Starting phenix.real_space_refine
on Fri Mar  6 13:21:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8a1y_15093/03_2026/8a1y_15093_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a1y_15093/03_2026/8a1y_15093.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8a1y_15093/03_2026/8a1y_15093.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a1y_15093/03_2026/8a1y_15093.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a1y_15093/03_2026/8a1y_15093_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a1y_15093/03_2026/8a1y_15093_trim.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.011 sd=   0.130
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: 7
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     P       7      5.49       5
     S      91      5.16       5
     C    9843      2.51       5
     N    2454      2.21       5
     O    2782      1.98       5
     H   14864      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 30045
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 6910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 448, 6910
          Classifications: {'peptide': 448}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 424}
    Chain: "B"
      Number of atoms: 6347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 412, 6347
          Classifications: {'peptide': 412}
          Link IDs: {'PTRANS': 15, 'TRANS': 396}
    Chain: "C"
      Number of atoms: 3840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 3840
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 7, 'TRANS': 245}
    Chain: "D"
      Number of atoms: 3166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 3166
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 9, 'TRANS': 192}
    Chain: "E"
      Number of atoms: 3078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 3078
          Classifications: {'peptide': 197}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 189}
    Chain: "F"
      Number of atoms: 6269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 408, 6269
          Classifications: {'peptide': 408}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 383}
    Chain: "B"
      Number of atoms: 274
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 274
          Unusual residues: {'3PE': 3, 'FMN': 1, 'HQO': 1, 'LMT': 2, 'RBF': 1}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 26
    Chain: "C"
      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
          Unresolved non-hydrogen dihedrals: 1
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 39
          Unusual residues: {'FES': 1, 'LMT': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'LMT': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 57
          Unusual residues: {'FAD': 1, 'FES': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  18773  SG  CYS D 112      67.035  82.568  59.443  1.00121.94           S
  ATOM  20665  SG  CYS E  26      64.349  82.937  62.001  1.00110.64           S
  ATOM  17447  SG  CYS D  29      67.030  84.311  65.651  1.00 92.56           S
  ATOM  22170  SG  CYS E 120      70.308  84.504  63.885  1.00117.42           S
  ATOM  24391  SG  CYS F  70      52.091  66.625  37.855  1.00276.78           S
  ATOM  24440  SG  CYS F  76      50.364  63.329  37.299  1.00271.01           S
  ATOM  24474  SG  CYS F  79      55.179  60.974  38.770  1.00261.99           S
  ATOM  24959  SG  CYS F 111      56.470  64.481  39.250  1.00255.78           S

  Time building chain proxies: 4.70, per 1000 atoms: 0.16
  Number of scatterers: 30045
  At special positions: 0
  Unit cell: (111.739, 136.849, 131.827, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Fe      4     26.01
     S      91     16.00
     P       7     15.00
     O    2782      8.00
     N    2454      7.00
     C    9843      6.00
     H   14864      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.56
  Conformation dependent library (CDL) restraints added in 860.3 milliseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" FES D1001 "
        pdb="FE2  FES D1001 " - pdb=" SG  CYS D  29 "
        pdb="FE1  FES D1001 " - pdb=" SG  CYS E  26 "
        pdb="FE1  FES D1001 " - pdb=" SG  CYS D 112 "
        pdb="FE2  FES D1001 " - pdb=" SG  CYS E 120 "
      pdb=" FES F1502 "
        pdb="FE2  FES F1502 " - pdb=" SG  CYS F  79 "
        pdb="FE1  FES F1502 " - pdb=" SG  CYS F  76 "
        pdb="FE1  FES F1502 " - pdb=" SG  CYS F  70 "
        pdb="FE2  FES F1502 " - pdb=" SG  CYS F 111 "
      Number of angles added : 12


  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3468

  Finding SS restraints...
    Secondary structure from input PDB file:
      91 helices and 13 sheets defined
      53.9% alpha, 10.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 83 through 85
      No H-bonds generated for 'chain 'A' and resid 83 through 85'
    Processing helix  chain 'A' and resid 107 through 111
    Processing helix  chain 'A' and resid 114 through 126
    Processing helix  chain 'A' and resid 127 through 131
    Processing helix  chain 'A' and resid 162 through 170
      removed outlier: 3.712A  pdb=" N   VAL A 166 " --> pdb=" O   GLU A 162 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLU A 169 " --> pdb=" O   VAL A 165 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLN A 170 " --> pdb=" O   VAL A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 185
    Processing helix  chain 'A' and resid 214 through 218
    Processing helix  chain 'A' and resid 219 through 228
    Processing helix  chain 'A' and resid 241 through 254
    Processing helix  chain 'A' and resid 282 through 287
    Processing helix  chain 'A' and resid 310 through 314
    Processing helix  chain 'A' and resid 351 through 356
    Processing helix  chain 'A' and resid 379 through 383
    Processing helix  chain 'A' and resid 389 through 400
    Processing helix  chain 'A' and resid 401 through 409
      removed outlier: 3.780A  pdb=" N   ARG A 407 " --> pdb=" O   ASP A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 424
    Processing helix  chain 'A' and resid 430 through 446
      removed outlier: 3.505A  pdb=" N   LEU A 434 " --> pdb=" O   GLU A 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 15
      removed outlier: 4.529A  pdb=" N   HIS B  12 " --> pdb=" O   GLU B   8 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   HIS B  13 " --> pdb=" O   ASP B   9 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   PHE B  14 " --> pdb=" O   ILE B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 22
      No H-bonds generated for 'chain 'B' and resid 20 through 22'
    Processing helix  chain 'B' and resid 23 through 35
    Processing helix  chain 'B' and resid 52 through 55
    Processing helix  chain 'B' and resid 56 through 62
      removed outlier: 3.589A  pdb=" N   VAL B  60 " --> pdb=" O   ILE B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 87
    Processing helix  chain 'B' and resid 89 through 99
      removed outlier: 3.699A  pdb=" N   ALA B  93 " --> pdb=" O   GLY B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 109
      removed outlier: 3.646A  pdb=" N   LEU B 104 " --> pdb=" O   TRP B 100 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   THR B 105 " --> pdb=" O   HIS B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 152
      Proline residue:  B 131  - end of helix
    Processing helix  chain 'B' and resid 159 through 167
      removed outlier: 3.560A  pdb=" N   ILE B 164 " --> pdb=" O   PHE B 160 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU B 165 " --> pdb=" O   VAL B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 189
    Processing helix  chain 'B' and resid 203 through 216
    Processing helix  chain 'B' and resid 217 through 221
      removed outlier: 3.873A  pdb=" N   SER B 221 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 244
    Processing helix  chain 'B' and resid 245 through 248
    Processing helix  chain 'B' and resid 259 through 266
    Processing helix  chain 'B' and resid 277 through 290
      removed outlier: 3.758A  pdb=" N   PHE B 286 " --> pdb=" O   ILE B 282 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ILE B 287 " --> pdb=" O   GLY B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 316
      removed outlier: 3.815A  pdb=" N   ILE B 298 " --> pdb=" O   SER B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 325
    Processing helix  chain 'B' and resid 326 through 332
      removed outlier: 3.763A  pdb=" N   VAL B 332 " --> pdb=" O   HIS B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 343
    Processing helix  chain 'B' and resid 353 through 374
      removed outlier: 3.572A  pdb=" N   TRP B 358 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA B 359 " --> pdb=" O   SER B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 410
      Proline residue:  B 394  - end of helix
    Processing helix  chain 'B' and resid 411 through 414
    Processing helix  chain 'C' and resid 7 through 33
    Processing helix  chain 'C' and resid 33 through 54
      removed outlier: 3.568A  pdb=" N   LYS C  45 " --> pdb=" O   ALA C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 70
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.709A  pdb=" N   TYR C  91 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 99
    Processing helix  chain 'C' and resid 177 through 181
      removed outlier: 3.724A  pdb=" N   VAL C 180 " --> pdb=" O   GLY C 177 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 182 through 188
    Processing helix  chain 'C' and resid 224 through 239
    Processing helix  chain 'C' and resid 244 through 253
    Processing helix  chain 'D' and resid 8 through 13
    Processing helix  chain 'D' and resid 14 through 16
      No H-bonds generated for 'chain 'D' and resid 14 through 16'
    Processing helix  chain 'D' and resid 27 through 35
      removed outlier: 3.981A  pdb=" N   ALA D  31 " --> pdb=" O   GLY D  27 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   THR D  35 " --> pdb=" O   ALA D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 62
    Processing helix  chain 'D' and resid 70 through 93
    Processing helix  chain 'D' and resid 94 through 102
    Processing helix  chain 'D' and resid 103 through 108
    Processing helix  chain 'D' and resid 111 through 121
    Processing helix  chain 'D' and resid 126 through 157
    Processing helix  chain 'D' and resid 168 through 172
    Processing helix  chain 'D' and resid 178 through 182
    Processing helix  chain 'D' and resid 183 through 202
      removed outlier: 4.205A  pdb=" N   ALA D 187 " --> pdb=" O   LEU D 183 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   PHE D 188 " --> pdb=" O   ALA D 184 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   TRP D 196 " --> pdb=" O   GLY D 192 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 203 through 206
    Processing helix  chain 'E' and resid 3 through 13
    Processing helix  chain 'E' and resid 24 through 31
    Processing helix  chain 'E' and resid 34 through 63
      Proline residue:  E  54  - end of helix
    Processing helix  chain 'E' and resid 75 through 77
      No H-bonds generated for 'chain 'E' and resid 75 through 77'
    Processing helix  chain 'E' and resid 78 through 102
      removed outlier: 3.895A  pdb=" N   ASP E  99 " --> pdb=" O   GLU E  95 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 102 through 110
      removed outlier: 3.523A  pdb=" N   ALA E 108 " --> pdb=" O   PRO E 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 112 through 117
      removed outlier: 3.633A  pdb=" N   ILE E 116 " --> pdb=" O   PHE E 112 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 119 through 132
      removed outlier: 3.543A  pdb=" N   PHE E 123 " --> pdb=" O   ASN E 119 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   VAL E 126 " --> pdb=" O   ILE E 122 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 135 through 164
    Processing helix  chain 'E' and resid 165 through 167
      No H-bonds generated for 'chain 'E' and resid 165 through 167'
    Processing helix  chain 'E' and resid 175 through 191
      removed outlier: 3.547A  pdb=" N   THR E 179 " --> pdb=" O   GLY E 175 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 192 through 196
      removed outlier: 4.303A  pdb=" N   GLY E 195 " --> pdb=" O   SER E 192 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 28
      removed outlier: 3.726A  pdb=" N   PHE F   6 " --> pdb=" O   SER F   2 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 54 through 63
      removed outlier: 3.866A  pdb=" N   ALA F  58 " --> pdb=" O   LYS F  54 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 91 through 98
      removed outlier: 4.136A  pdb=" N   HIS F  97 " --> pdb=" O   THR F  93 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 99 through 106
    Processing helix  chain 'F' and resid 124 through 130
    Processing helix  chain 'F' and resid 154 through 158
      removed outlier: 3.702A  pdb=" N   GLU F 158 " --> pdb=" O   PRO F 155 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 180 through 182
      No H-bonds generated for 'chain 'F' and resid 180 through 182'
    Processing helix  chain 'F' and resid 185 through 196
      removed outlier: 3.947A  pdb=" N   GLY F 190 " --> pdb=" O   GLU F 186 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   ASP F 191 " --> pdb=" O   LYS F 187 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   TRP F 192 " --> pdb=" O   TYR F 188 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 197 through 199
      No H-bonds generated for 'chain 'F' and resid 197 through 199'
    Processing helix  chain 'F' and resid 243 through 252
    Processing helix  chain 'F' and resid 284 through 297
      removed outlier: 3.701A  pdb=" N   MET F 288 " --> pdb=" O   GLY F 284 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 319 through 330
      removed outlier: 3.500A  pdb=" N   LEU F 326 " --> pdb=" O   ASP F 322 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 343 through 347
      removed outlier: 3.726A  pdb=" N   ASN F 347 " --> pdb=" O   PRO F 344 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 354 through 363
      removed outlier: 3.764A  pdb=" N   TYR F 360 " --> pdb=" O   HIS F 356 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 369 through 373
      removed outlier: 3.775A  pdb=" N   ASP F 372 " --> pdb=" O   ALA F 369 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 380 through 394
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1 through 3
    Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21
      removed outlier: 7.826A  pdb=" N   VAL A 323 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
      removed outlier: 5.827A  pdb=" N   SER A 263 " --> pdb=" O   VAL A 323 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   VAL A 325 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   ALA A 265 " --> pdb=" O   VAL A 325 " (cutoff:3.500A)
      removed outlier: 9.709A  pdb=" N   ARG A 327 " --> pdb=" O   ALA A 265 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32
      removed outlier: 6.764A  pdb=" N   LEU A  87 " --> pdb=" O   ARG A  81 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ARG A  81 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   SER A  89 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
      removed outlier: 4.899A  pdb=" N   ILE A  79 " --> pdb=" O   SER A  89 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   VAL A  91 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43
      removed outlier: 7.138A  pdb=" N   PHE A  68 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 250 through 251
      removed outlier: 3.560A  pdb=" N   GLN B 256 " --> pdb=" O   ASN B 251 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 83 through 84
      removed outlier: 4.158A  pdb=" N   LEU C  75 " --> pdb=" O   VAL C  84 " (cutoff:3.500A)
      removed outlier: 14.041A  pdb=" N   VAL C 121 " --> pdb=" O   HIS C 141 " (cutoff:3.500A)
      removed outlier: 12.313A  pdb=" N   HIS C 141 " --> pdb=" O   VAL C 121 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL C 123 " --> pdb=" O   PRO C 139 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LYS C 135 " --> pdb=" O   VAL C 127 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLU C 169 " --> pdb=" O   TYR C 150 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   PHE C 152 " --> pdb=" O   TYR C 167 " (cutoff:3.500A)
      removed outlier: 5.691A  pdb=" N   TYR C 167 " --> pdb=" O   PHE C 152 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   ALA C 154 " --> pdb=" O   LEU C 165 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   LEU C 165 " --> pdb=" O   ALA C 154 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   GLU C 156 " --> pdb=" O   SER C 163 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   SER C 163 " --> pdb=" O   GLU C 156 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 105
    Processing sheet with id=AA8, first strand: chain 'C' and resid 204 through 206
      removed outlier: 6.322A  pdb=" N   LYS C 204 " --> pdb=" O   VAL C 218 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'D' and resid 159 through 160
    Processing sheet with id=AB1, first strand: chain 'F' and resid 42 through 49
      removed outlier: 5.324A  pdb=" N   LYS F  45 " --> pdb=" O   ILE F  39 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   THR F  36 " --> pdb=" O   MET F 119 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   LEU F 121 " --> pdb=" O   THR F  36 " (cutoff:3.500A)
      removed outlier: 6.067A  pdb=" N   SER F  38 " --> pdb=" O   LEU F 121 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   ASP F 120 " --> pdb=" O   LYS F  84 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 208 through 213
      removed outlier: 6.712A  pdb=" N   TYR F 167 " --> pdb=" O   PRO F 263 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   THR F 259 " --> pdb=" O   GLU F 171 " (cutoff:3.500A)
      removed outlier: 5.883A  pdb=" N   VAL F 137 " --> pdb=" O   ALA F 153 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   ALA F 153 " --> pdb=" O   VAL F 137 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 175 through 178
    Processing sheet with id=AB4, first strand: chain 'F' and resid 334 through 339
      removed outlier: 6.013A  pdb=" N   MET F 305 " --> pdb=" O   VAL F 334 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   HIS F 336 " --> pdb=" O   MET F 305 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   TYR F 307 " --> pdb=" O   HIS F 336 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   ALA F 338 " --> pdb=" O   TYR F 307 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   TYR F 309 " --> pdb=" O   ALA F 338 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   MET F 276 " --> pdb=" O   SER F 306 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   TRP F 308 " --> pdb=" O   MET F 276 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   PHE F 278 " --> pdb=" O   TRP F 308 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   GLY F 310 " --> pdb=" O   PHE F 278 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   GLY F 280 " --> pdb=" O   GLY F 310 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   TYR F 375 " --> pdb=" O   LEU F 402 " (cutoff:3.500A)

    748 hydrogen bonds defined for protein.
    2106 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: 6.27

  Time building geometry restraints manager: 3.50 seconds

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

  Histogram of bond lengths:
        0.84 -     1.11: 14851
        1.11 -     1.39: 6010
        1.39 -     1.66: 9375
        1.66 -     1.93: 153
        1.93 -     2.20: 8
  Bond restraints: 30397
  Sorted by residual:
  bond pdb=" C4  FMN C1000 "
       pdb=" C4A FMN C1000 "
    ideal  model  delta    sigma   weight residual
    1.485  1.385  0.100 2.00e-02 2.50e+03 2.50e+01
  bond pdb=" N1  HQO B 607 "
       pdb=" O4  HQO B 607 "
    ideal  model  delta    sigma   weight residual
    1.285  1.383 -0.098 2.00e-02 2.50e+03 2.42e+01
  bond pdb=" C4  FMN B 600 "
       pdb=" C4A FMN B 600 "
    ideal  model  delta    sigma   weight residual
    1.485  1.387  0.098 2.00e-02 2.50e+03 2.38e+01
  bond pdb=" C1  HQO B 607 "
       pdb=" O1  HQO B 607 "
    ideal  model  delta    sigma   weight residual
    1.335  1.243  0.092 2.00e-02 2.50e+03 2.14e+01
  bond pdb=" C4A FMN B 600 "
       pdb=" N5  FMN B 600 "
    ideal  model  delta    sigma   weight residual
    1.300  1.376 -0.076 2.00e-02 2.50e+03 1.43e+01
  ... (remaining 30392 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 54580
        1.94 -     3.88: 233
        3.88 -     5.83: 51
        5.83 -     7.77: 10
        7.77 -     9.71: 12
  Bond angle restraints: 54886
  Sorted by residual:
  angle pdb=" C2  LMT E 201 "
        pdb=" C3  LMT E 201 "
        pdb=" C4  LMT E 201 "
      ideal   model   delta    sigma   weight residual
     117.09  107.38    9.71 3.00e+00 1.11e-01 1.05e+01
  angle pdb=" C2  LMT B 605 "
        pdb=" C3  LMT B 605 "
        pdb=" C4  LMT B 605 "
      ideal   model   delta    sigma   weight residual
     117.09  107.61    9.48 3.00e+00 1.11e-01 9.98e+00
  angle pdb=" C2  LMT D1002 "
        pdb=" C3  LMT D1002 "
        pdb=" C4  LMT D1002 "
      ideal   model   delta    sigma   weight residual
     117.09  107.64    9.45 3.00e+00 1.11e-01 9.92e+00
  angle pdb=" C2  LMT B 603 "
        pdb=" C3  LMT B 603 "
        pdb=" C4  LMT B 603 "
      ideal   model   delta    sigma   weight residual
     117.09  107.69    9.40 3.00e+00 1.11e-01 9.81e+00
  angle pdb=" C10 LMT B 603 "
        pdb=" C9  LMT B 603 "
        pdb=" C8  LMT B 603 "
      ideal   model   delta    sigma   weight residual
     116.03  107.29    8.74 3.00e+00 1.11e-01 8.49e+00
  ... (remaining 54881 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.73: 13497
       24.73 -    49.46: 751
       49.46 -    74.20: 230
       74.20 -    98.93: 30
       98.93 -   123.66: 13
  Dihedral angle restraints: 14521
    sinusoidal: 8026
      harmonic: 6495
  Sorted by residual:
  dihedral pdb=" O5' FAD F1501 "
           pdb=" O3P FAD F1501 "
           pdb=" P   FAD F1501 "
           pdb=" PA  FAD F1501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     298.23  174.57  123.66     1      3.00e+01 1.11e-03 1.66e+01
  dihedral pdb=" C3B LMT D1002 "
           pdb=" C4B LMT D1002 "
           pdb=" C5B LMT D1002 "
           pdb=" O5B LMT D1002 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.62   62.01 -119.63     1      3.00e+01 1.11e-03 1.59e+01
  dihedral pdb=" O2B LMT B 605 "
           pdb=" C1B LMT B 605 "
           pdb=" C2B LMT B 605 "
           pdb=" O5B LMT B 605 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -176.42  -58.83 -117.59     1      3.00e+01 1.11e-03 1.56e+01
  ... (remaining 14518 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1897
       0.044 -    0.088: 322
       0.088 -    0.132: 135
       0.132 -    0.176: 5
       0.176 -    0.221: 12
  Chirality restraints: 2371
  Sorted by residual:
  chirality pdb=" C4' LMT B 605 "
            pdb=" C3' LMT B 605 "
            pdb=" C5' LMT B 605 "
            pdb=" O1B LMT B 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.77    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" C3B LMT D1002 "
            pdb=" C2B LMT D1002 "
            pdb=" C4B LMT D1002 "
            pdb=" O3B LMT D1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    2.28    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" C5' LMT B 605 "
            pdb=" C4' LMT B 605 "
            pdb=" C6' LMT B 605 "
            pdb=" O5' LMT B 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.30   -0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 2368 not shown)

  Planarity restraints: 4445
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 213 "    0.016 5.00e-02 4.00e+02   2.42e-02 9.37e-01
        pdb=" N   PRO A 214 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO A 214 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 214 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL F 160 "   -0.015 5.00e-02 4.00e+02   2.31e-02 8.50e-01
        pdb=" N   PRO F 161 "    0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO F 161 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO F 161 "   -0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE E 102 "   -0.014 5.00e-02 4.00e+02   2.11e-02 7.12e-01
        pdb=" N   PRO E 103 "    0.036 5.00e-02 4.00e+02
        pdb=" CA  PRO E 103 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO E 103 "   -0.012 5.00e-02 4.00e+02
  ... (remaining 4442 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 1269
        2.18 -     2.79: 60128
        2.79 -     3.39: 84224
        3.39 -     4.00: 110268
        4.00 -     4.60: 171290
  Nonbonded interactions: 427179
  Sorted by model distance:
  nonbonded pdb=" H   LEU D  38 "
            pdb=" OE1 GLU D 153 "
     model   vdw
     1.577 2.450
  nonbonded pdb=" O   ASN F 140 "
            pdb=" HZ1 LYS F 148 "
     model   vdw
     1.597 2.450
  nonbonded pdb=" OE1 GLU C 109 "
            pdb=" H   GLU C 109 "
     model   vdw
     1.613 2.450
  nonbonded pdb=" H   GLY A 301 "
            pdb=" O   GLN A 322 "
     model   vdw
     1.623 2.450
  nonbonded pdb=" O   VAL D  48 "
            pdb=" HG1 THR D  52 "
     model   vdw
     1.635 2.450
  ... (remaining 427174 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  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:             0.170
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.090
  Set scattering table:                    0.080
  Process input model:                     33.540
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
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      :  0.005   0.100  15543  Z= 0.227
  Angle     :  0.562   9.709  21054  Z= 0.246
  Chirality :  0.041   0.221   2371
  Planarity :  0.002   0.024   2616
  Dihedral  : 17.134 123.662   5867
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  : 14.09 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.20), residues: 1908
  helix:  1.95 (0.19), residues: 871
  sheet: -0.26 (0.40), residues: 185
  loop :  0.02 (0.21), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 209 
 TYR   0.005   0.001   TYR B  27 
 PHE   0.006   0.001   PHE B 166 
 TRP   0.010   0.001   TRP B 103 
 HIS   0.002   0.000   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (15533)
  covalent geometry    : angle       0.56012 (21042)
  hydrogen bonds       : bond        0.24534 (  748)
  hydrogen bonds       : angle       7.60931 ( 2106)
  metal coordination   : bond        0.01822 (    8)
  metal coordination   : angle       1.82242 (   12)
  Misc. bond           : bond        0.04353 (    2)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  236 is missing expected H atoms. Skipping.
Residue THR  225 is missing expected H atoms. Skipping.
Residue SER   69 is missing expected H atoms. Skipping.
Evaluate side-chains
  293 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 292
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 THR cc_start: 0.9048 (m) cc_final: 0.8772 (p)
REVERT: A  349 ARG cc_start: 0.8252 (mtm-85) cc_final: 0.7447 (mtp85)
REVERT: A  445 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8038 (mt-10)
REVERT: B   57 MET cc_start: 0.8722 (mmt) cc_final: 0.8426 (mmt)
REVERT: B  122 MET cc_start: 0.8742 (ttm) cc_final: 0.8515 (ttp)
REVERT: B  382 MET cc_start: 0.8534 (tpt) cc_final: 0.7627 (tpt)
REVERT: C   84 VAL cc_start: 0.6120 (t) cc_final: 0.5887 (t)
REVERT: C   94 ARG cc_start: 0.7340 (mtt180) cc_final: 0.5932 (tpp80)
REVERT: D   32 LEU cc_start: 0.9017 (mt) cc_final: 0.8788 (mt)
REVERT: D  207 GLU cc_start: 0.7976 (tp30) cc_final: 0.7744 (tp30)
REVERT: F   24 PHE cc_start: 0.6945 (t80) cc_final: 0.6737 (m-80)
REVERT: F  210 ARG cc_start: 0.3751 (mmt-90) cc_final: 0.3416 (mmt90)
REVERT: F  264 PHE cc_start: 0.5706 (m-80) cc_final: 0.5111 (m-80)
REVERT: F  312 ARG cc_start: 0.4690 (ttp-170) cc_final: 0.3482 (mmm160)
REVERT: F  375 TYR cc_start: 0.6595 (m-80) cc_final: 0.6265 (m-80)
REVERT: F  383 MET cc_start: 0.1424 (ttm) cc_final: 0.1146 (ttm)
  outliers start: 1
  outliers final: 0
  residues processed: 292
  average time/residue: 0.2911
  time to fit residues: 123.1155
Evaluate side-chains
  212 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    6.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN
B  84 ASN
D  75 GLN
E  79 ASN
F 295 GLN
F 330 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.152480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.107600 restraints weight = 67989.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 2.64
r_work: 0.3314 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       64 |
|-----------------------------------------------------------------------------|
r_final: 0.3200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  15543  Z= 0.236
  Angle     :  0.605   8.670  21054  Z= 0.316
  Chirality :  0.044   0.202   2371
  Planarity :  0.004   0.034   2616
  Dihedral  : 11.822 118.474   2490
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 16.20 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.19), residues: 1908
  helix:  1.47 (0.18), residues: 875
  sheet: -0.46 (0.38), residues: 188
  loop : -0.25 (0.21), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG F 298 
 TYR   0.015   0.001   TYR B 360 
 PHE   0.024   0.001   PHE F  11 
 TRP   0.020   0.002   TRP F 308 
 HIS   0.004   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 (15533)
  covalent geometry    : angle       0.59288 (21042)
  hydrogen bonds       : bond        0.06113 (  748)
  hydrogen bonds       : angle       5.43933 ( 2106)
  metal coordination   : bond        0.01244 (    8)
  metal coordination   : angle       4.98434 (   12)
  Misc. bond           : bond        0.00569 (    2)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  236 is missing expected H atoms. Skipping.
Residue THR  225 is missing expected H atoms. Skipping.
Residue SER   69 is missing expected H atoms. Skipping.
Evaluate side-chains
  235 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 216
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7615 (mtp85)
REVERT: A  231 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8533 (p)
REVERT: A  349 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.7729 (mtp85)
REVERT: A  445 GLU cc_start: 0.8219 (mt-10) cc_final: 0.8018 (mt-10)
REVERT: B   57 MET cc_start: 0.9081 (mmt) cc_final: 0.8851 (mmt)
REVERT: B  122 MET cc_start: 0.8878 (ttm) cc_final: 0.8650 (ttp)
REVERT: B  382 MET cc_start: 0.8360 (tpt) cc_final: 0.7730 (tpt)
REVERT: C   94 ARG cc_start: 0.6441 (mtt180) cc_final: 0.5913 (mtt90)
REVERT: C  148 MET cc_start: 0.8623 (mmm) cc_final: 0.8422 (tpp)
REVERT: C  170 GLN cc_start: 0.8382 (pp30) cc_final: 0.7524 (pp30)
REVERT: E  120 CYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7358 (m)
REVERT: F  292 ILE cc_start: 0.8393 (mt) cc_final: 0.8100 (tp)
REVERT: F  308 TRP cc_start: 0.2523 (m100) cc_final: 0.2266 (m100)
REVERT: F  312 ARG cc_start: 0.4505 (ttp-170) cc_final: 0.3664 (mmm160)
REVERT: F  318 PHE cc_start: 0.5912 (OUTLIER) cc_final: 0.5581 (p90)
REVERT: F  374 GLU cc_start: 0.7069 (tp30) cc_final: 0.6695 (mt-10)
REVERT: F  375 TYR cc_start: 0.7050 (m-80) cc_final: 0.6131 (m-80)
REVERT: F  377 MET cc_start: 0.5781 (tpt) cc_final: 0.5255 (tpt)
REVERT: F  397 GLU cc_start: 0.6434 (mp0) cc_final: 0.6232 (mp0)
  outliers start: 19
  outliers final: 13
  residues processed: 229
  average time/residue: 0.2576
  time to fit residues: 89.1718
Evaluate side-chains
  208 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 192
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  302 SER
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  221 SER
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain D residue  133 ASP
Chi-restraints excluded: chain E residue  115 LEU
Chi-restraints excluded: chain E residue  117 THR
Chi-restraints excluded: chain E residue  120 CYS
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  214 MET
Chi-restraints excluded: chain F residue  306 SER
Chi-restraints excluded: chain F residue  318 PHE
Chi-restraints excluded: chain F residue  336 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 174 optimal weight:    7.9990
   chunk 96 optimal weight:    8.9990
   chunk 57 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0040
   chunk 63 optimal weight:    2.9990
   chunk 158 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 118 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 129 optimal weight:    2.9990
   chunk 141 optimal weight:    0.9990
   overall best weight:    1.8000

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

Flipped N/Q/H residues before XYZ refinement:
B 398 HIS
C 143 ASN
D 100 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.154680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.108304 restraints weight = 67615.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.54
r_work: 0.3314 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3203
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       64 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       75 |
|-----------------------------------------------------------------------------|
r_final: 0.3203
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15543  Z= 0.149
  Angle     :  0.514   7.013  21054  Z= 0.260
  Chirality :  0.042   0.323   2371
  Planarity :  0.003   0.032   2616
  Dihedral  : 10.248 117.397   2490
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 16.65 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.19), residues: 1908
  helix:  1.54 (0.18), residues: 877
  sheet: -0.57 (0.37), residues: 189
  loop : -0.27 (0.21), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 298 
 TYR   0.014   0.001   TYR B  27 
 PHE   0.026   0.001   PHE B  14 
 TRP   0.012   0.001   TRP B 103 
 HIS   0.004   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (15533)
  covalent geometry    : angle       0.50618 (21042)
  hydrogen bonds       : bond        0.05180 (  748)
  hydrogen bonds       : angle       4.94220 ( 2106)
  metal coordination   : bond        0.01520 (    8)
  metal coordination   : angle       3.70909 (   12)
  Misc. bond           : bond        0.00078 (    2)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  236 is missing expected H atoms. Skipping.
Residue THR  225 is missing expected H atoms. Skipping.
Residue SER   69 is missing expected H atoms. Skipping.
Evaluate side-chains
  222 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 205
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.7125 (t0) cc_final: 0.6810 (t0)
REVERT: A  231 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8510 (p)
REVERT: A  349 ARG cc_start: 0.8309 (mtm-85) cc_final: 0.7635 (mtp85)
REVERT: A  445 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7692 (mt-10)
REVERT: B   57 MET cc_start: 0.9051 (mmt) cc_final: 0.8837 (mmt)
REVERT: B  305 MET cc_start: 0.8340 (tmm) cc_final: 0.8037 (ttp)
REVERT: B  382 MET cc_start: 0.8490 (tpt) cc_final: 0.7783 (tpt)
REVERT: C   94 ARG cc_start: 0.6415 (mtt180) cc_final: 0.5884 (ttt90)
REVERT: C  148 MET cc_start: 0.8677 (mmm) cc_final: 0.8427 (tpp)
REVERT: C  170 GLN cc_start: 0.8370 (pp30) cc_final: 0.7536 (pp30)
REVERT: E  120 CYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7226 (m)
REVERT: F   55 LEU cc_start: 0.4887 (OUTLIER) cc_final: 0.4679 (tt)
REVERT: F  276 MET cc_start: 0.8357 (mtm) cc_final: 0.7942 (mtm)
REVERT: F  288 MET cc_start: 0.7090 (mmm) cc_final: 0.6719 (mmm)
REVERT: F  292 ILE cc_start: 0.8475 (mt) cc_final: 0.8244 (tp)
REVERT: F  312 ARG cc_start: 0.4604 (ttp-170) cc_final: 0.3768 (mmm160)
REVERT: F  318 PHE cc_start: 0.5805 (OUTLIER) cc_final: 0.5398 (p90)
REVERT: F  375 TYR cc_start: 0.7057 (m-80) cc_final: 0.6257 (m-80)
REVERT: F  377 MET cc_start: 0.5650 (tpt) cc_final: 0.5316 (tpt)
REVERT: F  390 MET cc_start: 0.0088 (mtp) cc_final: -0.0155 (mtp)
  outliers start: 17
  outliers final: 8
  residues processed: 218
  average time/residue: 0.2662
  time to fit residues: 87.8694
Evaluate side-chains
  202 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 190
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain D residue  133 ASP
Chi-restraints excluded: chain E residue  120 CYS
Chi-restraints excluded: chain F residue   55 LEU
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  214 MET
Chi-restraints excluded: chain F residue  258 CYS
Chi-restraints excluded: chain F residue  306 SER
Chi-restraints excluded: chain F residue  318 PHE
Chi-restraints excluded: chain F residue  326 LEU
Chi-restraints excluded: chain F residue  336 HIS
Chi-restraints excluded: chain F residue  339 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 134 optimal weight:    1.9990
   chunk 168 optimal weight:    9.9990
   chunk 144 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
E  61 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.152717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.107358 restraints weight = 67433.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.47
r_work: 0.3315 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3203
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       75 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       80 |
|-----------------------------------------------------------------------------|
r_final: 0.3203
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15543  Z= 0.134
  Angle     :  0.501   7.014  21054  Z= 0.251
  Chirality :  0.041   0.380   2371
  Planarity :  0.003   0.033   2616
  Dihedral  :  9.311 115.791   2490
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 17.03 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.19), residues: 1908
  helix:  1.60 (0.18), residues: 876
  sheet: -0.58 (0.37), residues: 189
  loop : -0.28 (0.21), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 298 
 TYR   0.025   0.001   TYR F 309 
 PHE   0.024   0.001   PHE F  11 
 TRP   0.012   0.001   TRP B 103 
 HIS   0.002   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (15533)
  covalent geometry    : angle       0.49216 (21042)
  hydrogen bonds       : bond        0.04336 (  748)
  hydrogen bonds       : angle       4.67315 ( 2106)
  metal coordination   : bond        0.01079 (    8)
  metal coordination   : angle       4.05497 (   12)
  Misc. bond           : bond        0.00053 (    2)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  236 is missing expected H atoms. Skipping.
Residue THR  225 is missing expected H atoms. Skipping.
Residue SER   69 is missing expected H atoms. Skipping.
Evaluate side-chains
  217 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 198
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.7184 (t0) cc_final: 0.6863 (t0)
REVERT: A  231 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8463 (p)
REVERT: A  349 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.7612 (mtp85)
REVERT: A  415 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8278 (mt-10)
REVERT: B   57 MET cc_start: 0.9016 (mmt) cc_final: 0.8794 (mmt)
REVERT: B  382 MET cc_start: 0.8342 (tpt) cc_final: 0.7638 (tpt)
REVERT: C  148 MET cc_start: 0.8627 (mmm) cc_final: 0.8352 (tpp)
REVERT: C  170 GLN cc_start: 0.8367 (pp30) cc_final: 0.7501 (pp30)
REVERT: E  120 CYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7242 (m)
REVERT: E  197 GLN cc_start: 0.5746 (OUTLIER) cc_final: 0.4633 (pm20)
REVERT: F  292 ILE cc_start: 0.8583 (mt) cc_final: 0.8199 (tp)
REVERT: F  312 ARG cc_start: 0.4409 (ttp-170) cc_final: 0.3633 (mmm160)
REVERT: F  318 PHE cc_start: 0.5732 (OUTLIER) cc_final: 0.5220 (p90)
REVERT: F  375 TYR cc_start: 0.6512 (m-80) cc_final: 0.6111 (m-80)
REVERT: F  377 MET cc_start: 0.5615 (tpt) cc_final: 0.5376 (tpt)
REVERT: F  390 MET cc_start: 0.0147 (mtp) cc_final: -0.0059 (mtp)
  outliers start: 19
  outliers final: 12
  residues processed: 210
  average time/residue: 0.2539
  time to fit residues: 80.4185
Evaluate side-chains
  199 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 183
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  417 ASP
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  380 GLU
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue  133 ASP
Chi-restraints excluded: chain E residue  120 CYS
Chi-restraints excluded: chain E residue  197 GLN
Chi-restraints excluded: chain F residue   55 LEU
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  214 MET
Chi-restraints excluded: chain F residue  258 CYS
Chi-restraints excluded: chain F residue  306 SER
Chi-restraints excluded: chain F residue  318 PHE
Chi-restraints excluded: chain F residue  326 LEU
Chi-restraints excluded: chain F residue  336 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 178 optimal weight:   10.0000
   chunk 118 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 168 optimal weight:    5.9990
   chunk 187 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 125 optimal weight:    7.9990
   overall best weight:    2.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.151284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.106377 restraints weight = 68173.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 2.75
r_work: 0.3254 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3145
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       80 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       83 |
|-----------------------------------------------------------------------------|
r_final: 0.3145
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  15543  Z= 0.219
  Angle     :  0.553  10.495  21054  Z= 0.279
  Chirality :  0.042   0.354   2371
  Planarity :  0.004   0.041   2616
  Dihedral  :  9.096 114.619   2490
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.65 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.19), residues: 1908
  helix:  1.50 (0.18), residues: 877
  sheet: -0.69 (0.37), residues: 189
  loop : -0.43 (0.21), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  94 
 TYR   0.017   0.002   TYR B  27 
 PHE   0.028   0.001   PHE F 333 
 TRP   0.015   0.001   TRP B 103 
 HIS   0.003   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 (15533)
  covalent geometry    : angle       0.53788 (21042)
  hydrogen bonds       : bond        0.04567 (  748)
  hydrogen bonds       : angle       4.71246 ( 2106)
  metal coordination   : bond        0.01868 (    8)
  metal coordination   : angle       5.39420 (   12)
  Misc. bond           : bond        0.00078 (    2)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  236 is missing expected H atoms. Skipping.
Residue THR  225 is missing expected H atoms. Skipping.
Residue SER   69 is missing expected H atoms. Skipping.
Evaluate side-chains
  219 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 187
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 SER cc_start: 0.8868 (OUTLIER) cc_final: 0.8603 (p)
REVERT: B   57 MET cc_start: 0.8965 (mmt) cc_final: 0.8710 (mmt)
REVERT: B  187 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8855 (t)
REVERT: B  305 MET cc_start: 0.8341 (tmm) cc_final: 0.8071 (ttp)
REVERT: B  322 MET cc_start: 0.8934 (tpp) cc_final: 0.8682 (tpp)
REVERT: B  382 MET cc_start: 0.8612 (tpt) cc_final: 0.7928 (tpt)
REVERT: C  170 GLN cc_start: 0.8416 (pp30) cc_final: 0.7537 (pp30)
REVERT: D   52 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8879 (t)
REVERT: E  120 CYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7432 (m)
REVERT: E  197 GLN cc_start: 0.5649 (OUTLIER) cc_final: 0.4498 (pm20)
REVERT: F  312 ARG cc_start: 0.4368 (ttp-170) cc_final: 0.3660 (mmm160)
REVERT: F  318 PHE cc_start: 0.5664 (OUTLIER) cc_final: 0.4881 (p90)
REVERT: F  375 TYR cc_start: 0.6939 (m-80) cc_final: 0.6521 (m-80)
  outliers start: 32
  outliers final: 18
  residues processed: 206
  average time/residue: 0.2513
  time to fit residues: 80.7764
Evaluate side-chains
  205 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 181
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  302 SER
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  221 SER
Chi-restraints excluded: chain B residue  310 THR
Chi-restraints excluded: chain B residue  380 GLU
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue  133 ASP
Chi-restraints excluded: chain D residue  200 THR
Chi-restraints excluded: chain E residue  120 CYS
Chi-restraints excluded: chain E residue  197 GLN
Chi-restraints excluded: chain F residue   12 THR
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  170 ILE
Chi-restraints excluded: chain F residue  214 MET
Chi-restraints excluded: chain F residue  306 SER
Chi-restraints excluded: chain F residue  318 PHE
Chi-restraints excluded: chain F residue  326 LEU
Chi-restraints excluded: chain F residue  336 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 119 optimal weight:    6.9990
   chunk 93 optimal weight:    3.9990
   chunk 159 optimal weight:    9.9990
   chunk 148 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 158 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 143 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 110 optimal weight:    0.4980
   overall best weight:    2.0988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.152289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.106966 restraints weight = 67667.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.46
r_work: 0.3280 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       83 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       85 |
|-----------------------------------------------------------------------------|
r_final: 0.3174
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  15543  Z= 0.152
  Angle     :  0.505   7.614  21054  Z= 0.254
  Chirality :  0.041   0.347   2371
  Planarity :  0.003   0.034   2616
  Dihedral  :  8.747 115.101   2490
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 17.22 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.19), residues: 1908
  helix:  1.58 (0.18), residues: 877
  sheet: -0.67 (0.37), residues: 187
  loop : -0.41 (0.21), residues: 844

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 298 
 TYR   0.013   0.001   TYR F 309 
 PHE   0.021   0.001   PHE F  11 
 TRP   0.013   0.001   TRP B 103 
 HIS   0.002   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (15533)
  covalent geometry    : angle       0.49281 (21042)
  hydrogen bonds       : bond        0.04152 (  748)
  hydrogen bonds       : angle       4.53040 ( 2106)
  metal coordination   : bond        0.01289 (    8)
  metal coordination   : angle       4.58997 (   12)
  Misc. bond           : bond        0.00052 (    2)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  236 is missing expected H atoms. Skipping.
Residue THR  225 is missing expected H atoms. Skipping.
Residue SER   69 is missing expected H atoms. Skipping.
Evaluate side-chains
  208 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 184
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 SER cc_start: 0.8857 (OUTLIER) cc_final: 0.8589 (p)
REVERT: B   57 MET cc_start: 0.8938 (mmt) cc_final: 0.8667 (mmt)
REVERT: B  187 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8860 (t)
REVERT: B  382 MET cc_start: 0.8531 (tpt) cc_final: 0.7855 (tpt)
REVERT: E  120 CYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7439 (m)
REVERT: E  197 GLN cc_start: 0.5624 (OUTLIER) cc_final: 0.4525 (pm20)
REVERT: F  312 ARG cc_start: 0.4313 (ttp-170) cc_final: 0.3590 (mmm160)
REVERT: F  375 TYR cc_start: 0.7014 (m-80) cc_final: 0.6633 (m-80)
  outliers start: 24
  outliers final: 18
  residues processed: 197
  average time/residue: 0.2433
  time to fit residues: 74.4949
Evaluate side-chains
  199 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 177
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  417 ASP
Chi-restraints excluded: chain B residue   12 HIS
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  380 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue  133 ASP
Chi-restraints excluded: chain E residue  120 CYS
Chi-restraints excluded: chain E residue  197 GLN
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  170 ILE
Chi-restraints excluded: chain F residue  306 SER
Chi-restraints excluded: chain F residue  318 PHE
Chi-restraints excluded: chain F residue  326 LEU
Chi-restraints excluded: chain F residue  336 HIS
Chi-restraints excluded: chain F residue  339 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 91 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 125 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   chunk 181 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 168 optimal weight:    3.9990
   chunk 112 optimal weight:    0.7980
   overall best weight:    1.8784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.150568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.105709 restraints weight = 67857.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.67
r_work: 0.3274 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3164
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       85 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       85 |
|-----------------------------------------------------------------------------|
r_final: 0.3164
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15543  Z= 0.148
  Angle     :  0.499   7.792  21054  Z= 0.250
  Chirality :  0.041   0.324   2371
  Planarity :  0.003   0.034   2616
  Dihedral  :  8.536 116.473   2490
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.96 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.19), residues: 1908
  helix:  1.65 (0.18), residues: 877
  sheet: -0.60 (0.37), residues: 185
  loop : -0.40 (0.21), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 395 
 TYR   0.012   0.001   TYR F 309 
 PHE   0.019   0.001   PHE F  11 
 TRP   0.013   0.001   TRP B 103 
 HIS   0.002   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (15533)
  covalent geometry    : angle       0.48666 (21042)
  hydrogen bonds       : bond        0.04046 (  748)
  hydrogen bonds       : angle       4.47188 ( 2106)
  metal coordination   : bond        0.01225 (    8)
  metal coordination   : angle       4.65928 (   12)
  Misc. bond           : bond        0.00052 (    2)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  236 is missing expected H atoms. Skipping.
Residue THR  225 is missing expected H atoms. Skipping.
Residue SER   69 is missing expected H atoms. Skipping.
Evaluate side-chains
  214 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 184
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 SER cc_start: 0.8857 (OUTLIER) cc_final: 0.8587 (p)
REVERT: B   57 MET cc_start: 0.8944 (mmt) cc_final: 0.8652 (mmt)
REVERT: B  187 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8857 (t)
REVERT: B  325 MET cc_start: 0.9012 (ttp) cc_final: 0.8766 (ttp)
REVERT: B  382 MET cc_start: 0.8523 (tpt) cc_final: 0.7823 (tpt)
REVERT: E  197 GLN cc_start: 0.5624 (OUTLIER) cc_final: 0.4535 (pm20)
REVERT: F  312 ARG cc_start: 0.3980 (ttp-170) cc_final: 0.3351 (mmm160)
REVERT: F  375 TYR cc_start: 0.7074 (m-80) cc_final: 0.6683 (m-80)
  outliers start: 30
  outliers final: 21
  residues processed: 202
  average time/residue: 0.2442
  time to fit residues: 76.9369
Evaluate side-chains
  202 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 178
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  417 ASP
Chi-restraints excluded: chain B residue   12 HIS
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  221 SER
Chi-restraints excluded: chain B residue  380 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue  133 ASP
Chi-restraints excluded: chain E residue  197 GLN
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  170 ILE
Chi-restraints excluded: chain F residue  214 MET
Chi-restraints excluded: chain F residue  306 SER
Chi-restraints excluded: chain F residue  318 PHE
Chi-restraints excluded: chain F residue  326 LEU
Chi-restraints excluded: chain F residue  336 HIS
Chi-restraints excluded: chain F residue  352 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 159 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 172 optimal weight:    0.7980
   chunk 44 optimal weight:   10.0000
   chunk 121 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9980
   chunk 148 optimal weight:    3.9990
   chunk 132 optimal weight:    4.9990
   chunk 95 optimal weight:    9.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
B 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.149611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.105459 restraints weight = 68296.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.45
r_work: 0.3270 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       85 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       85 |
|-----------------------------------------------------------------------------|
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15543  Z= 0.173
  Angle     :  0.514   8.607  21054  Z= 0.258
  Chirality :  0.041   0.317   2371
  Planarity :  0.004   0.035   2616
  Dihedral  :  8.571 119.282   2490
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 17.41 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.19), residues: 1908
  helix:  1.64 (0.18), residues: 876
  sheet: -0.62 (0.37), residues: 185
  loop : -0.44 (0.21), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 303 
 TYR   0.013   0.001   TYR B  27 
 PHE   0.020   0.001   PHE F  11 
 TRP   0.014   0.001   TRP B 103 
 HIS   0.003   0.001   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (15533)
  covalent geometry    : angle       0.50022 (21042)
  hydrogen bonds       : bond        0.04072 (  748)
  hydrogen bonds       : angle       4.48062 ( 2106)
  metal coordination   : bond        0.01364 (    8)
  metal coordination   : angle       4.95364 (   12)
  Misc. bond           : bond        0.00053 (    2)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  236 is missing expected H atoms. Skipping.
Residue THR  225 is missing expected H atoms. Skipping.
Residue SER   69 is missing expected H atoms. Skipping.
Evaluate side-chains
  209 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 185
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8613 (p)
REVERT: B   57 MET cc_start: 0.8923 (mmt) cc_final: 0.8627 (mmt)
REVERT: B  187 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8854 (t)
REVERT: B  382 MET cc_start: 0.8546 (tpt) cc_final: 0.7834 (tpt)
REVERT: E  197 GLN cc_start: 0.5649 (OUTLIER) cc_final: 0.4532 (pm20)
REVERT: F  312 ARG cc_start: 0.3970 (ttp-170) cc_final: 0.3424 (mmm160)
REVERT: F  375 TYR cc_start: 0.7142 (m-80) cc_final: 0.6827 (m-80)
  outliers start: 24
  outliers final: 19
  residues processed: 200
  average time/residue: 0.2467
  time to fit residues: 76.7066
Evaluate side-chains
  203 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 181
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain B residue   12 HIS
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  221 SER
Chi-restraints excluded: chain B residue  380 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue  133 ASP
Chi-restraints excluded: chain E residue  197 GLN
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  170 ILE
Chi-restraints excluded: chain F residue  258 CYS
Chi-restraints excluded: chain F residue  306 SER
Chi-restraints excluded: chain F residue  318 PHE
Chi-restraints excluded: chain F residue  326 LEU
Chi-restraints excluded: chain F residue  336 HIS
Chi-restraints excluded: chain F residue  352 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 150 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 134 optimal weight:    0.6980
   chunk 118 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 153 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.150256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.105349 restraints weight = 67752.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.43
r_work: 0.3281 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3170
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       85 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       85 |
|-----------------------------------------------------------------------------|
r_final: 0.3170
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15543  Z= 0.136
  Angle     :  0.493   7.874  21054  Z= 0.246
  Chirality :  0.041   0.305   2371
  Planarity :  0.003   0.034   2616
  Dihedral  :  8.430 122.501   2490
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 17.86 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.19), residues: 1908
  helix:  1.72 (0.18), residues: 876
  sheet: -0.59 (0.37), residues: 185
  loop : -0.39 (0.21), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 318 
 TYR   0.012   0.001   TYR F 309 
 PHE   0.021   0.001   PHE F 333 
 TRP   0.013   0.001   TRP B 103 
 HIS   0.003   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (15533)
  covalent geometry    : angle       0.48115 (21042)
  hydrogen bonds       : bond        0.03904 (  748)
  hydrogen bonds       : angle       4.40082 ( 2106)
  metal coordination   : bond        0.01107 (    8)
  metal coordination   : angle       4.44006 (   12)
  Misc. bond           : bond        0.00036 (    2)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  236 is missing expected H atoms. Skipping.
Residue THR  225 is missing expected H atoms. Skipping.
Residue SER   69 is missing expected H atoms. Skipping.
Evaluate side-chains
  212 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 187
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8573 (p)
REVERT: B   57 MET cc_start: 0.8910 (mmt) cc_final: 0.8595 (mmt)
REVERT: B  305 MET cc_start: 0.8244 (tmm) cc_final: 0.7884 (ttp)
REVERT: B  382 MET cc_start: 0.8493 (tpt) cc_final: 0.7779 (tpt)
REVERT: E  120 CYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7397 (m)
REVERT: E  197 GLN cc_start: 0.5579 (OUTLIER) cc_final: 0.4478 (pm20)
REVERT: F  133 TRP cc_start: 0.8054 (m100) cc_final: 0.7626 (m100)
REVERT: F  285 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7973 (tpp)
REVERT: F  312 ARG cc_start: 0.4026 (ttp-170) cc_final: 0.3307 (mmm160)
REVERT: F  375 TYR cc_start: 0.7212 (m-80) cc_final: 0.6807 (m-80)
REVERT: F  397 GLU cc_start: 0.6761 (mm-30) cc_final: 0.5381 (pm20)
  outliers start: 25
  outliers final: 18
  residues processed: 204
  average time/residue: 0.2499
  time to fit residues: 80.0000
Evaluate side-chains
  201 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 179
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  302 SER
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  221 SER
Chi-restraints excluded: chain B residue  380 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  145 LEU
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue  133 ASP
Chi-restraints excluded: chain E residue  120 CYS
Chi-restraints excluded: chain E residue  197 GLN
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  170 ILE
Chi-restraints excluded: chain F residue  258 CYS
Chi-restraints excluded: chain F residue  285 MET
Chi-restraints excluded: chain F residue  306 SER
Chi-restraints excluded: chain F residue  318 PHE
Chi-restraints excluded: chain F residue  326 LEU
Chi-restraints excluded: chain F residue  336 HIS
Chi-restraints excluded: chain F residue  352 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 90 optimal weight:    7.9990
   chunk 64 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 181 optimal weight:    8.9990
   chunk 187 optimal weight:    0.0030
   chunk 81 optimal weight:    3.9990
   chunk 126 optimal weight:    0.7980
   chunk 151 optimal weight:    0.0370
   chunk 94 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.5668

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

Flipped N/Q/H residues before XYZ refinement:
B 200 ASN
C 120 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.152335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.107796 restraints weight = 67357.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.44
r_work: 0.3310 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3200
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       85 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       85 |
|-----------------------------------------------------------------------------|
r_final: 0.3200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  15543  Z= 0.093
  Angle     :  0.461   7.573  21054  Z= 0.232
  Chirality :  0.040   0.280   2371
  Planarity :  0.003   0.034   2616
  Dihedral  :  8.038 126.279   2490
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 18.05 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.20), residues: 1908
  helix:  1.87 (0.18), residues: 879
  sheet: -0.48 (0.38), residues: 182
  loop : -0.24 (0.21), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 395 
 TYR   0.014   0.001   TYR F 309 
 PHE   0.019   0.001   PHE F 333 
 TRP   0.011   0.001   TRP B 260 
 HIS   0.002   0.000   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 (15533)
  covalent geometry    : angle       0.45351 (21042)
  hydrogen bonds       : bond        0.03556 (  748)
  hydrogen bonds       : angle       4.25180 ( 2106)
  metal coordination   : bond        0.00562 (    8)
  metal coordination   : angle       3.59739 (   12)
  Misc. bond           : bond        0.00008 (    2)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  236 is missing expected H atoms. Skipping.
Residue THR  225 is missing expected H atoms. Skipping.
Residue SER   69 is missing expected H atoms. Skipping.
Evaluate side-chains
  215 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 196
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 LEU cc_start: 0.9070 (tp) cc_final: 0.8844 (tp)
REVERT: B   57 MET cc_start: 0.8901 (mmt) cc_final: 0.8610 (mmt)
REVERT: B  261 MET cc_start: 0.8190 (tpt) cc_final: 0.7930 (tpp)
REVERT: B  382 MET cc_start: 0.8243 (tpt) cc_final: 0.7521 (tpt)
REVERT: E  120 CYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7277 (m)
REVERT: F  112 GLN cc_start: 0.7777 (mm110) cc_final: 0.7571 (mm110)
REVERT: F  194 LYS cc_start: 0.4423 (tttt) cc_final: 0.3910 (mtpt)
REVERT: F  285 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8038 (tpp)
REVERT: F  312 ARG cc_start: 0.3810 (ttp-170) cc_final: 0.3203 (mmm160)
REVERT: F  321 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7297 (pm20)
REVERT: F  375 TYR cc_start: 0.7179 (m-80) cc_final: 0.6774 (m-80)
REVERT: F  397 GLU cc_start: 0.6486 (mm-30) cc_final: 0.5437 (pm20)
  outliers start: 19
  outliers final: 13
  residues processed: 209
  average time/residue: 0.2336
  time to fit residues: 76.7064
Evaluate side-chains
  204 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 189
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  302 SER
Chi-restraints excluded: chain B residue  221 SER
Chi-restraints excluded: chain B residue  380 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain D residue   28 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue  120 CYS
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  285 MET
Chi-restraints excluded: chain F residue  306 SER
Chi-restraints excluded: chain F residue  318 PHE
Chi-restraints excluded: chain F residue  326 LEU
Chi-restraints excluded: chain F residue  336 HIS
Chi-restraints excluded: chain F residue  352 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 100 optimal weight:    0.0050
   chunk 135 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 162 optimal weight:    9.9990
   chunk 112 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 92 optimal weight:    8.9990
   chunk 160 optimal weight:    0.0070
   overall best weight:    1.2018

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

Flipped N/Q/H residues before XYZ refinement:
B 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.151649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.106960 restraints weight = 67867.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.61
r_work: 0.3295 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       85 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       86 |
|-----------------------------------------------------------------------------|
r_final: 0.3182
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  15543  Z= 0.115
  Angle     :  0.483  13.854  21054  Z= 0.239
  Chirality :  0.040   0.266   2371
  Planarity :  0.003   0.037   2616
  Dihedral  :  7.978 127.483   2490
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 18.56 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.20), residues: 1908
  helix:  1.92 (0.18), residues: 877
  sheet: -0.49 (0.38), residues: 188
  loop : -0.21 (0.21), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 303 
 TYR   0.020   0.001   TYR F 360 
 PHE   0.020   0.001   PHE F 333 
 TRP   0.012   0.001   TRP B 103 
 HIS   0.002   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (15533)
  covalent geometry    : angle       0.46538 (21042)
  hydrogen bonds       : bond        0.03588 (  748)
  hydrogen bonds       : angle       4.25689 ( 2106)
  metal coordination   : bond        0.01419 (    8)
  metal coordination   : angle       5.49876 (   12)
  Misc. bond           : bond        0.00025 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7972.34 seconds
wall clock time: 135 minutes 36.95 seconds (8136.95 seconds total)