Starting phenix.real_space_refine
on Sat Jan 18 17:02:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rb9_19029/01_2025/8rb9_19029.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rb9_19029/01_2025/8rb9_19029.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rb9_19029/01_2025/8rb9_19029.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rb9_19029/01_2025/8rb9_19029.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rb9_19029/01_2025/8rb9_19029.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rb9_19029/01_2025/8rb9_19029.cif"
  }
  resolution = 3.19
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.015
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: 6
    Type Number    sf(0)   Gaussians
     Fe     18      7.16       5
     P       4      5.49       5
     S      97      5.16       5
     C    8203      2.51       5
     N    2067      2.21       5
     O    2354      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 12743
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 1394
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1394
          Classifications: {'peptide': 189}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 179}
    Chain: "C"
      Number of atoms: 3511
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 476, 3511
          Classifications: {'peptide': 476}
          Link IDs: {'PTRANS': 37, 'TRANS': 438}
    Chain: "D"
      Number of atoms: 2629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2629
          Classifications: {'peptide': 349}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 325}
    Chain: "E"
      Number of atoms: 1601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1601
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 203}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "G"
      Number of atoms: 1489
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1489
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 6, 'TRANS': 188}
    Chain: "H"
      Number of atoms: 548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 548
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 4, 'TRANS': 66}
    Chain: "B"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 807
          Classifications: {'peptide': 112}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 106}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 124
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 124
          Unusual residues: {'FES': 1, 'LMT': 2, 'PTY': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 47
          Unusual residues: {'FMN': 1, 'SF4': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 442
          Unusual residues: {'FMN': 1, 'LMT': 11, 'RBF': 1}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
    Chain: "E"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 105
          Unusual residues: {'LMT': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "G"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'FMN': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
    Chain: "B"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {'SF4': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    184  SG  CYS A  25      37.800  81.555  53.659  1.00 55.48           S
  ATOM   8343  SG  CYS E 122      39.152  78.652  51.663  1.00 81.30           S
  ATOM    844  SG  CYS A 113      41.722  82.081  48.664  1.00 63.79           S
  ATOM   7734  SG  CYS E  39      40.476  84.999  51.135  1.00 69.20           S
  ATOM   4124  SG  CYS C 376      42.296  92.711  92.548  1.00 44.59           S
  ATOM   4439  SG  CYS C 419      37.916  94.279  93.154  1.00 26.17           S
  ATOM   4082  SG  CYS C 370      39.028  93.363  86.489  1.00 27.74           S
  ATOM   4107  SG  CYS C 373      41.835  98.038  90.225  1.00 31.60           S
  ATOM   4370  SG  CYS C 409      43.613  82.286  97.462  1.00 36.12           S
  ATOM   4392  SG  CYS C 412      45.419  87.269 101.448  1.00 30.47           S
  ATOM   4408  SG  CYS C 415      43.048  88.555  96.202  1.00 36.09           S
  ATOM   4150  SG  CYS C 380      48.328  87.195  96.044  1.00 37.59           S
  ATOM  11572  SG  CYS B 119      27.592  44.867  96.228  1.00 71.98           S
  ATOM  11745  SG  CYS B 145      22.006  46.170  96.213  1.00 82.52           S
  ATOM  11726  SG  CYS B 142      26.078  48.099  91.350  1.00 74.81           S
  ATOM  11709  SG  CYS B 139      25.334  51.568  96.502  1.00 42.56           S
  ATOM  11496  SG  CYS B 109      19.456  40.963 105.636  1.00 91.32           S
  ATOM  11514  SG  CYS B 112      18.525  36.556 100.470  1.00 87.95           S
  ATOM  11538  SG  CYS B 115      22.899  41.220 100.778  1.00 80.72           S
  ATOM  11775  SG  CYS B 149      16.079  41.125  99.925  1.00 99.88           S

  Time building chain proxies: 7.79, per 1000 atoms: 0.61
  Number of scatterers: 12743
  At special positions: 0
  Unit cell: (82.82, 150.06, 150.06, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe     18     26.01
     S      97     16.00
     P       4     15.00
     O    2354      8.00
     N    2067      7.00
     C    8203      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.59
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" FES A 201 "
        pdb="FE1  FES A 201 " - pdb=" SG  CYS A  25 "
        pdb="FE1  FES A 201 " - pdb=" SG  CYS E 122 "
        pdb="FE2  FES A 201 " - pdb=" SG  CYS A 113 "
        pdb="FE2  FES A 201 " - pdb=" SG  CYS E  39 "
      pdb=" SF4 B 201 "
        pdb="FE3  SF4 B 201 " - pdb=" SG  CYS B 142 "
        pdb="FE2  SF4 B 201 " - pdb=" SG  CYS B 145 "
        pdb="FE4  SF4 B 201 " - pdb=" SG  CYS B 139 "
        pdb="FE1  SF4 B 201 " - pdb=" SG  CYS B 119 "
      pdb=" SF4 B 202 "
        pdb="FE2  SF4 B 202 " - pdb=" SG  CYS B 112 "
        pdb="FE3  SF4 B 202 " - pdb=" SG  CYS B 115 "
        pdb="FE1  SF4 B 202 " - pdb=" SG  CYS B 109 "
        pdb="FE4  SF4 B 202 " - pdb=" SG  CYS B 149 "
      pdb=" SF4 C 501 "
        pdb="FE1  SF4 C 501 " - pdb=" SG  CYS C 376 "
        pdb="FE2  SF4 C 501 " - pdb=" SG  CYS C 419 "
        pdb="FE3  SF4 C 501 " - pdb=" SG  CYS C 370 "
        pdb="FE4  SF4 C 501 " - pdb=" SG  CYS C 373 "
      pdb=" SF4 C 502 "
        pdb="FE3  SF4 C 502 " - pdb=" SG  CYS C 415 "
        pdb="FE2  SF4 C 502 " - pdb=" SG  CYS C 412 "
        pdb="FE1  SF4 C 502 " - pdb=" SG  CYS C 409 "
        pdb="FE4  SF4 C 502 " - pdb=" SG  CYS C 380 "
      Number of angles added : 54


  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2900

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 11 sheets defined
      54.3% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 12
      removed outlier: 3.681A  pdb=" N   PHE A   6 " --> pdb=" O   GLU A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 31
      removed outlier: 3.700A  pdb=" N   PHE A  27 " --> pdb=" O   GLY A  23 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER A  31 " --> pdb=" O   PHE A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 62
      removed outlier: 3.665A  pdb=" N   SER A  37 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 67
    Processing helix  chain 'A' and resid 71 through 90
    Processing helix  chain 'A' and resid 105 through 110
      removed outlier: 3.540A  pdb=" N   THR A 110 " --> pdb=" O   PRO A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 126
      Proline residue:  A 119  - end of helix
      removed outlier: 3.510A  pdb=" N   ARG A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 158
    Processing helix  chain 'A' and resid 168 through 184
    Processing helix  chain 'A' and resid 185 through 187
      No H-bonds generated for 'chain 'A' and resid 185 through 187'
    Processing helix  chain 'C' and resid 124 through 134
      removed outlier: 3.557A  pdb=" N   LEU C 128 " --> pdb=" O   ASP C 124 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 146 through 157
      removed outlier: 3.543A  pdb=" N   LYS C 150 " --> pdb=" O   PRO C 146 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ARG C 156 " --> pdb=" O   LYS C 152 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   HIS C 157 " --> pdb=" O   GLN C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 174 through 183
    Processing helix  chain 'C' and resid 183 through 198
    Processing helix  chain 'C' and resid 211 through 222
    Processing helix  chain 'C' and resid 236 through 240
      removed outlier: 4.036A  pdb=" N   GLY C 240 " --> pdb=" O   TYR C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 241 through 250
      removed outlier: 3.610A  pdb=" N   GLN C 247 " --> pdb=" O   LYS C 243 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 263
    Processing helix  chain 'C' and resid 270 through 283
      removed outlier: 3.796A  pdb=" N   TYR C 274 " --> pdb=" O   ALA C 270 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 311 through 319
      removed outlier: 3.720A  pdb=" N   LEU C 315 " --> pdb=" O   PRO C 311 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 395
    Processing helix  chain 'C' and resid 397 through 404
      removed outlier: 3.649A  pdb=" N   TYR C 404 " --> pdb=" O   GLY C 400 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 415 through 419
      removed outlier: 3.891A  pdb=" N   CYS C 419 " --> pdb=" O   SER C 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 424 through 478
    Processing helix  chain 'D' and resid 17 through 41
      Proline residue:  D  31  - end of helix
    Processing helix  chain 'D' and resid 41 through 67
      removed outlier: 3.570A  pdb=" N   ILE D  45 " --> pdb=" O   GLY D  41 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 69 through 75
      removed outlier: 3.758A  pdb=" N   ASP D  75 " --> pdb=" O   ARG D  72 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 76 through 89
      removed outlier: 3.608A  pdb=" N   THR D  81 " --> pdb=" O   SER D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 106
      removed outlier: 3.752A  pdb=" N   GLY D  98 " --> pdb=" O   PRO D  94 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 110 through 114
      removed outlier: 3.627A  pdb=" N   GLY D 114 " --> pdb=" O   GLN D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 122 through 135
    Processing helix  chain 'D' and resid 155 through 164
    Processing helix  chain 'D' and resid 178 through 188
    Processing helix  chain 'D' and resid 191 through 198
      removed outlier: 3.613A  pdb=" N   ILE D 195 " --> pdb=" O   THR D 191 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LEU D 196 " --> pdb=" O   ALA D 192 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLY D 198 " --> pdb=" O   GLU D 194 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 201 through 208
    Processing helix  chain 'D' and resid 220 through 232
    Processing helix  chain 'D' and resid 237 through 258
    Processing helix  chain 'D' and resid 265 through 270
    Processing helix  chain 'D' and resid 273 through 281
    Processing helix  chain 'D' and resid 292 through 312
    Processing helix  chain 'D' and resid 318 through 337
      Proline residue:  D 331  - end of helix
    Processing helix  chain 'E' and resid 17 through 27
      removed outlier: 4.338A  pdb=" N   PHE E  21 " --> pdb=" O   PRO E  17 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU E  25 " --> pdb=" O   PHE E  21 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   TRP E  26 " --> pdb=" O   THR E  22 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 37 through 44
      removed outlier: 3.528A  pdb=" N   THR E  41 " --> pdb=" O   ALA E  37 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 47 through 72
    Processing helix  chain 'E' and resid 73 through 76
      removed outlier: 3.728A  pdb=" N   ILE E  76 " --> pdb=" O   ARG E  73 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 73 through 76'
    Processing helix  chain 'E' and resid 80 through 104
      removed outlier: 3.920A  pdb=" N   VAL E  92 " --> pdb=" O   VAL E  88 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ALA E 102 " --> pdb=" O   MET E  98 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 104 through 112
      removed outlier: 3.650A  pdb=" N   VAL E 110 " --> pdb=" O   GLU E 106 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 121 through 131
    Processing helix  chain 'E' and resid 136 through 168
    Processing helix  chain 'E' and resid 173 through 179
      removed outlier: 3.667A  pdb=" N   LEU E 177 " --> pdb=" O   GLN E 173 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 180 through 186
      removed outlier: 4.481A  pdb=" N   TRP E 184 " --> pdb=" O   HIS E 181 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 202 through 228
      removed outlier: 3.866A  pdb=" N   PHE E 206 " --> pdb=" O   PRO E 202 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ILE E 207 " --> pdb=" O   PRO E 203 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   VAL E 208 " --> pdb=" O   GLY E 204 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 35 through 79
      removed outlier: 3.542A  pdb=" N   GLY G  40 " --> pdb=" O   VAL G  36 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   CYS G  47 " --> pdb=" O   LEU G  43 " (cutoff:3.500A)
      removed outlier: 5.484A  pdb=" N   GLY G  63 " --> pdb=" O   ILE G  59 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   THR G  64 " --> pdb=" O   MET G  60 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLU G  79 " --> pdb=" O   ALA G  75 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 82 through 86
    Processing helix  chain 'G' and resid 89 through 93
      removed outlier: 3.826A  pdb=" N   ASP G  93 " --> pdb=" O   PRO G  90 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 168 through 172
    Processing helix  chain 'G' and resid 202 through 222
    Processing helix  chain 'H' and resid 25 through 34
    Processing helix  chain 'H' and resid 34 through 39
      removed outlier: 3.689A  pdb=" N   CYS H  38 " --> pdb=" O   GLY H  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 26
      removed outlier: 3.613A  pdb=" N   MET B  11 " --> pdb=" O   ALA B   7 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLY B  12 " --> pdb=" O   LEU B   8 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLY B  16 " --> pdb=" O   GLY B  12 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LEU B  19 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 85
      removed outlier: 3.549A  pdb=" N   LYS B  82 " --> pdb=" O   GLY B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 118
    Processing helix  chain 'B' and resid 162 through 166
    Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 28
    Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 38
      removed outlier: 3.652A  pdb=" N   ALA C  84 " --> pdb=" O   VAL C 102 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   GLU C 104 " --> pdb=" O   ILE C  82 " (cutoff:3.500A)
      removed outlier: 5.822A  pdb=" N   ILE C  82 " --> pdb=" O   GLU C 104 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 38
    Processing sheet with id=AA4, first strand: chain 'C' and resid 48 through 49
    Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 165
    Processing sheet with id=AA6, first strand: chain 'C' and resid 206 through 208
    Processing sheet with id=AA7, first strand: chain 'C' and resid 328 through 330
    Processing sheet with id=AA8, first strand: chain 'E' and resid 169 through 170
    Processing sheet with id=AA9, first strand: chain 'G' and resid 108 through 111
      removed outlier: 3.627A  pdb=" N   ALA G 118 " --> pdb=" O   ALA G 110 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   GLU G 133 " --> pdb=" O   LEU G 150 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLY G 146 " --> pdb=" O   SER G 137 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ASP G 139 " --> pdb=" O   ILE G 144 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ILE G 144 " --> pdb=" O   ASP G 139 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 14 through 18
      removed outlier: 6.214A  pdb=" N   SER H   4 " --> pdb=" O   ILE H  68 " (cutoff:3.500A)
      removed outlier: 7.894A  pdb=" N   ILE H  70 " --> pdb=" O   SER H   4 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   VAL H   6 " --> pdb=" O   ILE H  70 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 100 through 101

    641 hydrogen bonds defined for protein.
    1821 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: 3.32

  Time building geometry restraints manager: 3.97 seconds

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

  Histogram of bond lengths:
        1.20 -     1.42: 5097
        1.42 -     1.63: 7750
        1.63 -     1.85: 123
        1.85 -     2.07: 0
        2.07 -     2.28: 52
  Bond restraints: 13022
  Sorted by residual:
  bond pdb=" O5' FMN C 500 "
       pdb=" P   FMN C 500 "
    ideal  model  delta    sigma   weight residual
    1.610  1.817 -0.207 2.00e-02 2.50e+03 1.07e+02
  bond pdb=" C10 FMN C 500 "
       pdb=" C4A FMN C 500 "
    ideal  model  delta    sigma   weight residual
    1.390  1.479 -0.089 2.00e-02 2.50e+03 1.96e+01
  bond pdb=" C4A FMN C 500 "
       pdb=" N5  FMN C 500 "
    ideal  model  delta    sigma   weight residual
    1.380  1.294  0.086 2.00e-02 2.50e+03 1.84e+01
  bond pdb=" C4A FMN D 413 "
       pdb=" N5  FMN D 413 "
    ideal  model  delta    sigma   weight residual
    1.380  1.300  0.080 2.00e-02 2.50e+03 1.60e+01
  bond pdb=" C4A FMN G 301 "
       pdb=" N5  FMN G 301 "
    ideal  model  delta    sigma   weight residual
    1.380  1.301  0.079 2.00e-02 2.50e+03 1.57e+01
  ... (remaining 13017 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.88: 17353
        2.88 -     5.76: 281
        5.76 -     8.65: 59
        8.65 -    11.53: 27
       11.53 -    14.41: 1
  Bond angle restraints: 17721
  Sorted by residual:
  angle pdb=" C2' FMN C 500 "
        pdb=" C1' FMN C 500 "
        pdb=" N10 FMN C 500 "
      ideal   model   delta    sigma   weight residual
     109.47  123.88  -14.41 3.00e+00 1.11e-01 2.31e+01
  angle pdb=" C   ASN A 112 "
        pdb=" N   CYS A 113 "
        pdb=" CA  CYS A 113 "
      ideal   model   delta    sigma   weight residual
     121.54  129.22   -7.68 1.91e+00 2.74e-01 1.62e+01
  angle pdb=" N   THR G 202 "
        pdb=" CA  THR G 202 "
        pdb=" C   THR G 202 "
      ideal   model   delta    sigma   weight residual
     114.04  109.15    4.89 1.24e+00 6.50e-01 1.55e+01
  angle pdb=" C   ALA D 170 "
        pdb=" CA  ALA D 170 "
        pdb=" CB  ALA D 170 "
      ideal   model   delta    sigma   weight residual
     115.89  110.74    5.15 1.32e+00 5.74e-01 1.52e+01
  angle pdb=" O1P FMN C 500 "
        pdb=" P   FMN C 500 "
        pdb=" O5' FMN C 500 "
      ideal   model   delta    sigma   weight residual
     108.20   97.96   10.24 3.00e+00 1.11e-01 1.17e+01
  ... (remaining 17716 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.17: 8003
       34.17 -    68.35: 230
       68.35 -   102.52: 87
      102.52 -   136.70: 43
      136.70 -   170.87: 2
  Dihedral angle restraints: 8365
    sinusoidal: 3836
      harmonic: 4529
  Sorted by residual:
  dihedral pdb=" C10 FMN D 413 "
           pdb=" C1' FMN D 413 "
           pdb=" N10 FMN D 413 "
           pdb=" C2' FMN D 413 "
      ideal   model   delta sinusoidal    sigma   weight residual
     257.59   86.72  170.87     1      2.00e+01 2.50e-03 4.77e+01
  dihedral pdb=" C5' FMN G 301 "
           pdb=" O5' FMN G 301 "
           pdb=" P   FMN G 301 "
           pdb=" O1P FMN G 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
      75.26 -143.02 -141.72     1      2.00e+01 2.50e-03 4.28e+01
  dihedral pdb=" C5' FMN C 500 "
           pdb=" O5' FMN C 500 "
           pdb=" P   FMN C 500 "
           pdb=" O1P FMN C 500 "
      ideal   model   delta sinusoidal    sigma   weight residual
      75.26  -49.69  124.95     1      2.00e+01 2.50e-03 3.77e+01
  ... (remaining 8362 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.004: 2164
       1.004 -    2.008: 0
       2.008 -    3.013: 0
       3.013 -    4.017: 0
       4.017 -    5.021: 4
  Chirality restraints: 2168
  Sorted by residual:
  chirality pdb=" C2' FMN G 301 "
            pdb=" C1' FMN G 301 "
            pdb=" C3' FMN G 301 "
            pdb=" O2' FMN G 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47    2.55   -5.02 2.00e-01 2.50e+01 6.30e+02
  chirality pdb=" CB  THR G 202 "
            pdb=" CA  THR G 202 "
            pdb=" OG1 THR G 202 "
            pdb=" CG2 THR G 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55   -2.45    5.00 2.00e-01 2.50e+01 6.26e+02
  chirality pdb=" C4' FMN D 413 "
            pdb=" C3' FMN D 413 "
            pdb=" C5' FMN D 413 "
            pdb=" O4' FMN D 413 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47    2.42   -4.89 2.00e-01 2.50e+01 5.98e+02
  ... (remaining 2165 not shown)

  Planarity restraints: 2121
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' FMN G 301 "    0.097 2.00e-02 2.50e+03   2.73e-02 3.54e+01
        pdb=" C10 FMN G 301 "   -0.019 2.00e-02 2.50e+03
        pdb=" C2  FMN G 301 "   -0.009 2.00e-02 2.50e+03
        pdb=" C4  FMN G 301 "    0.008 2.00e-02 2.50e+03
        pdb=" C4A FMN G 301 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5A FMN G 301 "   -0.013 2.00e-02 2.50e+03
        pdb=" C6  FMN G 301 "    0.001 2.00e-02 2.50e+03
        pdb=" C7  FMN G 301 "    0.004 2.00e-02 2.50e+03
        pdb=" C7M FMN G 301 "    0.024 2.00e-02 2.50e+03
        pdb=" C8  FMN G 301 "   -0.006 2.00e-02 2.50e+03
        pdb=" C8M FMN G 301 "   -0.017 2.00e-02 2.50e+03
        pdb=" C9  FMN G 301 "   -0.019 2.00e-02 2.50e+03
        pdb=" C9A FMN G 301 "   -0.021 2.00e-02 2.50e+03
        pdb=" N1  FMN G 301 "   -0.022 2.00e-02 2.50e+03
        pdb=" N10 FMN G 301 "   -0.014 2.00e-02 2.50e+03
        pdb=" N3  FMN G 301 "    0.005 2.00e-02 2.50e+03
        pdb=" N5  FMN G 301 "   -0.010 2.00e-02 2.50e+03
        pdb=" O2  FMN G 301 "   -0.015 2.00e-02 2.50e+03
        pdb=" O4  FMN G 301 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA G 223 "   -0.018 2.00e-02 2.50e+03   3.55e-02 1.26e+01
        pdb=" C   ALA G 223 "    0.061 2.00e-02 2.50e+03
        pdb=" O   ALA G 223 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   GLU G 224 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' FMN D 413 "    0.028 2.00e-02 2.50e+03   1.15e-02 6.28e+00
        pdb=" C10 FMN D 413 "    0.004 2.00e-02 2.50e+03
        pdb=" C2  FMN D 413 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4  FMN D 413 "    0.001 2.00e-02 2.50e+03
        pdb=" C4A FMN D 413 "    0.003 2.00e-02 2.50e+03
        pdb=" C5A FMN D 413 "   -0.007 2.00e-02 2.50e+03
        pdb=" C6  FMN D 413 "   -0.004 2.00e-02 2.50e+03
        pdb=" C7  FMN D 413 "   -0.004 2.00e-02 2.50e+03
        pdb=" C7M FMN D 413 "    0.032 2.00e-02 2.50e+03
        pdb=" C8  FMN D 413 "   -0.010 2.00e-02 2.50e+03
        pdb=" C8M FMN D 413 "   -0.013 2.00e-02 2.50e+03
        pdb=" C9  FMN D 413 "   -0.013 2.00e-02 2.50e+03
        pdb=" C9A FMN D 413 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1  FMN D 413 "    0.003 2.00e-02 2.50e+03
        pdb=" N10 FMN D 413 "    0.001 2.00e-02 2.50e+03
        pdb=" N3  FMN D 413 "    0.000 2.00e-02 2.50e+03
        pdb=" N5  FMN D 413 "   -0.001 2.00e-02 2.50e+03
        pdb=" O2  FMN D 413 "   -0.007 2.00e-02 2.50e+03
        pdb=" O4  FMN D 413 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 2118 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 294
        2.70 -     3.25: 12457
        3.25 -     3.80: 19683
        3.80 -     4.35: 25092
        4.35 -     4.90: 43295
  Nonbonded interactions: 100821
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN D 119 "
            pdb=" O5' RBF D 403 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" O   LYS C 243 "
            pdb=" OH  TYR D 342 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OE2 GLU E  79 "
            pdb=" NE2 GLN G  39 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" O   LEU C 140 "
            pdb=" ND2 ASN C 269 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" OG1 THR D 191 "
            pdb=" OE1 GLU D 194 "
     model   vdw
     2.251 3.040
  ... (remaining 100816 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.800
  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:             0.020
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.080
  Set scattering table:                    0.130
  Process input model:                     32.340
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
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      :  0.007   0.207  13022  Z= 0.455
  Angle     :  0.940  14.411  17721  Z= 0.392
  Chirality :  0.219   5.021   2168
  Planarity :  0.004   0.040   2121
  Dihedral  : 20.534 170.873   5465
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.98 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  :  5.80 %
    Favored  : 92.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.22), residues: 1587
  helix:  1.46 (0.19), residues: 821
  sheet: -0.59 (0.56), residues: 109
  loop : -0.87 (0.25), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  83 
 HIS   0.002   0.001   HIS C 268 
 PHE   0.012   0.001   PHE D 298 
 TYR   0.009   0.001   TYR C 428 
 ARG   0.002   0.000   ARG E 227 

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 204
  time to evaluate  : 1.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7994 (mp0)
REVERT: C  449 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8877 (tt)
REVERT: E   19 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8051 (tm-30)
  outliers start: 25
  outliers final: 9
  residues processed: 225
  average time/residue: 0.3097
  time to fit residues: 95.4701
Evaluate side-chains
  150 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 1.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  449 ILE
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain G residue  202 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 132 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 80 optimal weight:    0.8980
   chunk 63 optimal weight:    9.9990
   chunk 123 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9990
   chunk 142 optimal weight:   20.0000
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
D 111 GLN
E  34 GLN
E 135 ASN
E 228 GLN
H  47 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.091134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.062696 restraints weight = 31085.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.2951 rms_B_bonded: 2.60
r_work: 0.2813 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13022  Z= 0.189
  Angle     :  0.688  13.719  17721  Z= 0.304
  Chirality :  0.046   0.351   2168
  Planarity :  0.004   0.038   2121
  Dihedral  : 17.989 177.622   2786
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.17 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 10.56 %
    Favored  : 86.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.22), residues: 1587
  helix:  1.69 (0.19), residues: 831
  sheet: -0.36 (0.57), residues: 107
  loop : -0.85 (0.25), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  83 
 HIS   0.002   0.000   HIS A  60 
 PHE   0.018   0.001   PHE A 143 
 TYR   0.017   0.001   TYR H   7 
 ARG   0.007   0.001   ARG C 451 

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 160
  time to evaluate  : 1.332 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8197 (tm-30)
REVERT: A   92 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.8001 (ttp-110)
REVERT: A  125 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8139 (mp0)
REVERT: D   75 ASP cc_start: 0.8700 (p0) cc_final: 0.8445 (p0)
REVERT: D  173 MET cc_start: 0.8469 (mtt) cc_final: 0.8259 (mtm)
REVERT: D  216 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8109 (pt0)
REVERT: E   19 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8119 (tm-30)
REVERT: E  106 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8992 (mm-30)
REVERT: G   71 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8498 (mm-40)
  outliers start: 35
  outliers final: 20
  residues processed: 187
  average time/residue: 0.2839
  time to fit residues: 74.0056
Evaluate side-chains
  165 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   35 ASP
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  449 ILE
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  216 GLU
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue   77 SER
Chi-restraints excluded: chain E residue  100 MET
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain G residue  165 SER
Chi-restraints excluded: chain G residue  173 PHE
Chi-restraints excluded: chain G residue  202 THR
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain B residue  162 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 147 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 115 optimal weight:    4.9990
   chunk 154 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 6 optimal weight:    8.9990
   chunk 117 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 111 GLN
** E  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.088928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.060375 restraints weight = 32063.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 2.59
r_work: 0.2827 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8820
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  13022  Z= 0.306
  Angle     :  0.706  13.566  17721  Z= 0.317
  Chirality :  0.046   0.383   2168
  Planarity :  0.004   0.039   2121
  Dihedral  : 14.358 175.416   2784
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.36 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 10.64 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.22), residues: 1587
  helix:  1.78 (0.19), residues: 832
  sheet: -0.52 (0.56), residues: 110
  loop : -0.95 (0.24), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 166 
 HIS   0.003   0.001   HIS A  14 
 PHE   0.014   0.001   PHE A 143 
 TYR   0.019   0.001   TYR H   7 
 ARG   0.009   0.001   ARG C 451 

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 154
  time to evaluate  : 1.506 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8880 (tm-30)
REVERT: A   71 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9303 (mm)
REVERT: A  125 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8211 (mp0)
REVERT: C    3 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.5756 (m-10)
REVERT: C  140 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9012 (mt)
REVERT: C  297 CYS cc_start: 0.8957 (m) cc_final: 0.8313 (t)
REVERT: C  344 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8406 (pm20)
REVERT: D   75 ASP cc_start: 0.8728 (p0) cc_final: 0.8501 (p0)
REVERT: D  260 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8974 (mm-30)
REVERT: E   19 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8097 (tm-30)
REVERT: G   67 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7800 (tm-30)
REVERT: H    9 ASP cc_start: 0.7882 (t0) cc_final: 0.7612 (t0)
REVERT: H   15 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8410 (tm-30)
REVERT: H   18 CYS cc_start: 0.6902 (t) cc_final: 0.6335 (t)
  outliers start: 44
  outliers final: 27
  residues processed: 188
  average time/residue: 0.2753
  time to fit residues: 73.7351
Evaluate side-chains
  173 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 141
  time to evaluate  : 1.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue    4 ASN
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  319 CYS
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  449 ILE
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  216 GLU
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue  100 MET
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  165 LEU
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain G residue  165 SER
Chi-restraints excluded: chain G residue  167 SER
Chi-restraints excluded: chain G residue  173 PHE
Chi-restraints excluded: chain G residue  202 THR
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  162 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 138 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 147 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 108 optimal weight:    0.0870
   chunk 22 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 131 optimal weight:    8.9990
   overall best weight:    3.0166

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.087992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.059496 restraints weight = 31707.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 2.57
r_work: 0.2811 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  13022  Z= 0.323
  Angle     :  0.690  13.793  17721  Z= 0.313
  Chirality :  0.045   0.381   2168
  Planarity :  0.004   0.050   2121
  Dihedral  : 12.453 175.541   2784
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.98 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 11.44 %
    Favored  : 85.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.22), residues: 1587
  helix:  1.87 (0.19), residues: 832
  sheet: -0.46 (0.57), residues: 108
  loop : -0.92 (0.24), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  96 
 HIS   0.002   0.001   HIS A  14 
 PHE   0.013   0.001   PHE A 143 
 TYR   0.015   0.001   TYR C 237 
 ARG   0.008   0.000   ARG A  92 

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 150
  time to evaluate  : 1.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8382 (ttm)
REVERT: A   59 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8643 (tm-30)
REVERT: A  100 ARG cc_start: 0.8625 (tpp80) cc_final: 0.8347 (tpp80)
REVERT: A  125 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8198 (mp0)
REVERT: A  161 ASN cc_start: 0.9117 (t0) cc_final: 0.8863 (t0)
REVERT: C    3 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.5771 (m-10)
REVERT: C  140 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.9011 (mt)
REVERT: C  297 CYS cc_start: 0.8958 (m) cc_final: 0.8327 (t)
REVERT: C  344 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8422 (pm20)
REVERT: D   75 ASP cc_start: 0.8708 (p0) cc_final: 0.8481 (p0)
REVERT: D  260 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8962 (mm-30)
REVERT: D  326 MET cc_start: 0.9279 (mmt) cc_final: 0.8757 (mmt)
REVERT: E   19 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8066 (tm-30)
REVERT: E  106 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8980 (mm-30)
REVERT: G   59 ILE cc_start: 0.9530 (tp) cc_final: 0.9298 (tp)
REVERT: G   67 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7901 (tm-30)
REVERT: G  133 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8975 (tp30)
REVERT: H    9 ASP cc_start: 0.8202 (t0) cc_final: 0.7830 (t0)
REVERT: H   12 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8149 (mtpp)
REVERT: B  159 GLN cc_start: 0.8197 (tp-100) cc_final: 0.7996 (tp-100)
REVERT: B  169 ASP cc_start: 0.8909 (p0) cc_final: 0.8516 (p0)
  outliers start: 40
  outliers final: 24
  residues processed: 181
  average time/residue: 0.2748
  time to fit residues: 70.3073
Evaluate side-chains
  171 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 141
  time to evaluate  : 1.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   48 MET
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue    4 ASN
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  319 CYS
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  449 ILE
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  216 GLU
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue  100 MET
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  165 LEU
Chi-restraints excluded: chain E residue  197 LEU
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain G residue  133 GLU
Chi-restraints excluded: chain G residue  165 SER
Chi-restraints excluded: chain G residue  173 PHE
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   63 LYS
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  162 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 135 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 105 optimal weight:    6.9990
   chunk 113 optimal weight:    4.9990
   chunk 127 optimal weight:   10.0000
   chunk 80 optimal weight:    1.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  32 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.083497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.055843 restraints weight = 29884.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.2778 rms_B_bonded: 2.83
r_work: 0.2639 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13022  Z= 0.234
  Angle     :  0.625  13.766  17721  Z= 0.288
  Chirality :  0.043   0.314   2168
  Planarity :  0.004   0.052   2121
  Dihedral  : 11.399 173.907   2783
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.04 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 13.42 %
    Favored  : 84.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.22), residues: 1587
  helix:  1.97 (0.19), residues: 832
  sheet: -0.28 (0.58), residues: 106
  loop : -0.89 (0.24), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  96 
 HIS   0.002   0.000   HIS B 132 
 PHE   0.014   0.001   PHE A 143 
 TYR   0.016   0.001   TYR C 237 
 ARG   0.009   0.000   ARG A  92 

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 148
  time to evaluate  : 1.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8584 (tm-30)
REVERT: A  100 ARG cc_start: 0.8698 (tpp80) cc_final: 0.8379 (tpp80)
REVERT: A  125 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8046 (mp0)
REVERT: A  161 ASN cc_start: 0.9018 (t0) cc_final: 0.8690 (t0)
REVERT: C  297 CYS cc_start: 0.9092 (m) cc_final: 0.8244 (t)
REVERT: C  344 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8510 (pm20)
REVERT: D   75 ASP cc_start: 0.8543 (p0) cc_final: 0.8282 (p0)
REVERT: D  260 GLU cc_start: 0.9346 (mt-10) cc_final: 0.8952 (mm-30)
REVERT: D  326 MET cc_start: 0.9145 (mmt) cc_final: 0.8867 (mmt)
REVERT: E   19 GLN cc_start: 0.8529 (tm-30) cc_final: 0.7970 (tm-30)
REVERT: G   59 ILE cc_start: 0.9444 (tp) cc_final: 0.9225 (tp)
REVERT: G   67 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7880 (tm-30)
REVERT: G  133 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.8871 (tp30)
REVERT: H    9 ASP cc_start: 0.7928 (t0) cc_final: 0.7452 (t0)
REVERT: H   12 LYS cc_start: 0.8479 (mmmt) cc_final: 0.8003 (mtpp)
REVERT: B  169 ASP cc_start: 0.8988 (p0) cc_final: 0.8549 (p0)
  outliers start: 32
  outliers final: 24
  residues processed: 173
  average time/residue: 0.2648
  time to fit residues: 65.0426
Evaluate side-chains
  166 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 139
  time to evaluate  : 1.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   35 ASP
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  319 CYS
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  449 ILE
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  216 GLU
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue  100 MET
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  197 LEU
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain G residue  133 GLU
Chi-restraints excluded: chain G residue  165 SER
Chi-restraints excluded: chain G residue  167 SER
Chi-restraints excluded: chain G residue  173 PHE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue  100 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 137 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 91 optimal weight:    5.9990
   chunk 132 optimal weight:    0.7980
   chunk 148 optimal weight:   30.0000
   chunk 142 optimal weight:   10.0000
   chunk 29 optimal weight:    0.1980
   chunk 53 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 228 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.083516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.056970 restraints weight = 30122.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.2798 rms_B_bonded: 2.77
r_work: 0.2656 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13022  Z= 0.206
  Angle     :  0.598  13.287  17721  Z= 0.279
  Chirality :  0.041   0.226   2168
  Planarity :  0.004   0.057   2121
  Dihedral  : 10.701 173.793   2783
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.66 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 13.66 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.22), residues: 1587
  helix:  2.08 (0.19), residues: 832
  sheet: -0.17 (0.59), residues: 106
  loop : -0.86 (0.25), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 166 
 HIS   0.002   0.000   HIS B 132 
 PHE   0.016   0.001   PHE A 143 
 TYR   0.016   0.001   TYR C 237 
 ARG   0.004   0.000   ARG H   2 

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 150
  time to evaluate  : 1.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8553 (tm-30)
REVERT: A  100 ARG cc_start: 0.8726 (tpp80) cc_final: 0.8516 (tpp80)
REVERT: A  125 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8015 (mp0)
REVERT: A  161 ASN cc_start: 0.9016 (t0) cc_final: 0.8597 (t0)
REVERT: C    3 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.5951 (m-10)
REVERT: C  344 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8533 (pm20)
REVERT: D   75 ASP cc_start: 0.8470 (p0) cc_final: 0.8220 (p0)
REVERT: D  260 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8928 (mm-30)
REVERT: D  326 MET cc_start: 0.9105 (mmt) cc_final: 0.8904 (mmt)
REVERT: E   19 GLN cc_start: 0.8499 (tm-30) cc_final: 0.7913 (tm-30)
REVERT: E  173 GLN cc_start: 0.8653 (pm20) cc_final: 0.8410 (pm20)
REVERT: G   59 ILE cc_start: 0.9444 (tp) cc_final: 0.9219 (tp)
REVERT: G   67 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7870 (tm-30)
REVERT: G  133 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8843 (tp30)
REVERT: G  179 GLU cc_start: 0.9139 (pt0) cc_final: 0.8736 (pm20)
REVERT: H    9 ASP cc_start: 0.7886 (t0) cc_final: 0.7420 (t0)
REVERT: H   12 LYS cc_start: 0.8570 (mmmt) cc_final: 0.8199 (mtpt)
REVERT: B  169 ASP cc_start: 0.8985 (p0) cc_final: 0.8544 (p0)
  outliers start: 40
  outliers final: 30
  residues processed: 183
  average time/residue: 0.2743
  time to fit residues: 71.5747
Evaluate side-chains
  173 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 139
  time to evaluate  : 1.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  319 CYS
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  449 ILE
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  216 GLU
Chi-restraints excluded: chain D residue  269 LEU
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue  100 MET
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  165 LEU
Chi-restraints excluded: chain E residue  197 LEU
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain G residue  133 GLU
Chi-restraints excluded: chain G residue  165 SER
Chi-restraints excluded: chain G residue  167 SER
Chi-restraints excluded: chain G residue  173 PHE
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  155 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 152 optimal weight:    0.4980
   chunk 148 optimal weight:    2.9990
   chunk 141 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 77 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 134 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.085617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.060375 restraints weight = 29831.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 2.28
r_work: 0.2778 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8819
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  13022  Z= 0.164
  Angle     :  0.578  12.619  17721  Z= 0.274
  Chirality :  0.040   0.189   2168
  Planarity :  0.004   0.057   2121
  Dihedral  : 10.290 172.822   2783
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.47 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 13.90 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.22), residues: 1587
  helix:  2.24 (0.19), residues: 826
  sheet: -0.05 (0.59), residues: 106
  loop : -0.74 (0.25), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  96 
 HIS   0.002   0.000   HIS C  17 
 PHE   0.019   0.001   PHE A 143 
 TYR   0.016   0.001   TYR C 237 
 ARG   0.007   0.000   ARG B 103 

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 157
  time to evaluate  : 1.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8580 (tm-30)
REVERT: A  100 ARG cc_start: 0.8466 (tpp80) cc_final: 0.8241 (tpp80)
REVERT: A  105 TYR cc_start: 0.8446 (m-80) cc_final: 0.8122 (m-80)
REVERT: A  125 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8093 (mp0)
REVERT: A  161 ASN cc_start: 0.9047 (t0) cc_final: 0.8814 (t0)
REVERT: C    3 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.5666 (m-10)
REVERT: C  344 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8393 (pm20)
REVERT: E   19 GLN cc_start: 0.8496 (tm-30) cc_final: 0.7913 (tm-30)
REVERT: G   59 ILE cc_start: 0.9553 (tp) cc_final: 0.9277 (tp)
REVERT: G   67 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7953 (tm-30)
REVERT: H    9 ASP cc_start: 0.8004 (t0) cc_final: 0.7473 (t0)
REVERT: H   12 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8169 (mtpp)
REVERT: B  169 ASP cc_start: 0.8783 (p0) cc_final: 0.8467 (p0)
  outliers start: 39
  outliers final: 26
  residues processed: 187
  average time/residue: 0.2686
  time to fit residues: 71.6369
Evaluate side-chains
  176 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 147
  time to evaluate  : 1.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  319 CYS
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  449 ILE
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  216 GLU
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  165 LEU
Chi-restraints excluded: chain E residue  197 LEU
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain G residue  165 SER
Chi-restraints excluded: chain G residue  167 SER
Chi-restraints excluded: chain G residue  173 PHE
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  162 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 154 optimal weight:    8.9990
   chunk 91 optimal weight:    4.9990
   chunk 110 optimal weight:    3.9990
   chunk 120 optimal weight:    9.9990
   chunk 62 optimal weight:    3.9990
   chunk 33 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 149 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9990
   chunk 136 optimal weight:   10.0000
   chunk 135 optimal weight:    2.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 236 HIS
D 327 ASN
** E  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.082997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.057326 restraints weight = 30233.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 2.29
r_work: 0.2700 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2570 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8968
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  13022  Z= 0.360
  Angle     :  0.661  11.603  17721  Z= 0.313
  Chirality :  0.043   0.193   2168
  Planarity :  0.004   0.060   2121
  Dihedral  : 10.420 176.619   2782
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.61 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.01 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.22), residues: 1587
  helix:  2.13 (0.19), residues: 827
  sheet: -0.15 (0.57), residues: 106
  loop : -0.75 (0.25), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  96 
 HIS   0.003   0.001   HIS A  14 
 PHE   0.015   0.001   PHE A 143 
 TYR   0.012   0.001   TYR C 237 
 ARG   0.005   0.000   ARG B 103 

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 140
  time to evaluate  : 1.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8894 (tm-30)
REVERT: A   88 GLU cc_start: 0.8355 (tp30) cc_final: 0.8127 (tp30)
REVERT: A  125 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8266 (mp0)
REVERT: A  161 ASN cc_start: 0.9170 (t0) cc_final: 0.8903 (t0)
REVERT: C    3 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.5831 (m-10)
REVERT: C  344 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8632 (pm20)
REVERT: D   75 ASP cc_start: 0.8816 (p0) cc_final: 0.8595 (p0)
REVERT: E   19 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8055 (tm-30)
REVERT: E  106 GLU cc_start: 0.9350 (mm-30) cc_final: 0.9100 (mm-30)
REVERT: E  173 GLN cc_start: 0.8950 (pm20) cc_final: 0.8642 (pm20)
REVERT: G   38 TYR cc_start: 0.7614 (t80) cc_final: 0.7217 (t80)
REVERT: G   59 ILE cc_start: 0.9589 (tp) cc_final: 0.9324 (tp)
REVERT: G   67 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8150 (tm-30)
REVERT: G  106 GLU cc_start: 0.8619 (tp30) cc_final: 0.8296 (tp30)
REVERT: G  179 GLU cc_start: 0.8745 (pm20) cc_final: 0.8544 (pm20)
REVERT: H    9 ASP cc_start: 0.8064 (t0) cc_final: 0.7548 (t0)
REVERT: H   12 LYS cc_start: 0.8693 (mmmt) cc_final: 0.8173 (mtpp)
REVERT: B  169 ASP cc_start: 0.9048 (p0) cc_final: 0.8707 (p0)
  outliers start: 31
  outliers final: 24
  residues processed: 167
  average time/residue: 0.2689
  time to fit residues: 64.4098
Evaluate side-chains
  162 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 1.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  449 ILE
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  216 GLU
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  165 LEU
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain G residue  165 SER
Chi-restraints excluded: chain G residue  167 SER
Chi-restraints excluded: chain G residue  173 PHE
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   63 LYS
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  162 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 98 optimal weight:    7.9990
   chunk 106 optimal weight:    0.8980
   chunk 132 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 145 optimal weight:    0.8980
   chunk 28 optimal weight:   10.0000
   chunk 81 optimal weight:    7.9990
   chunk 125 optimal weight:   10.0000
   chunk 56 optimal weight:    0.6980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 327 ASN
** E  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.085022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.059881 restraints weight = 29749.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 2.27
r_work: 0.2754 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2624 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8919
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13022  Z= 0.178
  Angle     :  0.585  10.831  17721  Z= 0.280
  Chirality :  0.041   0.184   2168
  Planarity :  0.004   0.060   2121
  Dihedral  : 10.060 172.826   2782
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.47 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.09 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.22), residues: 1587
  helix:  2.24 (0.19), residues: 826
  sheet: -0.11 (0.58), residues: 106
  loop : -0.67 (0.25), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  96 
 HIS   0.002   0.000   HIS C  17 
 PHE   0.021   0.001   PHE A 143 
 TYR   0.015   0.001   TYR C 237 
 ARG   0.006   0.000   ARG B 167 

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 146
  time to evaluate  : 1.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8675 (tm-30)
REVERT: A  125 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8270 (mp0)
REVERT: A  161 ASN cc_start: 0.9140 (t0) cc_final: 0.8896 (t0)
REVERT: C  297 CYS cc_start: 0.9059 (m) cc_final: 0.8506 (t)
REVERT: C  344 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8614 (pm20)
REVERT: E  106 GLU cc_start: 0.9311 (mm-30) cc_final: 0.9095 (mm-30)
REVERT: G   38 TYR cc_start: 0.7650 (t80) cc_final: 0.7221 (t80)
REVERT: G   59 ILE cc_start: 0.9584 (tp) cc_final: 0.9296 (tp)
REVERT: G   67 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8159 (tm-30)
REVERT: G  179 GLU cc_start: 0.8735 (pm20) cc_final: 0.8534 (pm20)
REVERT: H    9 ASP cc_start: 0.7948 (t0) cc_final: 0.7425 (t0)
REVERT: H   12 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8221 (mtpp)
REVERT: B  169 ASP cc_start: 0.9035 (p0) cc_final: 0.8704 (p0)
  outliers start: 29
  outliers final: 25
  residues processed: 170
  average time/residue: 0.2627
  time to fit residues: 63.6132
Evaluate side-chains
  171 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 1.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  449 ILE
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  216 GLU
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  165 LEU
Chi-restraints excluded: chain E residue  197 LEU
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain G residue  165 SER
Chi-restraints excluded: chain G residue  167 SER
Chi-restraints excluded: chain G residue  173 PHE
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   63 LYS
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  162 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 150 optimal weight:   10.0000
   chunk 52 optimal weight:    0.6980
   chunk 13 optimal weight:    4.9990
   chunk 141 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
D 327 ASN
** E  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.083797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.058099 restraints weight = 30025.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 2.31
r_work: 0.2725 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8857
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13022  Z= 0.280
  Angle     :  0.637  10.377  17721  Z= 0.308
  Chirality :  0.042   0.179   2168
  Planarity :  0.004   0.061   2121
  Dihedral  : 10.034 174.953   2782
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.29 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.49 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.22), residues: 1587
  helix:  2.19 (0.19), residues: 827
  sheet: -0.01 (0.58), residues: 104
  loop : -0.66 (0.25), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 166 
 HIS   0.002   0.001   HIS A  14 
 PHE   0.021   0.001   PHE A 143 
 TYR   0.015   0.001   TYR C 237 
 ARG   0.009   0.000   ARG B 167 

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

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

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3174 Ramachandran restraints generated.
    1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 142
  time to evaluate  : 1.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8769 (tm-30)
REVERT: A  125 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8116 (mp0)
REVERT: A  161 ASN cc_start: 0.9079 (t0) cc_final: 0.8819 (t0)
REVERT: C  297 CYS cc_start: 0.8867 (m) cc_final: 0.8373 (t)
REVERT: C  344 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8412 (pm20)
REVERT: E  106 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8957 (mm-30)
REVERT: G   38 TYR cc_start: 0.7639 (t80) cc_final: 0.7228 (t80)
REVERT: G   59 ILE cc_start: 0.9573 (tp) cc_final: 0.9299 (tp)
REVERT: G   67 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8022 (tm-30)
REVERT: G  106 GLU cc_start: 0.8222 (tp30) cc_final: 0.7943 (tp30)
REVERT: H    9 ASP cc_start: 0.7780 (t0) cc_final: 0.7224 (t0)
REVERT: H   12 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8237 (mtpp)
REVERT: B  169 ASP cc_start: 0.8913 (p0) cc_final: 0.8566 (p0)
  outliers start: 29
  outliers final: 24
  residues processed: 167
  average time/residue: 0.2602
  time to fit residues: 61.8583
Evaluate side-chains
  166 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 1.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  344 GLU
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  352 THR
Chi-restraints excluded: chain C residue  449 ILE
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  216 GLU
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  165 LEU
Chi-restraints excluded: chain E residue  197 LEU
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain G residue  165 SER
Chi-restraints excluded: chain G residue  167 SER
Chi-restraints excluded: chain G residue  173 PHE
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   63 LYS
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  162 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 107 optimal weight:    9.9990
   chunk 149 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   chunk 133 optimal weight:    0.0060
   chunk 112 optimal weight:    7.9990
   chunk 110 optimal weight:    4.9990
   overall best weight:    1.9402

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

Flipped N/Q/H residues before XYZ refinement:
** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 327 ASN
** E  29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.084157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.058315 restraints weight = 29888.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 2.33
r_work: 0.2742 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2611 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8930
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13022  Z= 0.237
  Angle     :  0.626   9.688  17721  Z= 0.304
  Chirality :  0.041   0.179   2168
  Planarity :  0.004   0.060   2121
  Dihedral  :  9.858 174.151   2782
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.60 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 15.81 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.22), residues: 1587
  helix:  2.25 (0.19), residues: 821
  sheet:  0.03 (0.58), residues: 104
  loop : -0.65 (0.25), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  96 
 HIS   0.002   0.000   HIS A  60 
 PHE   0.022   0.001   PHE A 143 
 TYR   0.015   0.001   TYR C 237 
 ARG   0.014   0.000   ARG A  92 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6197.11 seconds
wall clock time: 110 minutes 40.46 seconds (6640.46 seconds total)