482 (m-80)
REVERT: E   78 SER cc_start: 0.7951 (OUTLIER) cc_final: 0.7733 (p)
REVERT: E   97 LEU cc_start: 0.7429 (tp) cc_final: 0.7167 (tm)
REVERT: E  160 TYR cc_start: 0.5046 (t80) cc_final: 0.4826 (t80)
REVERT: E  174 TYR cc_start: 0.6490 (OUTLIER) cc_final: 0.5580 (m-80)
REVERT: E  392 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8391 (OUTLIER)
REVERT: A    8 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7659 (pm20)
REVERT: A   21 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8380 (mtpp)
REVERT: A   26 ASP cc_start: 0.7632 (m-30) cc_final: 0.7408 (m-30)
REVERT: A  271 LYS cc_start: 0.7379 (mmtm) cc_final: 0.6894 (mtpt)
REVERT: A  309 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6535 (tm-30)
REVERT: A  311 LYS cc_start: 0.7766 (mmmt) cc_final: 0.7472 (mmtm)
REVERT: B  101 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8240 (mtm)
REVERT: B  133 VAL cc_start: 0.8416 (t) cc_final: 0.8124 (p)
REVERT: B  135 VAL cc_start: 0.8725 (t) cc_final: 0.8477 (p)
REVERT: B  220 GLN cc_start: 0.8786 (mt0) cc_final: 0.8463 (mt0)
REVERT: B  221 THR cc_start: 0.8599 (m) cc_final: 0.8282 (t)
REVERT: B  251 ARG cc_start: 0.8355 (mtt90) cc_final: 0.8023 (mtp85)
REVERT: B  261 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7899 (mp)
REVERT: B  335 PHE cc_start: 0.8515 (m-80) cc_final: 0.8186 (m-10)
REVERT: G   47 GLU cc_start: 0.7595 (mp0) cc_final: 0.7217 (mp0)
REVERT: G   50 LEU cc_start: 0.7951 (mt) cc_final: 0.7624 (mt)
REVERT: H    6 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7509 (pt0)
REVERT: H   21 SER cc_start: 0.8463 (m) cc_final: 0.8123 (p)
REVERT: H   53 SER cc_start: 0.8393 (m) cc_final: 0.7961 (p)
REVERT: H   68 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7844 (m-10)
REVERT: H  100 ILE cc_start: 0.8141 (tp) cc_final: 0.7877 (tp)
REVERT: H  215 THR cc_start: 0.8594 (m) cc_final: 0.8283 (t)
  outliers start: 38
  outliers final: 23
  residues processed: 223
  average time/residue: 0.3165
  time to fit residues: 76.7026
Evaluate side-chains
  222 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 192
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   78 SER
Chi-restraints excluded: chain E residue   95 CYS
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain E residue  138 THR
Chi-restraints excluded: chain E residue  145 CYS
Chi-restraints excluded: chain E residue  174 TYR
Chi-restraints excluded: chain E residue  324 THR
Chi-restraints excluded: chain E residue  332 THR
Chi-restraints excluded: chain E residue  392 LEU
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   68 PHE
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  154 SER
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  189 ILE
Chi-restraints excluded: chain H residue  193 SER
Chi-restraints excluded: chain H residue  243 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 100 optimal weight:    0.0070
   chunk 1 optimal weight:   10.0000
   chunk 72 optimal weight:    0.2980
   chunk 77 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 49 optimal weight:    6.9990
   chunk 71 optimal weight:    0.7980
   chunk 39 optimal weight:    0.3980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
** E  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 196 HIS
B  75 GLN
B  91 HIS
H  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.137371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.118401 restraints weight = 12132.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 1.81
r_work: 0.3470 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3337 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8350  Z= 0.151
  Angle     :  0.559   7.282  11399  Z= 0.288
  Chirality :  0.043   0.242   1340
  Planarity :  0.004   0.046   1448
  Dihedral  :  4.606  46.368   1194
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 19.72 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.43 (0.26), residues: 1104
  helix:  1.55 (0.26), residues: 412
  sheet: -0.55 (0.29), residues: 276
  loop : -0.26 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  49 
 TYR   0.013   0.001   TYR H 103 
 PHE   0.025   0.001   PHE E  69 
 TRP   0.009   0.001   TRP E 383 
 HIS   0.006   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8347)
  covalent geometry    : angle       0.55877 (11393)
  SS BOND              : bond        0.00510 (    3)
  SS BOND              : angle       1.06843 (    6)
  hydrogen bonds       : bond        0.03538 (  449)
  hydrogen bonds       : angle       4.84094 ( 1287)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 198
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: E   45 LEU cc_start: 0.8043 (tp) cc_final: 0.7840 (tm)
REVERT: E   52 MET cc_start: 0.5552 (mtt) cc_final: 0.5278 (mtt)
REVERT: E   61 PHE cc_start: 0.7849 (m-80) cc_final: 0.7443 (m-80)
REVERT: E   78 SER cc_start: 0.7927 (OUTLIER) cc_final: 0.7695 (p)
REVERT: E   97 LEU cc_start: 0.7370 (tp) cc_final: 0.7144 (tm)
REVERT: E  160 TYR cc_start: 0.5027 (t80) cc_final: 0.4827 (t80)
REVERT: E  174 TYR cc_start: 0.6369 (OUTLIER) cc_final: 0.5527 (m-80)
REVERT: E  392 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8376 (mt)
REVERT: A    8 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7660 (pm20)
REVERT: A   21 LYS cc_start: 0.8571 (ttmm) cc_final: 0.8365 (mtpp)
REVERT: A   26 ASP cc_start: 0.7670 (m-30) cc_final: 0.7445 (m-30)
REVERT: A  213 ILE cc_start: 0.8685 (tt) cc_final: 0.8324 (tp)
REVERT: A  271 LYS cc_start: 0.7256 (mmtm) cc_final: 0.6847 (mtpt)
REVERT: A  309 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6537 (tm-30)
REVERT: B   90 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8190 (m)
REVERT: B  101 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8192 (mtm)
REVERT: B  133 VAL cc_start: 0.8409 (t) cc_final: 0.8147 (p)
REVERT: B  135 VAL cc_start: 0.8721 (t) cc_final: 0.8486 (p)
REVERT: B  220 GLN cc_start: 0.8896 (mt0) cc_final: 0.8590 (mt0)
REVERT: B  221 THR cc_start: 0.8564 (m) cc_final: 0.8277 (t)
REVERT: B  251 ARG cc_start: 0.8345 (mtt90) cc_final: 0.8010 (mtp85)
REVERT: B  261 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7866 (mp)
REVERT: B  335 PHE cc_start: 0.8471 (m-80) cc_final: 0.8145 (m-10)
REVERT: G   47 GLU cc_start: 0.7624 (mp0) cc_final: 0.7239 (mp0)
REVERT: G   50 LEU cc_start: 0.7963 (mt) cc_final: 0.7660 (mt)
REVERT: H    6 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7451 (pt0)
REVERT: H   21 SER cc_start: 0.8465 (m) cc_final: 0.8104 (p)
REVERT: H   52 SER cc_start: 0.8499 (t) cc_final: 0.8202 (p)
REVERT: H   53 SER cc_start: 0.8354 (m) cc_final: 0.8033 (p)
REVERT: H  215 THR cc_start: 0.8597 (m) cc_final: 0.8284 (t)
  outliers start: 32
  outliers final: 18
  residues processed: 215
  average time/residue: 0.3183
  time to fit residues: 74.3417
Evaluate side-chains
  215 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 189
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   78 SER
Chi-restraints excluded: chain E residue   95 CYS
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain E residue  138 THR
Chi-restraints excluded: chain E residue  145 CYS
Chi-restraints excluded: chain E residue  174 TYR
Chi-restraints excluded: chain E residue  324 THR
Chi-restraints excluded: chain E residue  332 THR
Chi-restraints excluded: chain E residue  392 LEU
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  193 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0970
   chunk 34 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
** E  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 196 HIS
A 307 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.137045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.117999 restraints weight = 12165.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 1.84
r_work: 0.3463 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8350  Z= 0.168
  Angle     :  0.568   7.289  11399  Z= 0.293
  Chirality :  0.043   0.243   1340
  Planarity :  0.004   0.040   1448
  Dihedral  :  4.646  46.523   1194
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 18.69 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.39 (0.26), residues: 1104
  helix:  1.56 (0.26), residues: 408
  sheet: -0.57 (0.29), residues: 275
  loop : -0.31 (0.32), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  49 
 TYR   0.015   0.001   TYR H 103 
 PHE   0.010   0.001   PHE A 336 
 TRP   0.013   0.001   TRP E 383 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 8347)
  covalent geometry    : angle       0.56797 (11393)
  SS BOND              : bond        0.00509 (    3)
  SS BOND              : angle       1.06213 (    6)
  hydrogen bonds       : bond        0.03607 (  449)
  hydrogen bonds       : angle       4.82885 ( 1287)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 199
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: E   45 LEU cc_start: 0.8058 (tp) cc_final: 0.7849 (tm)
REVERT: E   52 MET cc_start: 0.5561 (mtt) cc_final: 0.5271 (mtt)
REVERT: E   61 PHE cc_start: 0.7854 (m-80) cc_final: 0.7246 (m-80)
REVERT: E   78 SER cc_start: 0.7931 (OUTLIER) cc_final: 0.7706 (p)
REVERT: E   97 LEU cc_start: 0.7374 (tp) cc_final: 0.7135 (tm)
REVERT: E  160 TYR cc_start: 0.5028 (t80) cc_final: 0.4810 (t80)
REVERT: E  174 TYR cc_start: 0.6327 (OUTLIER) cc_final: 0.5547 (m-80)
REVERT: E  392 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8225 (mt)
REVERT: A    8 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7559 (pm20)
REVERT: A   21 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8376 (mtpp)
REVERT: A   26 ASP cc_start: 0.7660 (m-30) cc_final: 0.7426 (m-30)
REVERT: A  271 LYS cc_start: 0.7274 (mmtm) cc_final: 0.6855 (mtpt)
REVERT: A  309 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6491 (tm-30)
REVERT: B   90 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8221 (m)
REVERT: B  101 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8203 (mtm)
REVERT: B  133 VAL cc_start: 0.8407 (t) cc_final: 0.8140 (p)
REVERT: B  135 VAL cc_start: 0.8722 (t) cc_final: 0.8475 (p)
REVERT: B  163 ASP cc_start: 0.7327 (p0) cc_final: 0.6977 (p0)
REVERT: B  221 THR cc_start: 0.8625 (m) cc_final: 0.8293 (t)
REVERT: B  251 ARG cc_start: 0.8375 (mtt90) cc_final: 0.8036 (mtp85)
REVERT: B  261 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7876 (mp)
REVERT: B  335 PHE cc_start: 0.8471 (m-80) cc_final: 0.8149 (m-10)
REVERT: G   47 GLU cc_start: 0.7629 (mp0) cc_final: 0.7219 (mp0)
REVERT: G   50 LEU cc_start: 0.8061 (mt) cc_final: 0.7748 (mt)
REVERT: H    6 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7491 (pt0)
REVERT: H   21 SER cc_start: 0.8478 (m) cc_final: 0.8112 (p)
REVERT: H   52 SER cc_start: 0.8484 (t) cc_final: 0.8175 (p)
REVERT: H   53 SER cc_start: 0.8383 (m) cc_final: 0.8045 (p)
REVERT: H  100 ILE cc_start: 0.7951 (tp) cc_final: 0.7735 (tp)
REVERT: H  215 THR cc_start: 0.8593 (m) cc_final: 0.8270 (t)
  outliers start: 41
  outliers final: 21
  residues processed: 219
  average time/residue: 0.3368
  time to fit residues: 80.1621
Evaluate side-chains
  224 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 195
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   78 SER
Chi-restraints excluded: chain E residue   95 CYS
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain E residue  138 THR
Chi-restraints excluded: chain E residue  174 TYR
Chi-restraints excluded: chain E residue  324 THR
Chi-restraints excluded: chain E residue  332 THR
Chi-restraints excluded: chain E residue  392 LEU
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  154 SER
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  193 SER
Chi-restraints excluded: chain H residue  243 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0970
   chunk 52 optimal weight:    0.0870
   chunk 46 optimal weight:    0.0970
   chunk 41 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.3154

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

Flipped N/Q/H residues before XYZ refinement:
** E  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 196 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.138235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.119424 restraints weight = 12097.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 1.80
r_work: 0.3486 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8350  Z= 0.128
  Angle     :  0.548   7.565  11399  Z= 0.282
  Chirality :  0.042   0.254   1340
  Planarity :  0.003   0.040   1448
  Dihedral  :  4.535  46.716   1194
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 21.90 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.44 (0.26), residues: 1104
  helix:  1.63 (0.26), residues: 408
  sheet: -0.62 (0.29), residues: 277
  loop : -0.25 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  49 
 TYR   0.012   0.001   TYR H 190 
 PHE   0.011   0.001   PHE E  77 
 TRP   0.014   0.001   TRP E 383 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8347)
  covalent geometry    : angle       0.54810 (11393)
  SS BOND              : bond        0.00433 (    3)
  SS BOND              : angle       0.95488 (    6)
  hydrogen bonds       : bond        0.03341 (  449)
  hydrogen bonds       : angle       4.72057 ( 1287)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 202
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: E   52 MET cc_start: 0.5519 (mtt) cc_final: 0.5242 (mtt)
REVERT: E   61 PHE cc_start: 0.7845 (m-80) cc_final: 0.7407 (m-80)
REVERT: E   78 SER cc_start: 0.7925 (OUTLIER) cc_final: 0.7715 (p)
REVERT: E   97 LEU cc_start: 0.7333 (tp) cc_final: 0.7122 (tm)
REVERT: E  174 TYR cc_start: 0.6184 (OUTLIER) cc_final: 0.5389 (m-80)
REVERT: E  392 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8215 (mt)
REVERT: A    8 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7531 (pm20)
REVERT: A   21 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8383 (mtpp)
REVERT: A   26 ASP cc_start: 0.7630 (m-30) cc_final: 0.7394 (m-30)
REVERT: A  209 ARG cc_start: 0.8178 (mtm110) cc_final: 0.7772 (mtm110)
REVERT: A  271 LYS cc_start: 0.7270 (mmtm) cc_final: 0.6904 (mtpt)
REVERT: A  303 TYR cc_start: 0.7023 (t80) cc_final: 0.6717 (t80)
REVERT: A  309 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6540 (tm-30)
REVERT: A  323 MET cc_start: 0.7833 (mmm) cc_final: 0.7522 (mmm)
REVERT: B   90 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.8223 (m)
REVERT: B  101 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8211 (mtm)
REVERT: B  133 VAL cc_start: 0.8411 (t) cc_final: 0.8162 (p)
REVERT: B  135 VAL cc_start: 0.8696 (t) cc_final: 0.8458 (p)
REVERT: B  139 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7721 (mt)
REVERT: B  163 ASP cc_start: 0.7280 (p0) cc_final: 0.6957 (p0)
REVERT: B  220 GLN cc_start: 0.8741 (mt0) cc_final: 0.8418 (mt0)
REVERT: B  221 THR cc_start: 0.8660 (m) cc_final: 0.8354 (t)
REVERT: B  251 ARG cc_start: 0.8298 (mtt90) cc_final: 0.7997 (mtp85)
REVERT: B  261 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7850 (mp)
REVERT: B  335 PHE cc_start: 0.8435 (m-80) cc_final: 0.8115 (m-10)
REVERT: G   47 GLU cc_start: 0.7622 (mp0) cc_final: 0.7241 (mp0)
REVERT: G   50 LEU cc_start: 0.8042 (mt) cc_final: 0.7726 (mt)
REVERT: H   21 SER cc_start: 0.8431 (m) cc_final: 0.8069 (p)
REVERT: H   52 SER cc_start: 0.8378 (t) cc_final: 0.8082 (p)
REVERT: H   53 SER cc_start: 0.8349 (m) cc_final: 0.8061 (p)
REVERT: H  194 ASN cc_start: 0.8667 (m-40) cc_final: 0.8284 (m110)
REVERT: H  215 THR cc_start: 0.8593 (m) cc_final: 0.8275 (t)
  outliers start: 27
  outliers final: 16
  residues processed: 217
  average time/residue: 0.3093
  time to fit residues: 72.8903
Evaluate side-chains
  227 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 203
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   78 SER
Chi-restraints excluded: chain E residue   95 CYS
Chi-restraints excluded: chain E residue  138 THR
Chi-restraints excluded: chain E residue  174 TYR
Chi-restraints excluded: chain E residue  324 THR
Chi-restraints excluded: chain E residue  332 THR
Chi-restraints excluded: chain E residue  392 LEU
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  193 SER
Chi-restraints excluded: chain H residue  243 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 86 optimal weight:    0.3980
   chunk 75 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 94 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** E  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 196 HIS
A 307 GLN
H  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.136567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.117809 restraints weight = 12053.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 1.82
r_work: 0.3464 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3332 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8350  Z= 0.197
  Angle     :  0.591   8.073  11399  Z= 0.305
  Chirality :  0.044   0.262   1340
  Planarity :  0.003   0.033   1448
  Dihedral  :  4.709  47.174   1194
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 21.77 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.30 (0.26), residues: 1104
  helix:  1.46 (0.26), residues: 408
  sheet: -0.62 (0.29), residues: 283
  loop : -0.33 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  49 
 TYR   0.013   0.002   TYR G  40 
 PHE   0.026   0.002   PHE E  69 
 TRP   0.014   0.001   TRP E 383 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 8347)
  covalent geometry    : angle       0.59058 (11393)
  SS BOND              : bond        0.00559 (    3)
  SS BOND              : angle       1.06941 (    6)
  hydrogen bonds       : bond        0.03710 (  449)
  hydrogen bonds       : angle       4.84748 ( 1287)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 195
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: E   52 MET cc_start: 0.5574 (mtt) cc_final: 0.5293 (mtt)
REVERT: E   61 PHE cc_start: 0.7848 (m-80) cc_final: 0.7249 (m-80)
REVERT: E   97 LEU cc_start: 0.7384 (tp) cc_final: 0.7145 (tm)
REVERT: E  174 TYR cc_start: 0.6383 (OUTLIER) cc_final: 0.5430 (m-80)
REVERT: E  392 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8254 (mt)
REVERT: A    8 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7580 (pm20)
REVERT: A   26 ASP cc_start: 0.7632 (m-30) cc_final: 0.7391 (m-30)
REVERT: A  271 LYS cc_start: 0.7418 (mmtm) cc_final: 0.6927 (mtpt)
REVERT: A  309 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6498 (tm-30)
REVERT: B   90 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8243 (m)
REVERT: B  101 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8232 (mtm)
REVERT: B  133 VAL cc_start: 0.8410 (t) cc_final: 0.8144 (p)
REVERT: B  135 VAL cc_start: 0.8700 (t) cc_final: 0.8467 (p)
REVERT: B  163 ASP cc_start: 0.7360 (p0) cc_final: 0.7011 (p0)
REVERT: B  220 GLN cc_start: 0.8738 (mt0) cc_final: 0.8368 (mt0)
REVERT: B  221 THR cc_start: 0.8658 (m) cc_final: 0.8343 (t)
REVERT: B  251 ARG cc_start: 0.8373 (mtt90) cc_final: 0.8043 (mtp85)
REVERT: B  261 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7880 (mp)
REVERT: B  335 PHE cc_start: 0.8480 (m-80) cc_final: 0.8181 (m-10)
REVERT: G   47 GLU cc_start: 0.7657 (mp0) cc_final: 0.7248 (mp0)
REVERT: G   50 LEU cc_start: 0.8060 (mt) cc_final: 0.7752 (mt)
REVERT: H    6 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7391 (pt0)
REVERT: H   21 SER cc_start: 0.8517 (m) cc_final: 0.8149 (p)
REVERT: H   52 SER cc_start: 0.8391 (t) cc_final: 0.8042 (p)
REVERT: H   53 SER cc_start: 0.8403 (m) cc_final: 0.8052 (p)
REVERT: H  139 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8458 (t)
REVERT: H  215 THR cc_start: 0.8595 (m) cc_final: 0.8276 (t)
  outliers start: 30
  outliers final: 18
  residues processed: 212
  average time/residue: 0.4370
  time to fit residues: 100.3844
Evaluate side-chains
  224 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 198
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   95 CYS
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain E residue  138 THR
Chi-restraints excluded: chain E residue  140 PHE
Chi-restraints excluded: chain E residue  174 TYR
Chi-restraints excluded: chain E residue  324 THR
Chi-restraints excluded: chain E residue  392 LEU
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  154 SER
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  189 ILE
Chi-restraints excluded: chain H residue  193 SER
Chi-restraints excluded: chain H residue  243 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 78 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 48 optimal weight:    0.4980
   chunk 65 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 37 optimal weight:    0.2980
   chunk 4 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** E  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 196 HIS
A 307 GLN
H  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.136812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.118115 restraints weight = 12093.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 1.80
r_work: 0.3469 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3337 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.2940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8350  Z= 0.176
  Angle     :  0.610  11.569  11399  Z= 0.308
  Chirality :  0.044   0.266   1340
  Planarity :  0.003   0.033   1448
  Dihedral  :  4.704  44.466   1194
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 22.92 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.30 (0.26), residues: 1104
  helix:  1.40 (0.26), residues: 409
  sheet: -0.58 (0.29), residues: 277
  loop : -0.31 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  49 
 TYR   0.012   0.001   TYR G  40 
 PHE   0.013   0.001   PHE E  77 
 TRP   0.019   0.001   TRP E 383 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 8347)
  covalent geometry    : angle       0.60911 (11393)
  SS BOND              : bond        0.00576 (    3)
  SS BOND              : angle       1.32180 (    6)
  hydrogen bonds       : bond        0.03638 (  449)
  hydrogen bonds       : angle       4.85420 ( 1287)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 194
  time to evaluate  : 0.251 
Fit side-chains
REVERT: E   52 MET cc_start: 0.5600 (mtt) cc_final: 0.5309 (mtt)
REVERT: E   61 PHE cc_start: 0.7854 (m-80) cc_final: 0.7248 (m-80)
REVERT: E   97 LEU cc_start: 0.7421 (tp) cc_final: 0.7163 (tm)
REVERT: E  140 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7722 (t80)
REVERT: E  174 TYR cc_start: 0.6212 (OUTLIER) cc_final: 0.5229 (m-80)
REVERT: E  335 VAL cc_start: 0.8092 (t) cc_final: 0.7867 (p)
REVERT: E  392 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8294 (mt)
REVERT: A    8 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7591 (pm20)
REVERT: A   26 ASP cc_start: 0.7633 (m-30) cc_final: 0.7393 (m-30)
REVERT: A  209 ARG cc_start: 0.8212 (mtm110) cc_final: 0.7808 (mtm110)
REVERT: A  271 LYS cc_start: 0.7430 (mmtm) cc_final: 0.6988 (mtpt)
REVERT: A  303 TYR cc_start: 0.7064 (t80) cc_final: 0.6717 (t80)
REVERT: A  309 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6476 (tm-30)
REVERT: B   90 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8256 (m)
REVERT: B  101 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8228 (mtm)
REVERT: B  133 VAL cc_start: 0.8389 (t) cc_final: 0.8134 (p)
REVERT: B  135 VAL cc_start: 0.8690 (t) cc_final: 0.8465 (p)
REVERT: B  163 ASP cc_start: 0.7389 (p0) cc_final: 0.7017 (p0)
REVERT: B  220 GLN cc_start: 0.8736 (mt0) cc_final: 0.8400 (mt0)
REVERT: B  221 THR cc_start: 0.8644 (m) cc_final: 0.8343 (t)
REVERT: B  251 ARG cc_start: 0.8349 (mtt90) cc_final: 0.8024 (mtp85)
REVERT: B  261 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7870 (mp)
REVERT: B  335 PHE cc_start: 0.8500 (m-80) cc_final: 0.8214 (m-10)
REVERT: G   47 GLU cc_start: 0.7635 (mp0) cc_final: 0.7232 (mp0)
REVERT: G   50 LEU cc_start: 0.8061 (mt) cc_final: 0.7767 (mt)
REVERT: H    6 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7363 (pt0)
REVERT: H   21 SER cc_start: 0.8503 (m) cc_final: 0.8146 (p)
REVERT: H   52 SER cc_start: 0.8494 (t) cc_final: 0.8170 (p)
REVERT: H   53 SER cc_start: 0.8422 (m) cc_final: 0.8043 (p)
REVERT: H  139 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8463 (t)
REVERT: H  215 THR cc_start: 0.8593 (m) cc_final: 0.8276 (t)
  outliers start: 28
  outliers final: 17
  residues processed: 210
  average time/residue: 0.4026
  time to fit residues: 91.7641
Evaluate side-chains
  220 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 194
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  138 THR
Chi-restraints excluded: chain E residue  140 PHE
Chi-restraints excluded: chain E residue  174 TYR
Chi-restraints excluded: chain E residue  324 THR
Chi-restraints excluded: chain E residue  392 LEU
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  247 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  154 SER
Chi-restraints excluded: chain H residue  187 LEU
Chi-restraints excluded: chain H residue  189 ILE
Chi-restraints excluded: chain H residue  193 SER
Chi-restraints excluded: chain H residue  243 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 72 optimal weight:    0.0980
   chunk 38 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 82 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** E  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 196 HIS
H  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.136511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.117917 restraints weight = 11995.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 1.79
r_work: 0.3467 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8350  Z= 0.194
  Angle     :  0.623  10.547  11399  Z= 0.316
  Chirality :  0.045   0.266   1340
  Planarity :  0.004   0.041   1448
  Dihedral  :  4.717  46.037   1193
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 22.66 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: 1104
  helix:  1.34 (0.26), residues: 409
  sheet: -0.46 (0.30), residues: 278
  loop : -0.37 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  49 
 TYR   0.013   0.002   TYR G  40 
 PHE   0.027   0.002   PHE E  69 
 TRP   0.018   0.002   TRP E 383 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 8347)
  covalent geometry    : angle       0.62202 (11393)
  SS BOND              : bond        0.00620 (    3)
  SS BOND              : angle       1.58139 (    6)
  hydrogen bonds       : bond        0.03749 (  449)
  hydrogen bonds       : angle       4.93518 ( 1287)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2925.89 seconds
wall clock time: 50 minutes 35.03 seconds (3035.03 seconds total)