Starting phenix.real_space_refine
on Wed Jul 30 12:07:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8glu_40218/07_2025/8glu_40218.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8glu_40218/07_2025/8glu_40218.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8glu_40218/07_2025/8glu_40218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8glu_40218/07_2025/8glu_40218.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8glu_40218/07_2025/8glu_40218.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8glu_40218/07_2025/8glu_40218.cif"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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
     Zn      1      6.06       5
     P       8      5.49       5
     Mg      3      5.21       5
     S      43      5.16       5
     C    7795      2.51       5
     N    2227      2.21       5
     O    2261      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12338
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "G"
      Number of atoms: 3193
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 3193
          Classifications: {'peptide': 402}
          Link IDs: {'PTRANS': 14, 'TRANS': 387}
    Chain: "X"
      Number of atoms: 2523
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2523
          Classifications: {'peptide': 310}
          Link IDs: {'PTRANS': 15, 'TRANS': 294}
    Chain: "F"
      Number of atoms: 3203
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 403, 3203
          Classifications: {'peptide': 403}
          Link IDs: {'PTRANS': 14, 'TRANS': 388}
    Chain: "E"
      Number of atoms: 3326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 418, 3326
          Classifications: {'peptide': 418}
          Link IDs: {'PTRANS': 15, 'TRANS': 402}
    Chain: "G"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "X"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4188  SG  CYS X 124      53.942  61.985  38.668  1.00 45.24           S
  ATOM   4209  SG  CYS X 127      50.862  64.091  39.821  1.00 45.34           S
  ATOM   4427  SG  CYS X 152      50.421  61.433  37.072  1.00 60.05           S

  Residues with excluded nonbonded symmetry interactions: 11
    residue:
      pdb=" N   ASP G 278 " occ=0.00
      ... (6 atoms not shown)
      pdb=" OD2 ASP G 278 " occ=0.00
    residue:
      pdb=" N   LEU G 279 " occ=0.00
      ... (6 atoms not shown)
      pdb=" CD2 LEU G 279 " occ=0.00
    residue:
      pdb=" N   ARG G 280 " occ=0.00
      ... (9 atoms not shown)
      pdb=" NH2 ARG G 280 " occ=0.00
    residue:
      pdb=" N   SER G 281 " occ=0.00
      ... (4 atoms not shown)
      pdb=" OG  SER G 281 " occ=0.00
    residue:
      pdb=" N   ALA G 282 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA G 282 " occ=0.00
    residue:
      pdb=" N   ARG G 283 " occ=0.00
      ... (9 atoms not shown)
      pdb=" NH2 ARG G 283 " occ=0.00
    residue:
      pdb=" N   ARG G 284 " occ=0.00
      ... (9 atoms not shown)
      pdb=" NH2 ARG G 284 " occ=0.00
    residue:
      pdb=" N   GLY G 285 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY G 285 " occ=0.00
    residue:
      pdb=" N   ALA G 286 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA G 286 " occ=0.00
    residue:
      pdb=" N   GLY G 287 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY G 287 " occ=0.00
    residue:
      pdb=" N   PHE G 288 " occ=0.00
      ... (9 atoms not shown)
      pdb=" CZ  PHE G 288 " occ=0.00
  Time building chain proxies: 8.06, per 1000 atoms: 0.65
  Number of scatterers: 12338
  At special positions: 0
  Unit cell: (88.065, 120.555, 172.71, 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)
     Zn      1     29.99
     S      43     16.00
     P       8     15.00
     Mg      3     11.99
     O    2261      8.00
     N    2227      7.00
     C    7795      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.09
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN X 601 "
        pdb="ZN    ZN X 601 " - pdb=" ND1 HIS X 155 "
        pdb="ZN    ZN X 601 " - pdb=" SG  CYS X 127 "
        pdb="ZN    ZN X 601 " - pdb=" SG  CYS X 152 "
        pdb="ZN    ZN X 601 " - pdb=" SG  CYS X 124 "
      Number of angles added : 3


  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2870

  Finding SS restraints...
    Secondary structure from input PDB file:
      83 helices and 8 sheets defined
      54.9% alpha, 4.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'G' and resid 21 through 25
    Processing helix  chain 'G' and resid 34 through 38
      removed outlier: 3.850A  pdb=" N   ALA G  37 " --> pdb=" O   VAL G  34 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 47 through 53
      removed outlier: 4.149A  pdb=" N   LEU G  51 " --> pdb=" O   SER G  48 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   GLN G  52 " --> pdb=" O   SER G  49 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LYS G  53 " --> pdb=" O   ASP G  50 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 54 through 63
      removed outlier: 3.506A  pdb=" N   HIS G  60 " --> pdb=" O   VAL G  56 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   THR G  61 " --> pdb=" O   ILE G  57 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ILE G  62 " --> pdb=" O   ARG G  58 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   CYS G  63 " --> pdb=" O   ALA G  59 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 75 through 89
    Processing helix  chain 'G' and resid 100 through 115
      removed outlier: 3.541A  pdb=" N   HIS G 104 " --> pdb=" O   ASP G 100 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TYR G 109 " --> pdb=" O   LEU G 105 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   GLU G 110 " --> pdb=" O   GLN G 106 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   ARG G 111 " --> pdb=" O   ASN G 107 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 141 through 150
      removed outlier: 3.609A  pdb=" N   LEU G 146 " --> pdb=" O   LYS G 142 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 151 through 153
      No H-bonds generated for 'chain 'G' and resid 151 through 153'
    Processing helix  chain 'G' and resid 181 through 196
      removed outlier: 3.575A  pdb=" N   PHE G 188 " --> pdb=" O   CYS G 184 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG G 193 " --> pdb=" O   ARG G 189 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 209 through 224
      removed outlier: 3.550A  pdb=" N   HIS G 224 " --> pdb=" O   ILE G 220 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 233 through 240
    Processing helix  chain 'G' and resid 243 through 256
      removed outlier: 4.303A  pdb=" N   MET G 248 " --> pdb=" O   GLY G 244 " (cutoff:3.500A)
      removed outlier: 4.924A  pdb=" N   LEU G 249 " --> pdb=" O   SER G 245 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL G 253 " --> pdb=" O   LEU G 249 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   VAL G 256 " --> pdb=" O   PHE G 252 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 268 through 270
      No H-bonds generated for 'chain 'G' and resid 268 through 270'
    Processing helix  chain 'G' and resid 271 through 276
    Processing helix  chain 'G' and resid 278 through 283
    Processing helix  chain 'G' and resid 305 through 316
      removed outlier: 3.695A  pdb=" N   ASN G 314 " --> pdb=" O   ALA G 310 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 329 through 339
    Processing helix  chain 'G' and resid 343 through 362
      removed outlier: 3.565A  pdb=" N   VAL G 347 " --> pdb=" O   VAL G 343 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL G 348 " --> pdb=" O   MET G 344 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLY G 362 " --> pdb=" O   ALA G 358 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 367 through 379
    Processing helix  chain 'G' and resid 382 through 392
      removed outlier: 3.586A  pdb=" N   LEU G 386 " --> pdb=" O   VAL G 382 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 393 through 399
      removed outlier: 4.101A  pdb=" N   ARG G 399 " --> pdb=" O   GLU G 395 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 12 through 24
      removed outlier: 3.662A  pdb=" N   GLN X  24 " --> pdb=" O   ALA X  20 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 28 through 37
    Processing helix  chain 'X' and resid 53 through 59
    Processing helix  chain 'X' and resid 66 through 74
    Processing helix  chain 'X' and resid 76 through 85
      removed outlier: 3.826A  pdb=" N   TYR X  80 " --> pdb=" O   LEU X  76 " (cutoff:3.500A)
      Proline residue:  X  82  - end of helix
      removed outlier: 4.250A  pdb=" N   GLY X  85 " --> pdb=" O   ALA X  81 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 86 through 97
      removed outlier: 4.231A  pdb=" N   GLU X  97 " --> pdb=" O   ILE X  93 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 100 through 108
      removed outlier: 3.781A  pdb=" N   VAL X 104 " --> pdb=" O   ALA X 100 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   HIS X 105 " --> pdb=" O   GLN X 101 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LEU X 108 " --> pdb=" O   VAL X 104 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 124 through 135
      removed outlier: 3.704A  pdb=" N   VAL X 128 " --> pdb=" O   CYS X 124 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ALA X 129 " --> pdb=" O   PRO X 125 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 164 through 168
    Processing helix  chain 'X' and resid 189 through 200
      removed outlier: 4.124A  pdb=" N   THR X 193 " --> pdb=" O   LEU X 189 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ALA X 194 " --> pdb=" O   SER X 190 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   LEU X 195 " --> pdb=" O   GLN X 191 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 201 through 203
      No H-bonds generated for 'chain 'X' and resid 201 through 203'
    Processing helix  chain 'X' and resid 205 through 211
      removed outlier: 3.557A  pdb=" N   GLU X 210 " --> pdb=" O   ARG X 207 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU X 211 " --> pdb=" O   ALA X 208 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 214 through 230
    Processing helix  chain 'X' and resid 240 through 250
      removed outlier: 3.517A  pdb=" N   VAL X 246 " --> pdb=" O   VAL X 242 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 251 through 258
    Processing helix  chain 'X' and resid 269 through 276
    Processing helix  chain 'X' and resid 283 through 295
      removed outlier: 3.687A  pdb=" N   HIS X 287 " --> pdb=" O   SER X 283 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   VAL X 290 " --> pdb=" O   GLN X 286 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 299 through 310
      removed outlier: 3.944A  pdb=" N   LEU X 310 " --> pdb=" O   GLN X 306 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 21 through 26
    Processing helix  chain 'F' and resid 33 through 37
      removed outlier: 3.715A  pdb=" N   ALA F  37 " --> pdb=" O   VAL F  34 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 55 through 63
      removed outlier: 3.834A  pdb=" N   ILE F  62 " --> pdb=" O   ARG F  58 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   CYS F  63 " --> pdb=" O   ALA F  59 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 75 through 90
      removed outlier: 4.018A  pdb=" N   LEU F  79 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 100 through 115
      removed outlier: 3.604A  pdb=" N   HIS F 104 " --> pdb=" O   ASP F 100 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 143 through 151
    Processing helix  chain 'F' and resid 179 through 195
      removed outlier: 3.556A  pdb=" N   ILE F 183 " --> pdb=" O   SER F 179 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE F 187 " --> pdb=" O   ILE F 183 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   PHE F 188 " --> pdb=" O   CYS F 184 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ARG F 193 " --> pdb=" O   ARG F 189 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA F 194 " --> pdb=" O   ALA F 190 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 209 through 222
      removed outlier: 3.544A  pdb=" N   ALA F 215 " --> pdb=" O   GLU F 211 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ILE F 220 " --> pdb=" O   LEU F 216 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 233 through 238
    Processing helix  chain 'F' and resid 246 through 259
      removed outlier: 3.526A  pdb=" N   PHE F 251 " --> pdb=" O   GLU F 247 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   PHE F 252 " --> pdb=" O   MET F 248 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR F 254 " --> pdb=" O   ASN F 250 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 268 through 270
      No H-bonds generated for 'chain 'F' and resid 268 through 270'
    Processing helix  chain 'F' and resid 271 through 276
      removed outlier: 3.925A  pdb=" N   PHE F 275 " --> pdb=" O   ALA F 271 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 278 through 286
      removed outlier: 3.928A  pdb=" N   ARG F 284 " --> pdb=" O   ARG F 280 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 305 through 316
      removed outlier: 3.536A  pdb=" N   ILE F 309 " --> pdb=" O   ASN F 305 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 317 through 319
      No H-bonds generated for 'chain 'F' and resid 317 through 319'
    Processing helix  chain 'F' and resid 329 through 341
    Processing helix  chain 'F' and resid 344 through 362
      removed outlier: 3.944A  pdb=" N   VAL F 348 " --> pdb=" O   MET F 344 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU F 350 " --> pdb=" O   ILE F 346 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA F 354 " --> pdb=" O   LEU F 350 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 367 through 379
    Processing helix  chain 'F' and resid 382 through 392
    Processing helix  chain 'F' and resid 393 through 399
    Processing helix  chain 'E' and resid 15 through 19
    Processing helix  chain 'E' and resid 21 through 27
      removed outlier: 3.633A  pdb=" N   LEU E  27 " --> pdb=" O   PHE E  23 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 32 through 39
    Processing helix  chain 'E' and resid 47 through 51
      removed outlier: 3.587A  pdb=" N   LEU E  51 " --> pdb=" O   SER E  48 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 54 through 64
    Processing helix  chain 'E' and resid 64 through 69
    Processing helix  chain 'E' and resid 75 through 90
    Processing helix  chain 'E' and resid 100 through 113
      removed outlier: 3.920A  pdb=" N   HIS E 104 " --> pdb=" O   ASP E 100 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 143 through 151
    Processing helix  chain 'E' and resid 181 through 195
      removed outlier: 4.001A  pdb=" N   LEU E 185 " --> pdb=" O   LYS E 181 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ARG E 193 " --> pdb=" O   ARG E 189 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 198 through 203
    Processing helix  chain 'E' and resid 209 through 224
    Processing helix  chain 'E' and resid 233 through 237
    Processing helix  chain 'E' and resid 246 through 255
    Processing helix  chain 'E' and resid 268 through 270
      No H-bonds generated for 'chain 'E' and resid 268 through 270'
    Processing helix  chain 'E' and resid 271 through 276
      removed outlier: 3.811A  pdb=" N   PHE E 275 " --> pdb=" O   ALA E 271 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 278 through 285
    Processing helix  chain 'E' and resid 305 through 317
    Processing helix  chain 'E' and resid 329 through 341
    Processing helix  chain 'E' and resid 343 through 361
      removed outlier: 4.289A  pdb=" N   VAL E 348 " --> pdb=" O   MET E 344 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   LYS E 349 " --> pdb=" O   ASP E 345 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU E 359 " --> pdb=" O   GLN E 355 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 367 through 379
      removed outlier: 3.945A  pdb=" N   LEU E 379 " --> pdb=" O   TYR E 375 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 382 through 392
    Processing helix  chain 'E' and resid 393 through 400
      removed outlier: 3.506A  pdb=" N   ILE E 397 " --> pdb=" O   ILE E 393 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 407 through 421
      removed outlier: 3.596A  pdb=" N   ARG E 411 " --> pdb=" O   GLU E 407 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'G' and resid 6 through 7
      removed outlier: 6.375A  pdb=" N   ILE G   6 " --> pdb=" O   TYR G 158 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'G' and resid 169 through 173
      removed outlier: 6.222A  pdb=" N   LEU G 170 " --> pdb=" O   VAL G 230 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   ASP G 232 " --> pdb=" O   LEU G 170 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   ILE G 172 " --> pdb=" O   ASP G 232 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   LEU G 229 " --> pdb=" O   MET G 264 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   ILE G 266 " --> pdb=" O   LEU G 229 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ILE G 231 " --> pdb=" O   ILE G 266 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY G 136 " --> pdb=" O   GLY G 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 5 through 7
    Processing sheet with id=AA4, first strand: chain 'F' and resid 171 through 173
      removed outlier: 6.976A  pdb=" N   ILE F 172 " --> pdb=" O   ASP F 232 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 299 through 300
    Processing sheet with id=AA6, first strand: chain 'E' and resid 5 through 7
      removed outlier: 3.679A  pdb=" N   TYR E 158 " --> pdb=" O   ILE E   6 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 131 through 133
      removed outlier: 6.239A  pdb=" N   LEU E 229 " --> pdb=" O   MET E 264 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 135 through 136
      removed outlier: 7.094A  pdb=" N   ILE E 135 " --> pdb=" O   TRP E 293 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    478 hydrogen bonds defined for protein.
    1362 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.15

  Time building geometry restraints manager: 3.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3895
        1.34 -     1.45: 1613
        1.45 -     1.57: 6987
        1.57 -     1.69: 14
        1.69 -     1.81: 70
  Bond restraints: 12579
  Sorted by residual:
  bond pdb=" CA  ASN G 198 "
       pdb=" CB  ASN G 198 "
    ideal  model  delta    sigma   weight residual
    1.527  1.604 -0.077 2.48e-02 1.63e+03 9.55e+00
  bond pdb=" CA  ASN G 198 "
       pdb=" C   ASN G 198 "
    ideal  model  delta    sigma   weight residual
    1.526  1.543 -0.017 1.35e-02 5.49e+03 1.53e+00
  bond pdb=" CA  ASP F  20 "
       pdb=" CB  ASP F  20 "
    ideal  model  delta    sigma   weight residual
    1.528  1.558 -0.030 2.61e-02 1.47e+03 1.30e+00
  bond pdb=" CB  ASN G 198 "
       pdb=" CG  ASN G 198 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 2.50e-02 1.60e+03 1.22e+00
  bond pdb=" CA  ILE E  65 "
       pdb=" CB  ILE E  65 "
    ideal  model  delta    sigma   weight residual
    1.539  1.534  0.005 5.40e-03 3.43e+04 9.60e-01
  ... (remaining 12574 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 16792
        1.81 -     3.63: 192
        3.63 -     5.44: 46
        5.44 -     7.25: 11
        7.25 -     9.07: 2
  Bond angle restraints: 17043
  Sorted by residual:
  angle pdb=" OG1 THR X  45 "
        pdb=" CB  THR X  45 "
        pdb=" CG2 THR X  45 "
      ideal   model   delta    sigma   weight residual
     109.30  103.31    5.99 2.00e+00 2.50e-01 8.97e+00
  angle pdb=" CA  ASN G 198 "
        pdb=" CB  ASN G 198 "
        pdb=" CG  ASN G 198 "
      ideal   model   delta    sigma   weight residual
     112.60  115.55   -2.95 1.00e+00 1.00e+00 8.70e+00
  angle pdb=" N   GLN E 414 "
        pdb=" CA  GLN E 414 "
        pdb=" CB  GLN E 414 "
      ideal   model   delta    sigma   weight residual
     110.28  114.84   -4.56 1.55e+00 4.16e-01 8.66e+00
  angle pdb=" C   ASN G 198 "
        pdb=" CA  ASN G 198 "
        pdb=" CB  ASN G 198 "
      ideal   model   delta    sigma   weight residual
     111.77  116.16   -4.39 1.52e+00 4.33e-01 8.34e+00
  angle pdb=" C   ARG X 238 "
        pdb=" N   HIS X 239 "
        pdb=" CA  HIS X 239 "
      ideal   model   delta    sigma   weight residual
     121.54  127.03   -5.49 1.91e+00 2.74e-01 8.27e+00
  ... (remaining 17038 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.07: 7245
       28.07 -    56.15: 355
       56.15 -    84.22: 37
       84.22 -   112.29: 4
      112.29 -   140.37: 3
  Dihedral angle restraints: 7644
    sinusoidal: 3190
      harmonic: 4454
  Sorted by residual:
  dihedral pdb=" O2A ADP E 601 "
           pdb=" O3A ADP E 601 "
           pdb=" PA  ADP E 601 "
           pdb=" PB  ADP E 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   80.37 -140.37     1      2.00e+01 2.50e-03 4.25e+01
  dihedral pdb=" C5' ADP E 601 "
           pdb=" O5' ADP E 601 "
           pdb=" PA  ADP E 601 "
           pdb=" O2A ADP E 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   79.29 -139.28     1      2.00e+01 2.50e-03 4.22e+01
  dihedral pdb=" O1B ADP E 601 "
           pdb=" O3A ADP E 601 "
           pdb=" PB  ADP E 601 "
           pdb=" PA  ADP E 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   74.71 -134.72     1      2.00e+01 2.50e-03 4.09e+01
  ... (remaining 7641 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1220
       0.033 -    0.066: 513
       0.066 -    0.099: 107
       0.099 -    0.132: 62
       0.132 -    0.164: 3
  Chirality restraints: 1905
  Sorted by residual:
  chirality pdb=" CB  THR X  45 "
            pdb=" CA  THR X  45 "
            pdb=" OG1 THR X  45 "
            pdb=" CG2 THR X  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.16 2.00e-01 2.50e+01 6.75e-01
  chirality pdb=" CB  ILE E 393 "
            pdb=" CA  ILE E 393 "
            pdb=" CG1 ILE E 393 "
            pdb=" CG2 ILE E 393 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 4.92e-01
  chirality pdb=" CA  GLN E 414 "
            pdb=" N   GLN E 414 "
            pdb=" C   GLN E 414 "
            pdb=" CB  GLN E 414 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.76e-01
  ... (remaining 1902 not shown)

  Planarity restraints: 2190
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F 268 "   -0.034 5.00e-02 4.00e+02   5.09e-02 4.15e+00
        pdb=" N   PRO F 269 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO F 269 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO F 269 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR G 268 "   -0.033 5.00e-02 4.00e+02   5.03e-02 4.05e+00
        pdb=" N   PRO G 269 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO G 269 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO G 269 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU X 146 "    0.032 5.00e-02 4.00e+02   4.93e-02 3.88e+00
        pdb=" N   PRO X 147 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO X 147 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO X 147 "    0.027 5.00e-02 4.00e+02
  ... (remaining 2187 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 125
        2.62 -     3.19: 10638
        3.19 -     3.76: 18069
        3.76 -     4.33: 24406
        4.33 -     4.90: 40583
  Nonbonded interactions: 93821
  Sorted by model distance:
  nonbonded pdb=" O1B ADP E 601 "
            pdb="MG    MG E 602 "
     model   vdw
     2.053 2.170
  nonbonded pdb=" O3B ATP F 601 "
            pdb="MG    MG F 602 "
     model   vdw
     2.055 2.170
  nonbonded pdb=" OG1 THR E 143 "
            pdb="MG    MG E 602 "
     model   vdw
     2.077 2.170
  nonbonded pdb=" O3G ATP F 601 "
            pdb="MG    MG F 602 "
     model   vdw
     2.081 2.170
  nonbonded pdb=" O3G ATP G 601 "
            pdb="MG    MG G 602 "
     model   vdw
     2.111 2.170
  ... (remaining 93816 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
Found NCS groups:
ncs_group {
  reference = (chain 'E' and (resid 4 through 403 or resid 602))
  selection = (chain 'F' and (resid 4 through 403 or resid 602))
  selection = (chain 'G' and (resid 4 through 403 or resid 602))
}

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=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.960
  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:             0.010
  Extract box with map and model:          0.580
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     32.130
  Find NCS groups from input model:        0.510
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  12583  Z= 0.120
  Angle     :  0.557   9.065  17046  Z= 0.278
  Chirality :  0.040   0.164   1905
  Planarity :  0.004   0.051   2190
  Dihedral  : 15.701 140.366   4774
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.22), residues: 1525
  helix:  0.02 (0.20), residues: 726
  sheet: -0.00 (0.68), residues: 69
  loop : -1.24 (0.22), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP X 270 
 HIS   0.006   0.001   HIS X 177 
 PHE   0.013   0.001   PHE F 187 
 TYR   0.013   0.001   TYR X  14 
 ARG   0.006   0.000   ARG G 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19143 (  478)
  hydrogen bonds       : angle       6.17458 ( 1362)
  metal coordination   : bond        0.01064 (    4)
  metal coordination   : angle       2.15125 (    3)
  covalent geometry    : bond        0.00265 (12579)
  covalent geometry    : angle       0.55620 (17043)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.441 
Fit side-chains
   revert: symmetry clash
REVERT: G  181 LYS cc_start: 0.8424 (tttt) cc_final: 0.8211 (mtpp)
REVERT: X  107 MET cc_start: 0.6728 (tmm) cc_final: 0.6513 (tmm)
REVERT: F  375 TYR cc_start: 0.6798 (t80) cc_final: 0.6493 (t80)
REVERT: E  276 GLU cc_start: 0.6368 (mp0) cc_final: 0.5542 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.2831
  time to fit residues: 64.3314
Evaluate side-chains
  119 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 1.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:   20.0000
   chunk 115 optimal weight:   20.0000
   chunk 63 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0270
   chunk 119 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   chunk 88 optimal weight:    6.9990
   chunk 138 optimal weight:    5.9990
   overall best weight:    1.7242

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

Flipped N/Q/H residues before XYZ refinement:
** X 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 222 ASN
** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 305 ASN
E 306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.184634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.138994 restraints weight = 17070.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.138549 restraints weight = 19950.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.140326 restraints weight = 17758.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3763
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3763 r_free = 0.3763    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3763 r_free = 0.3763    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
r_final: 0.3763
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.1281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  12583  Z= 0.213
  Angle     :  0.656   8.436  17046  Z= 0.326
  Chirality :  0.043   0.146   1905
  Planarity :  0.005   0.058   2190
  Dihedral  :  9.473 143.944   1788
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  8.59 %
    Favored  : 90.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.22), residues: 1525
  helix: -0.05 (0.20), residues: 742
  sheet: -0.52 (0.61), residues: 77
  loop : -1.42 (0.22), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP G 316 
 HIS   0.006   0.001   HIS X 287 
 PHE   0.015   0.002   PHE X 161 
 TYR   0.022   0.002   TYR G 375 
 ARG   0.006   0.000   ARG E  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04713 (  478)
  hydrogen bonds       : angle       4.71790 ( 1362)
  metal coordination   : bond        0.01403 (    4)
  metal coordination   : angle       3.61560 (    3)
  covalent geometry    : bond        0.00518 (12579)
  covalent geometry    : angle       0.65451 (17043)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 1.526 
Fit side-chains
   revert: symmetry clash
REVERT: G  198 ASN cc_start: 0.7729 (p0) cc_final: 0.7453 (p0)
REVERT: X   35 GLU cc_start: 0.6754 (tp30) cc_final: 0.6539 (mm-30)
REVERT: X   99 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7694 (mm-40)
REVERT: F  385 MET cc_start: 0.7257 (mpp) cc_final: 0.4574 (tpt)
REVERT: E   86 MET cc_start: 0.7482 (mtp) cc_final: 0.7030 (ttm)
REVERT: E  276 GLU cc_start: 0.6246 (mp0) cc_final: 0.5395 (tp30)
REVERT: E  300 GLN cc_start: 0.5234 (tp40) cc_final: 0.4875 (mm-40)
  outliers start: 13
  outliers final: 8
  residues processed: 133
  average time/residue: 0.2737
  time to fit residues: 52.7288
Evaluate side-chains
  121 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 1.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  135 ILE
Chi-restraints excluded: chain G residue  231 ILE
Chi-restraints excluded: chain X residue  106 LEU
Chi-restraints excluded: chain X residue  190 SER
Chi-restraints excluded: chain X residue  219 THR
Chi-restraints excluded: chain X residue  275 PHE
Chi-restraints excluded: chain E residue  367 THR
Chi-restraints excluded: chain E residue  379 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 135 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 147 optimal weight:   20.0000
   chunk 27 optimal weight:    0.9990
   chunk 142 optimal weight:   10.0000
   chunk 110 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** X 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 222 ASN
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.183773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.139264 restraints weight = 16782.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.139644 restraints weight = 17697.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.140071 restraints weight = 20397.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3773
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3773 r_free = 0.3773    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3773 r_free = 0.3773    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
r_final: 0.3773
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12583  Z= 0.184
  Angle     :  0.609   9.353  17046  Z= 0.301
  Chirality :  0.041   0.145   1905
  Planarity :  0.004   0.060   2190
  Dihedral  :  9.175 140.360   1788
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.94 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.22), residues: 1525
  helix:  0.03 (0.20), residues: 742
  sheet: -0.72 (0.61), residues: 79
  loop : -1.43 (0.22), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP G 316 
 HIS   0.006   0.001   HIS X 287 
 PHE   0.015   0.002   PHE X 161 
 TYR   0.019   0.002   TYR G 375 
 ARG   0.002   0.000   ARG F 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04105 (  478)
  hydrogen bonds       : angle       4.54577 ( 1362)
  metal coordination   : bond        0.01371 (    4)
  metal coordination   : angle       3.62919 (    3)
  covalent geometry    : bond        0.00449 (12579)
  covalent geometry    : angle       0.60696 (17043)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 1.561 
Fit side-chains
   revert: symmetry clash
REVERT: G  198 ASN cc_start: 0.7788 (p0) cc_final: 0.7457 (p0)
REVERT: X   99 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7731 (mm-40)
REVERT: F  385 MET cc_start: 0.7387 (mpp) cc_final: 0.4520 (tpt)
REVERT: E   86 MET cc_start: 0.7478 (mtp) cc_final: 0.7080 (ttm)
  outliers start: 21
  outliers final: 14
  residues processed: 133
  average time/residue: 0.2522
  time to fit residues: 49.4114
Evaluate side-chains
  126 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 1.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  135 ILE
Chi-restraints excluded: chain G residue  231 ILE
Chi-restraints excluded: chain G residue  256 VAL
Chi-restraints excluded: chain G residue  359 LEU
Chi-restraints excluded: chain X residue  190 SER
Chi-restraints excluded: chain X residue  255 LEU
Chi-restraints excluded: chain X residue  259 ASP
Chi-restraints excluded: chain X residue  275 PHE
Chi-restraints excluded: chain F residue  191 LEU
Chi-restraints excluded: chain F residue  230 VAL
Chi-restraints excluded: chain F residue  253 VAL
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  379 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 117 optimal weight:    5.9990
   chunk 103 optimal weight:    9.9990
   chunk 93 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
G  52 GLN
** X  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 222 ASN
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.184573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.142484 restraints weight = 17084.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.140787 restraints weight = 23911.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.142492 restraints weight = 22006.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3836
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3836 r_free = 0.3836    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3836 r_free = 0.3836    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
r_final: 0.3836
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12583  Z= 0.204
  Angle     :  0.632  12.317  17046  Z= 0.310
  Chirality :  0.042   0.148   1905
  Planarity :  0.004   0.061   2190
  Dihedral  :  9.019 134.921   1788
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.38 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.21), residues: 1525
  helix: -0.06 (0.20), residues: 751
  sheet: -0.81 (0.61), residues: 79
  loop : -1.54 (0.22), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP G 316 
 HIS   0.006   0.001   HIS X 287 
 PHE   0.017   0.002   PHE X 161 
 TYR   0.020   0.002   TYR G 375 
 ARG   0.003   0.000   ARG F 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04141 (  478)
  hydrogen bonds       : angle       4.52962 ( 1362)
  metal coordination   : bond        0.01547 (    4)
  metal coordination   : angle       4.04909 (    3)
  covalent geometry    : bond        0.00501 (12579)
  covalent geometry    : angle       0.62944 (17043)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 1.459 
Fit side-chains
   revert: symmetry clash
REVERT: G  198 ASN cc_start: 0.7728 (p0) cc_final: 0.7293 (p0)
REVERT: G  344 MET cc_start: 0.7574 (mmt) cc_final: 0.7189 (mmt)
REVERT: X   99 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7657 (mm-40)
REVERT: E   86 MET cc_start: 0.7444 (mtp) cc_final: 0.6963 (ttm)
REVERT: E  191 LEU cc_start: 0.8418 (pp) cc_final: 0.8002 (tp)
  outliers start: 29
  outliers final: 22
  residues processed: 145
  average time/residue: 0.2624
  time to fit residues: 54.8814
Evaluate side-chains
  137 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 1.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  135 ILE
Chi-restraints excluded: chain G residue  231 ILE
Chi-restraints excluded: chain G residue  256 VAL
Chi-restraints excluded: chain G residue  359 LEU
Chi-restraints excluded: chain G residue  363 ASN
Chi-restraints excluded: chain X residue  170 HIS
Chi-restraints excluded: chain X residue  190 SER
Chi-restraints excluded: chain X residue  219 THR
Chi-restraints excluded: chain X residue  255 LEU
Chi-restraints excluded: chain X residue  258 LEU
Chi-restraints excluded: chain X residue  259 ASP
Chi-restraints excluded: chain X residue  275 PHE
Chi-restraints excluded: chain F residue  191 LEU
Chi-restraints excluded: chain F residue  230 VAL
Chi-restraints excluded: chain F residue  253 VAL
Chi-restraints excluded: chain F residue  344 MET
Chi-restraints excluded: chain E residue    9 VAL
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  256 VAL
Chi-restraints excluded: chain E residue  367 THR
Chi-restraints excluded: chain E residue  383 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 111 optimal weight:    8.9990
   chunk 57 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 127 optimal weight:   10.0000
   chunk 87 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
G  52 GLN
** X  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 222 ASN
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.184369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.142428 restraints weight = 17021.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.141078 restraints weight = 24008.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.142827 restraints weight = 21402.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3839 r_free = 0.3839    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3839 r_free = 0.3839    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
r_final: 0.3839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12583  Z= 0.193
  Angle     :  0.617   9.761  17046  Z= 0.306
  Chirality :  0.041   0.148   1905
  Planarity :  0.004   0.064   2190
  Dihedral  :  8.817 129.729   1788
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.98 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.21), residues: 1525
  helix: -0.09 (0.20), residues: 752
  sheet: -0.76 (0.61), residues: 79
  loop : -1.59 (0.22), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP G 316 
 HIS   0.006   0.001   HIS X 287 
 PHE   0.033   0.002   PHE E 187 
 TYR   0.018   0.002   TYR G 375 
 ARG   0.002   0.000   ARG F 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03987 (  478)
  hydrogen bonds       : angle       4.46465 ( 1362)
  metal coordination   : bond        0.01580 (    4)
  metal coordination   : angle       3.92343 (    3)
  covalent geometry    : bond        0.00472 (12579)
  covalent geometry    : angle       0.61471 (17043)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 126
  time to evaluate  : 1.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  181 LYS cc_start: 0.8586 (tttt) cc_final: 0.8154 (mtpp)
REVERT: G  198 ASN cc_start: 0.7688 (p0) cc_final: 0.7327 (p0)
REVERT: X   99 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7604 (mm-40)
REVERT: F  385 MET cc_start: 0.7443 (mpp) cc_final: 0.4797 (tpt)
REVERT: E   86 MET cc_start: 0.7273 (mtp) cc_final: 0.7020 (ttm)
REVERT: E  191 LEU cc_start: 0.8529 (pp) cc_final: 0.8291 (tp)
  outliers start: 32
  outliers final: 22
  residues processed: 149
  average time/residue: 0.2617
  time to fit residues: 57.3391
Evaluate side-chains
  139 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 1.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  135 ILE
Chi-restraints excluded: chain G residue  231 ILE
Chi-restraints excluded: chain G residue  254 THR
Chi-restraints excluded: chain G residue  256 VAL
Chi-restraints excluded: chain G residue  359 LEU
Chi-restraints excluded: chain X residue  170 HIS
Chi-restraints excluded: chain X residue  190 SER
Chi-restraints excluded: chain X residue  219 THR
Chi-restraints excluded: chain X residue  255 LEU
Chi-restraints excluded: chain X residue  258 LEU
Chi-restraints excluded: chain X residue  259 ASP
Chi-restraints excluded: chain X residue  274 ILE
Chi-restraints excluded: chain X residue  275 PHE
Chi-restraints excluded: chain F residue  191 LEU
Chi-restraints excluded: chain F residue  230 VAL
Chi-restraints excluded: chain F residue  253 VAL
Chi-restraints excluded: chain F residue  344 MET
Chi-restraints excluded: chain E residue    9 VAL
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  256 VAL
Chi-restraints excluded: chain E residue  367 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 141 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 22 optimal weight:    0.3980
   chunk 111 optimal weight:    8.9990
   chunk 150 optimal weight:    6.9990
   chunk 86 optimal weight:    2.9990
   chunk 147 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
G  52 GLN
** X  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 105 HIS
F 222 ASN
E 102 GLN
** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.184830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.140534 restraints weight = 16895.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.140375 restraints weight = 19768.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.141178 restraints weight = 20214.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3778 r_free = 0.3778    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3778 r_free = 0.3778    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
r_final: 0.3778
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12583  Z= 0.118
  Angle     :  0.574  10.678  17046  Z= 0.282
  Chirality :  0.039   0.177   1905
  Planarity :  0.004   0.063   2190
  Dihedral  :  8.479 125.431   1788
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.05 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.22), residues: 1525
  helix:  0.15 (0.20), residues: 744
  sheet: -0.63 (0.63), residues: 79
  loop : -1.45 (0.22), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 308 
 HIS   0.006   0.001   HIS G 383 
 PHE   0.028   0.001   PHE E 187 
 TYR   0.028   0.001   TYR E 109 
 ARG   0.002   0.000   ARG G 189 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03262 (  478)
  hydrogen bonds       : angle       4.30526 ( 1362)
  metal coordination   : bond        0.01374 (    4)
  metal coordination   : angle       2.58260 (    3)
  covalent geometry    : bond        0.00276 (12579)
  covalent geometry    : angle       0.57340 (17043)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 1.320 
Fit side-chains
   revert: symmetry clash
REVERT: G  181 LYS cc_start: 0.8413 (tttt) cc_final: 0.7998 (mtpp)
REVERT: G  198 ASN cc_start: 0.7728 (p0) cc_final: 0.7410 (p0)
REVERT: G  344 MET cc_start: 0.7441 (mmt) cc_final: 0.7205 (mmt)
REVERT: X   50 SER cc_start: 0.7390 (m) cc_final: 0.7018 (p)
REVERT: X   99 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7739 (mm-40)
REVERT: E   86 MET cc_start: 0.7311 (mtp) cc_final: 0.6989 (ttm)
REVERT: E  385 MET cc_start: 0.4823 (mtm) cc_final: 0.4452 (mtm)
  outliers start: 28
  outliers final: 19
  residues processed: 149
  average time/residue: 0.2446
  time to fit residues: 52.8851
Evaluate side-chains
  136 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 1.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  231 ILE
Chi-restraints excluded: chain G residue  232 ASP
Chi-restraints excluded: chain G residue  256 VAL
Chi-restraints excluded: chain G residue  359 LEU
Chi-restraints excluded: chain X residue  170 HIS
Chi-restraints excluded: chain X residue  190 SER
Chi-restraints excluded: chain X residue  232 THR
Chi-restraints excluded: chain X residue  255 LEU
Chi-restraints excluded: chain X residue  258 LEU
Chi-restraints excluded: chain X residue  275 PHE
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  191 LEU
Chi-restraints excluded: chain F residue  344 MET
Chi-restraints excluded: chain E residue    9 VAL
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue  133 LEU
Chi-restraints excluded: chain E residue  256 VAL
Chi-restraints excluded: chain E residue  367 THR
Chi-restraints excluded: chain E residue  383 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 111 optimal weight:    9.9990
   chunk 126 optimal weight:    5.9990
   chunk 132 optimal weight:    1.9990
   chunk 103 optimal weight:   10.0000
   chunk 82 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 51 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 120 optimal weight:   20.0000
   chunk 121 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
G  52 GLN
X  51 HIS
** X  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 222 ASN
F 322 GLN
** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 305 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.183630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.140991 restraints weight = 17165.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.139898 restraints weight = 23422.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.141320 restraints weight = 21468.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3823
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3823 r_free = 0.3823    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3823 r_free = 0.3823    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
r_final: 0.3823
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12583  Z= 0.210
  Angle     :  0.645  11.259  17046  Z= 0.318
  Chirality :  0.042   0.193   1905
  Planarity :  0.005   0.065   2190
  Dihedral  :  8.435 120.453   1788
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 17.19 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.22), residues: 1525
  helix: -0.01 (0.20), residues: 739
  sheet: -0.70 (0.63), residues: 79
  loop : -1.56 (0.22), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP E 308 
 HIS   0.006   0.001   HIS X 287 
 PHE   0.017   0.002   PHE X 161 
 TYR   0.025   0.002   TYR E 109 
 ARG   0.013   0.000   ARG E  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04018 (  478)
  hydrogen bonds       : angle       4.41549 ( 1362)
  metal coordination   : bond        0.01592 (    4)
  metal coordination   : angle       4.32374 (    3)
  covalent geometry    : bond        0.00516 (12579)
  covalent geometry    : angle       0.64235 (17043)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 119
  time to evaluate  : 1.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  181 LYS cc_start: 0.8604 (tttt) cc_final: 0.8160 (mtpp)
REVERT: G  198 ASN cc_start: 0.7673 (p0) cc_final: 0.7352 (p0)
REVERT: G  344 MET cc_start: 0.7520 (mmt) cc_final: 0.7211 (mmt)
REVERT: X   50 SER cc_start: 0.7427 (m) cc_final: 0.7010 (p)
REVERT: X   99 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7460 (mm-40)
REVERT: X  276 ARG cc_start: 0.6029 (ptp-110) cc_final: 0.5785 (ttm110)
REVERT: F  222 ASN cc_start: 0.7658 (t0) cc_final: 0.7405 (t0)
REVERT: E   86 MET cc_start: 0.7350 (mtp) cc_final: 0.7092 (ttm)
REVERT: E  300 GLN cc_start: 0.5132 (mm110) cc_final: 0.4925 (mm-40)
REVERT: E  308 TRP cc_start: 0.5627 (t60) cc_final: 0.5412 (t60)
  outliers start: 28
  outliers final: 21
  residues processed: 142
  average time/residue: 0.2487
  time to fit residues: 51.6993
Evaluate side-chains
  138 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  231 ILE
Chi-restraints excluded: chain G residue  249 LEU
Chi-restraints excluded: chain G residue  256 VAL
Chi-restraints excluded: chain G residue  359 LEU
Chi-restraints excluded: chain X residue  106 LEU
Chi-restraints excluded: chain X residue  170 HIS
Chi-restraints excluded: chain X residue  190 SER
Chi-restraints excluded: chain X residue  232 THR
Chi-restraints excluded: chain X residue  255 LEU
Chi-restraints excluded: chain X residue  258 LEU
Chi-restraints excluded: chain X residue  259 ASP
Chi-restraints excluded: chain X residue  274 ILE
Chi-restraints excluded: chain X residue  275 PHE
Chi-restraints excluded: chain F residue  230 VAL
Chi-restraints excluded: chain F residue  253 VAL
Chi-restraints excluded: chain F residue  344 MET
Chi-restraints excluded: chain E residue    9 VAL
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue  256 VAL
Chi-restraints excluded: chain E residue  367 THR
Chi-restraints excluded: chain E residue  383 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9990
   chunk 103 optimal weight:    4.9990
   chunk 93 optimal weight:    0.6980
   chunk 147 optimal weight:    9.9990
   chunk 89 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 141 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
G  52 GLN
** X  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.183809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.140177 restraints weight = 16710.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.139785 restraints weight = 20642.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.141198 restraints weight = 19979.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3826
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3826 r_free = 0.3826    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3826 r_free = 0.3826    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
r_final: 0.3826
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12583  Z= 0.167
  Angle     :  0.604   9.749  17046  Z= 0.298
  Chirality :  0.041   0.193   1905
  Planarity :  0.004   0.064   2190
  Dihedral  :  8.236 115.667   1788
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.41 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.22), residues: 1525
  helix:  0.04 (0.20), residues: 744
  sheet: -0.75 (0.63), residues: 79
  loop : -1.55 (0.22), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP E 308 
 HIS   0.005   0.001   HIS G 383 
 PHE   0.014   0.001   PHE X 161 
 TYR   0.024   0.002   TYR E 109 
 ARG   0.002   0.000   ARG G 323 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03611 (  478)
  hydrogen bonds       : angle       4.31443 ( 1362)
  metal coordination   : bond        0.01602 (    4)
  metal coordination   : angle       3.72171 (    3)
  covalent geometry    : bond        0.00406 (12579)
  covalent geometry    : angle       0.60199 (17043)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 122
  time to evaluate  : 1.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  181 LYS cc_start: 0.8556 (tttt) cc_final: 0.8124 (mtpp)
REVERT: G  198 ASN cc_start: 0.7610 (p0) cc_final: 0.7308 (p0)
REVERT: G  344 MET cc_start: 0.7495 (mmt) cc_final: 0.7261 (mmt)
REVERT: X   50 SER cc_start: 0.7362 (m) cc_final: 0.6953 (p)
REVERT: X   99 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7356 (mm-40)
REVERT: X  276 ARG cc_start: 0.5983 (ptp-110) cc_final: 0.5704 (ttm110)
REVERT: F  373 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7642 (tm-30)
REVERT: E   86 MET cc_start: 0.7347 (mtp) cc_final: 0.7065 (ttm)
REVERT: E  300 GLN cc_start: 0.5326 (mm110) cc_final: 0.5125 (mm-40)
REVERT: E  385 MET cc_start: 0.4842 (mtm) cc_final: 0.4409 (mtm)
  outliers start: 30
  outliers final: 23
  residues processed: 145
  average time/residue: 0.2332
  time to fit residues: 49.7166
Evaluate side-chains
  142 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 1.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain G residue  135 ILE
Chi-restraints excluded: chain G residue  249 LEU
Chi-restraints excluded: chain G residue  254 THR
Chi-restraints excluded: chain G residue  256 VAL
Chi-restraints excluded: chain G residue  359 LEU
Chi-restraints excluded: chain X residue  106 LEU
Chi-restraints excluded: chain X residue  170 HIS
Chi-restraints excluded: chain X residue  190 SER
Chi-restraints excluded: chain X residue  229 LEU
Chi-restraints excluded: chain X residue  232 THR
Chi-restraints excluded: chain X residue  255 LEU
Chi-restraints excluded: chain X residue  258 LEU
Chi-restraints excluded: chain X residue  259 ASP
Chi-restraints excluded: chain X residue  275 PHE
Chi-restraints excluded: chain F residue  230 VAL
Chi-restraints excluded: chain F residue  253 VAL
Chi-restraints excluded: chain F residue  344 MET
Chi-restraints excluded: chain E residue    9 VAL
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue  256 VAL
Chi-restraints excluded: chain E residue  367 THR
Chi-restraints excluded: chain E residue  383 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 133 optimal weight:    5.9990
   chunk 142 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 70 optimal weight:    0.5980
   chunk 6 optimal weight:    0.2980
   chunk 108 optimal weight:    2.9990
   chunk 80 optimal weight:    6.9990
   chunk 140 optimal weight:   20.0000
   chunk 84 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
G  52 GLN
** X  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.184800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.141196 restraints weight = 17133.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.140171 restraints weight = 22138.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.141882 restraints weight = 20629.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3834
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3834 r_free = 0.3834    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3834 r_free = 0.3834    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
r_final: 0.3834
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12583  Z= 0.154
  Angle     :  0.595   9.830  17046  Z= 0.293
  Chirality :  0.040   0.182   1905
  Planarity :  0.004   0.063   2190
  Dihedral  :  8.072 112.447   1788
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 18.17 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.22), residues: 1525
  helix:  0.07 (0.20), residues: 741
  sheet: -0.56 (0.65), residues: 73
  loop : -1.56 (0.22), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.001   TRP E 308 
 HIS   0.005   0.001   HIS G 383 
 PHE   0.013   0.001   PHE X 161 
 TYR   0.023   0.002   TYR E 109 
 ARG   0.002   0.000   ARG G 323 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03484 (  478)
  hydrogen bonds       : angle       4.31854 ( 1362)
  metal coordination   : bond        0.01567 (    4)
  metal coordination   : angle       3.47928 (    3)
  covalent geometry    : bond        0.00376 (12579)
  covalent geometry    : angle       0.59329 (17043)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 1.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  181 LYS cc_start: 0.8507 (tttt) cc_final: 0.8116 (mtpp)
REVERT: G  198 ASN cc_start: 0.7630 (p0) cc_final: 0.7366 (p0)
REVERT: G  344 MET cc_start: 0.7466 (mmt) cc_final: 0.7223 (mmt)
REVERT: X   50 SER cc_start: 0.7260 (m) cc_final: 0.6856 (p)
REVERT: X   99 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7373 (mm-40)
REVERT: X  276 ARG cc_start: 0.5955 (ptp-110) cc_final: 0.5637 (ttm110)
REVERT: F  276 GLU cc_start: 0.7225 (mp0) cc_final: 0.6836 (mp0)
REVERT: F  373 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7645 (tm-30)
REVERT: E   86 MET cc_start: 0.7351 (mtp) cc_final: 0.7063 (ttm)
REVERT: E  385 MET cc_start: 0.4912 (mtm) cc_final: 0.4475 (mtm)
  outliers start: 23
  outliers final: 23
  residues processed: 142
  average time/residue: 0.2412
  time to fit residues: 50.6594
Evaluate side-chains
  140 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 1.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain G residue  249 LEU
Chi-restraints excluded: chain G residue  254 THR
Chi-restraints excluded: chain G residue  256 VAL
Chi-restraints excluded: chain G residue  359 LEU
Chi-restraints excluded: chain X residue  106 LEU
Chi-restraints excluded: chain X residue  170 HIS
Chi-restraints excluded: chain X residue  190 SER
Chi-restraints excluded: chain X residue  229 LEU
Chi-restraints excluded: chain X residue  232 THR
Chi-restraints excluded: chain X residue  255 LEU
Chi-restraints excluded: chain X residue  258 LEU
Chi-restraints excluded: chain X residue  259 ASP
Chi-restraints excluded: chain X residue  275 PHE
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  230 VAL
Chi-restraints excluded: chain F residue  253 VAL
Chi-restraints excluded: chain F residue  344 MET
Chi-restraints excluded: chain E residue    9 VAL
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue  256 VAL
Chi-restraints excluded: chain E residue  367 THR
Chi-restraints excluded: chain E residue  383 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 120 optimal weight:   20.0000
   chunk 83 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 63 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 146 optimal weight:   20.0000
   chunk 50 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0770
   chunk 52 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.9342

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

Flipped N/Q/H residues before XYZ refinement:
G  52 GLN
** X  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.185471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.141640 restraints weight = 16478.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.141709 restraints weight = 19048.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.142433 restraints weight = 19863.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3843
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3843 r_free = 0.3843    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3843 r_free = 0.3843    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
r_final: 0.3843
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12583  Z= 0.136
  Angle     :  0.591  13.827  17046  Z= 0.289
  Chirality :  0.040   0.179   1905
  Planarity :  0.004   0.063   2190
  Dihedral  :  7.897 111.331   1788
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 18.56 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.22), residues: 1525
  helix:  0.14 (0.20), residues: 741
  sheet: -0.57 (0.65), residues: 73
  loop : -1.52 (0.22), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP E 308 
 HIS   0.005   0.001   HIS G 383 
 PHE   0.013   0.001   PHE E 187 
 TYR   0.022   0.002   TYR E 109 
 ARG   0.002   0.000   ARG E 189 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03305 (  478)
  hydrogen bonds       : angle       4.26887 ( 1362)
  metal coordination   : bond        0.01542 (    4)
  metal coordination   : angle       3.15490 (    3)
  covalent geometry    : bond        0.00330 (12579)
  covalent geometry    : angle       0.58961 (17043)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 1.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  181 LYS cc_start: 0.8482 (tttt) cc_final: 0.8135 (mtpp)
REVERT: G  198 ASN cc_start: 0.7577 (p0) cc_final: 0.7363 (p0)
REVERT: G  344 MET cc_start: 0.7433 (mmt) cc_final: 0.7205 (mmt)
REVERT: X   50 SER cc_start: 0.7201 (m) cc_final: 0.6818 (p)
REVERT: X   99 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7369 (mm-40)
REVERT: X  276 ARG cc_start: 0.5920 (ptp-110) cc_final: 0.5639 (ttm110)
REVERT: F  373 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7674 (tm-30)
REVERT: E   86 MET cc_start: 0.7325 (mtp) cc_final: 0.7048 (ttm)
REVERT: E  301 ARG cc_start: 0.5517 (mmt180) cc_final: 0.5262 (mpt90)
REVERT: E  385 MET cc_start: 0.4895 (mtm) cc_final: 0.4473 (mtm)
  outliers start: 23
  outliers final: 21
  residues processed: 142
  average time/residue: 0.2576
  time to fit residues: 53.4479
Evaluate side-chains
  140 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 1.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  249 LEU
Chi-restraints excluded: chain G residue  254 THR
Chi-restraints excluded: chain G residue  256 VAL
Chi-restraints excluded: chain G residue  359 LEU
Chi-restraints excluded: chain X residue  106 LEU
Chi-restraints excluded: chain X residue  170 HIS
Chi-restraints excluded: chain X residue  190 SER
Chi-restraints excluded: chain X residue  229 LEU
Chi-restraints excluded: chain X residue  232 THR
Chi-restraints excluded: chain X residue  255 LEU
Chi-restraints excluded: chain X residue  259 ASP
Chi-restraints excluded: chain X residue  275 PHE
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  230 VAL
Chi-restraints excluded: chain F residue  253 VAL
Chi-restraints excluded: chain F residue  344 MET
Chi-restraints excluded: chain E residue    9 VAL
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue  256 VAL
Chi-restraints excluded: chain E residue  367 THR
Chi-restraints excluded: chain E residue  383 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 73 optimal weight:    0.4980
   chunk 121 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 91 optimal weight:    0.0570
   chunk 18 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 134 optimal weight:    6.9990
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
G  52 GLN
** X  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.186497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.143404 restraints weight = 16565.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.144707 restraints weight = 20007.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.145363 restraints weight = 18400.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3879 r_free = 0.3879    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3879 r_free = 0.3879    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       84 |
|-----------------------------------------------------------------------------|
r_final: 0.3879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12583  Z= 0.114
  Angle     :  0.581  11.907  17046  Z= 0.286
  Chirality :  0.039   0.171   1905
  Planarity :  0.004   0.062   2190
  Dihedral  :  7.724 110.321   1788
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 18.86 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.22), residues: 1525
  helix:  0.23 (0.20), residues: 735
  sheet: -0.77 (0.62), residues: 79
  loop : -1.42 (0.22), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP E 308 
 HIS   0.005   0.001   HIS G 383 
 PHE   0.013   0.001   PHE E 187 
 TYR   0.021   0.001   TYR E 109 
 ARG   0.009   0.000   ARG F 189 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03131 (  478)
  hydrogen bonds       : angle       4.20983 ( 1362)
  metal coordination   : bond        0.01461 (    4)
  metal coordination   : angle       2.49192 (    3)
  covalent geometry    : bond        0.00267 (12579)
  covalent geometry    : angle       0.58035 (17043)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3947.63 seconds
wall clock time: 69 minutes 16.56 seconds (4156.56 seconds total)