Starting phenix.real_space_refine
on Sat Aug 23 17:26:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8utu_42550/08_2025/8utu_42550.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8utu_42550/08_2025/8utu_42550.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8utu_42550/08_2025/8utu_42550.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8utu_42550/08_2025/8utu_42550.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8utu_42550/08_2025/8utu_42550.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8utu_42550/08_2025/8utu_42550.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      11      5.49       5
     Mg      3      5.21       5
     S      87      5.16       5
     C    8515      2.51       5
     N    2326      2.21       5
     O    2673      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13615
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "K"
      Number of atoms: 3039
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 386, 3039
          Classifications: {'peptide': 386}
          Link IDs: {'PTRANS': 12, 'TRANS': 373}
    Chain: "A"
      Number of atoms: 3437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 440, 3437
          Classifications: {'peptide': 440}
          Link IDs: {'PTRANS': 20, 'TRANS': 419}
    Chain: "B"
      Number of atoms: 3427
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 432, 3398
          Classifications: {'peptide': 432}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411}
      Conformer: "B"
        Number of residues, atoms: 432, 3398
          Classifications: {'peptide': 432}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411}
          bond proxies already assigned to first conformer: 3444
    Chain: "E"
      Number of atoms: 3524
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 451, 3524
          Classifications: {'peptide': 451}
          Link IDs: {'PTRANS': 20, 'TRANS': 430}
    Chain: "K"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 62
          Unusual residues: {'TA1': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  ATHR B 429 " occ=0.52
      ... (12 atoms not shown)
      pdb=" CG2BTHR B 429 " occ=0.48
    residue:
      pdb=" N  AALA B 430 " occ=0.52
      ... (8 atoms not shown)
      pdb=" CB BALA B 430 " occ=0.48
    residue:
      pdb=" N  AASP B 431 " occ=0.52
      ... (14 atoms not shown)
      pdb=" OD2BASP B 431 " occ=0.48
    residue:
      pdb=" N  AGLU B 432 " occ=0.52
      ... (16 atoms not shown)
      pdb=" OE2BGLU B 432 " occ=0.48
  Time building chain proxies: 4.15, per 1000 atoms: 0.30
  Number of scatterers: 13615
  At special positions: 0
  Unit cell: (103.812, 113.096, 154.452, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      87     16.00
     P      11     15.00
     Mg      3     11.99
     O    2673      8.00
     N    2326      7.00
     C    8515      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: 1.28
  Conformation dependent library (CDL) restraints added in 708.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3180

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 13 sheets defined
      49.2% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'K' and resid 16 through 22
      removed outlier: 3.587A  pdb=" N   ARG K  22 " --> pdb=" O   ARG K  18 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 69 through 77
    Processing helix  chain 'K' and resid 77 through 88
    Processing helix  chain 'K' and resid 102 through 108
    Processing helix  chain 'K' and resid 119 through 134
    Processing helix  chain 'K' and resid 188 through 203
    Processing helix  chain 'K' and resid 262 through 295
      Proline residue:  K 292  - end of helix
    Processing helix  chain 'K' and resid 309 through 315
    Processing helix  chain 'K' and resid 315 through 320
    Processing helix  chain 'K' and resid 334 through 336
      No H-bonds generated for 'chain 'K' and resid 334 through 336'
    Processing helix  chain 'K' and resid 337 through 353
      removed outlier: 3.744A  pdb=" N   GLN K 353 " --> pdb=" O   ASP K 349 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 363 through 386
    Processing helix  chain 'A' and resid 10 through 29
    Processing helix  chain 'A' and resid 36 through 43
      removed outlier: 4.178A  pdb=" N   LYS A  40 " --> pdb=" O   MET A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 80
      removed outlier: 4.858A  pdb=" N   ILE A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   GLU A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   VAL A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 114 through 129
      removed outlier: 3.537A  pdb=" N   GLN A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   CYS A 129 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 161
      removed outlier: 4.204A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 190
      removed outlier: 3.614A  pdb=" N   ASN A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   THR A 190 " --> pdb=" O   ASN A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 197
    Processing helix  chain 'A' and resid 205 through 216
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 3.797A  pdb=" N   LEU A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 4.955A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   ARG A 243 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 260
    Processing helix  chain 'A' and resid 262 through 266
      removed outlier: 4.209A  pdb=" N   HIS A 266 " --> pdb=" O   PRO A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 4.067A  pdb=" N   TYR A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 4.232A  pdb=" N   PHE A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 301
      removed outlier: 3.599A  pdb=" N   GLN A 301 " --> pdb=" O   PRO A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 324 through 338
      removed outlier: 3.630A  pdb=" N   VAL A 328 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 400
      removed outlier: 4.201A  pdb=" N   ALA A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   LEU A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
    Processing helix  chain 'A' and resid 415 through 432
      removed outlier: 4.031A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA A 421 " --> pdb=" O   GLU A 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 29
      removed outlier: 3.796A  pdb=" N   ASP B  26 " --> pdb=" O   GLU B  22 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLU B  27 " --> pdb=" O   VAL B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 49
    Processing helix  chain 'B' and resid 69 through 78
      removed outlier: 4.287A  pdb=" N   MET B  73 " --> pdb=" O   GLU B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 88
      No H-bonds generated for 'chain 'B' and resid 86 through 88'
    Processing helix  chain 'B' and resid 100 through 106
    Processing helix  chain 'B' and resid 108 through 126
      removed outlier: 3.894A  pdb=" N   LEU B 112 " --> pdb=" O   GLU B 108 " (cutoff:3.500A)
      removed outlier: 4.832A  pdb=" N   ASP B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   SER B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 159
      removed outlier: 3.757A  pdb=" N   SER B 145 " --> pdb=" O   GLY B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 193
      removed outlier: 3.630A  pdb=" N   ASN B 184 " --> pdb=" O   VAL B 180 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   GLN B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 214
    Processing helix  chain 'B' and resid 221 through 242
      removed outlier: 3.770A  pdb=" N   LEU B 225 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   THR B 237 " --> pdb=" O   MET B 233 " (cutoff:3.500A)
      removed outlier: 5.201A  pdb=" N   CYS B 239 " --> pdb=" O   GLY B 235 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   LEU B 240 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ARG B 241 " --> pdb=" O   THR B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 258
    Processing helix  chain 'B' and resid 285 through 294
    Processing helix  chain 'B' and resid 295 through 299
      removed outlier: 3.632A  pdb=" N   ASN B 298 " --> pdb=" O   ASP B 295 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   MET B 299 " --> pdb=" O   SER B 296 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 295 through 299'
    Processing helix  chain 'B' and resid 304 through 308
      removed outlier: 3.618A  pdb=" N   GLY B 308 " --> pdb=" O   PRO B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 337
      removed outlier: 3.652A  pdb=" N   VAL B 326 " --> pdb=" O   SER B 322 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ASN B 337 " --> pdb=" O   VAL B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 341
    Processing helix  chain 'B' and resid 373 through 390
      removed outlier: 4.281A  pdb=" N   LEU B 377 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE B 378 " --> pdb=" O   ILE B 374 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 400
    Processing helix  chain 'B' and resid 404 through 425
      removed outlier: 3.874A  pdb=" N   PHE B 408 " --> pdb=" O   ASP B 404 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   TYR B 425 " --> pdb=" O   GLU B 421 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 10 through 29
    Processing helix  chain 'E' and resid 36 through 43
      removed outlier: 3.764A  pdb=" N   LYS E  40 " --> pdb=" O   MET E  36 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 71 through 80
      removed outlier: 4.323A  pdb=" N   ILE E  75 " --> pdb=" O   GLU E  71 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLU E  77 " --> pdb=" O   THR E  73 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL E  78 " --> pdb=" O   VAL E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 102 through 108
    Processing helix  chain 'E' and resid 114 through 129
    Processing helix  chain 'E' and resid 143 through 161
      removed outlier: 4.251A  pdb=" N   THR E 150 " --> pdb=" O   GLY E 146 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 182 through 197
      removed outlier: 3.715A  pdb=" N   ASN E 186 " --> pdb=" O   VAL E 182 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   HIS E 192 " --> pdb=" O   ILE E 188 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   THR E 193 " --> pdb=" O   LEU E 189 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   HIS E 197 " --> pdb=" O   THR E 193 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 205 through 216
    Processing helix  chain 'E' and resid 223 through 244
      removed outlier: 3.852A  pdb=" N   LEU E 227 " --> pdb=" O   THR E 223 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   SER E 241 " --> pdb=" O   SER E 237 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   LEU E 242 " --> pdb=" O   ILE E 238 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ARG E 243 " --> pdb=" O   THR E 239 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 251 through 260
      removed outlier: 3.650A  pdb=" N   GLN E 256 " --> pdb=" O   LEU E 252 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 277 through 282
      removed outlier: 4.268A  pdb=" N   TYR E 282 " --> pdb=" O   ALA E 278 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 287 through 296
      removed outlier: 3.804A  pdb=" N   PHE E 296 " --> pdb=" O   THR E 292 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 297 through 301
      removed outlier: 3.613A  pdb=" N   GLN E 301 " --> pdb=" O   PRO E 298 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 306 through 310
    Processing helix  chain 'E' and resid 324 through 338
      removed outlier: 3.672A  pdb=" N   VAL E 328 " --> pdb=" O   VAL E 324 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   THR E 337 " --> pdb=" O   ALA E 333 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LYS E 338 " --> pdb=" O   THR E 334 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 383 through 400
      removed outlier: 4.185A  pdb=" N   ALA E 387 " --> pdb=" O   ALA E 383 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 405 through 410
    Processing helix  chain 'E' and resid 414 through 417
    Processing helix  chain 'E' and resid 418 through 437
      removed outlier: 3.638A  pdb=" N   GLU E 433 " --> pdb=" O   GLU E 429 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY E 436 " --> pdb=" O   TYR E 432 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   VAL E 437 " --> pdb=" O   GLU E 433 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 54 through 57
      removed outlier: 6.601A  pdb=" N   CYS K  92 " --> pdb=" O   ALA K 326 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   VAL K 328 " --> pdb=" O   CYS K  92 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   PHE K  94 " --> pdb=" O   VAL K 328 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   ALA K 330 " --> pdb=" O   PHE K  94 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   TYR K  96 " --> pdb=" O   ALA K 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 54 through 57
      removed outlier: 6.601A  pdb=" N   CYS K  92 " --> pdb=" O   ALA K 326 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   VAL K 328 " --> pdb=" O   CYS K  92 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   PHE K  94 " --> pdb=" O   VAL K 328 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   ALA K 330 " --> pdb=" O   PHE K  94 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   TYR K  96 " --> pdb=" O   ALA K 330 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   VAL K 142 " --> pdb=" O   VAL K 186 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'K' and resid 28 through 31
    Processing sheet with id=AA4, first strand: chain 'K' and resid 168 through 171
    Processing sheet with id=AA5, first strand: chain 'K' and resid 205 through 206
    Processing sheet with id=AA6, first strand: chain 'A' and resid 65 through 68
      removed outlier: 7.680A  pdb=" N   GLU A   3 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   PHE A 135 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   ILE A   5 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 5.473A  pdb=" N   VAL A 137 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ILE A   7 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   SER A 165 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   LYS A 166 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   PHE A 202 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   GLU A 168 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   VAL A 204 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   SER A 170 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA8, first strand: chain 'A' and resid 269 through 272
    Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 91
      removed outlier: 5.936A  pdb=" N   LEU B  65 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 8.195A  pdb=" N   VAL B  66 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   GLN B   8 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   GLU B   3 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   PHE B 133 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   VAL B   5 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 5.723A  pdb=" N   LEU B 135 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   ILE B   7 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   HIS B 137 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   ALA B   9 " --> pdb=" O   HIS B 137 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   GLN B 131 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
      removed outlier: 8.424A  pdb=" N   ASN B 165 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   PHE B 133 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   PHE B 167 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   LEU B 135 " --> pdb=" O   PHE B 167 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   VAL B 169 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   HIS B 137 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 8.673A  pdb=" N   ASP B 203 " --> pdb=" O   PRO B 268 " (cutoff:3.500A)
      removed outlier: 12.247A  pdb=" N   PHE B 270 " --> pdb=" O   ASP B 203 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   PHE B 265 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   SER B 371 " --> pdb=" O   PHE B 265 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 51 through 54
    Processing sheet with id=AB2, first strand: chain 'E' and resid 65 through 68
      removed outlier: 7.000A  pdb=" N   GLU E   3 " --> pdb=" O   GLY E 134 " (cutoff:3.500A)
      removed outlier: 8.245A  pdb=" N   LEU E 136 " --> pdb=" O   GLU E   3 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   ILE E   5 " --> pdb=" O   LEU E 136 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   PHE E 138 " --> pdb=" O   ILE E   5 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ILE E   7 " --> pdb=" O   PHE E 138 " (cutoff:3.500A)
      removed outlier: 8.785A  pdb=" N   SER E 140 " --> pdb=" O   ILE E   7 " (cutoff:3.500A)
      removed outlier: 8.903A  pdb=" N   VAL E   9 " --> pdb=" O   SER E 140 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   SER E 165 " --> pdb=" O   GLN E 133 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   HIS E 139 " --> pdb=" O   PHE E 169 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ILE E 171 " --> pdb=" O   HIS E 139 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 55
    Processing sheet with id=AB4, first strand: chain 'E' and resid 269 through 272

    684 hydrogen bonds defined for protein.
    1947 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: 2.49

  Time building geometry restraints manager: 1.62 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2332
        1.32 -     1.44: 3680
        1.44 -     1.57: 7731
        1.57 -     1.69: 21
        1.69 -     1.82: 139
  Bond restraints: 13903
  Sorted by residual:
  bond pdb=" N   TYR A 262 "
       pdb=" CA  TYR A 262 "
    ideal  model  delta    sigma   weight residual
    1.453  1.491 -0.038 8.30e-03 1.45e+04 2.14e+01
  bond pdb=" O3A ANP K 502 "
       pdb=" PB  ANP K 502 "
    ideal  model  delta    sigma   weight residual
    1.700  1.608  0.092 2.00e-02 2.50e+03 2.11e+01
  bond pdb=" C4  ANP K 502 "
       pdb=" C5  ANP K 502 "
    ideal  model  delta    sigma   weight residual
    1.387  1.468 -0.081 2.00e-02 2.50e+03 1.64e+01
  bond pdb=" CA  SER B  25 "
       pdb=" CB  SER B  25 "
    ideal  model  delta    sigma   weight residual
    1.530  1.464  0.065 1.63e-02 3.76e+03 1.61e+01
  bond pdb=" C   PRO B  61 "
       pdb=" O   PRO B  61 "
    ideal  model  delta    sigma   weight residual
    1.233  1.190  0.043 1.10e-02 8.26e+03 1.53e+01
  ... (remaining 13898 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 18304
        2.58 -     5.17: 501
        5.17 -     7.75: 58
        7.75 -    10.33: 9
       10.33 -    12.92: 4
  Bond angle restraints: 18876
  Sorted by residual:
  angle pdb=" N   VAL A 435 "
        pdb=" CA  VAL A 435 "
        pdb=" C   VAL A 435 "
      ideal   model   delta    sigma   weight residual
     113.43  103.38   10.05 1.09e+00 8.42e-01 8.50e+01
  angle pdb=" N   GLU E 417 "
        pdb=" CA  GLU E 417 "
        pdb=" C   GLU E 417 "
      ideal   model   delta    sigma   weight residual
     112.88  102.69   10.19 1.29e+00 6.01e-01 6.24e+01
  angle pdb=" C   ARG B  62 "
        pdb=" CA  ARG B  62 "
        pdb=" CB  ARG B  62 "
      ideal   model   delta    sigma   weight residual
     112.12  101.75   10.37 1.50e+00 4.44e-01 4.78e+01
  angle pdb=" N   LEU K 122 "
        pdb=" CA  LEU K 122 "
        pdb=" C   LEU K 122 "
      ideal   model   delta    sigma   weight residual
     111.07  105.33    5.74 1.07e+00 8.73e-01 2.88e+01
  angle pdb=" N   LYS A 336 "
        pdb=" CA  LYS A 336 "
        pdb=" C   LYS A 336 "
      ideal   model   delta    sigma   weight residual
     112.89  106.44    6.45 1.24e+00 6.50e-01 2.71e+01
  ... (remaining 18871 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.42: 7997
       31.42 -    62.84: 366
       62.84 -    94.27: 38
       94.27 -   125.69: 11
      125.69 -   157.11: 11
  Dihedral angle restraints: 8423
    sinusoidal: 3465
      harmonic: 4958
  Sorted by residual:
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -133.62 -157.11     1      2.00e+01 2.50e-03 4.61e+01
  dihedral pdb=" C5' GTP E 501 "
           pdb=" O5' GTP E 501 "
           pdb=" PA  GTP E 501 "
           pdb=" O3A GTP E 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  -85.06  154.33     1      2.00e+01 2.50e-03 4.56e+01
  dihedral pdb=" C8  GTP E 501 "
           pdb=" C1' GTP E 501 "
           pdb=" N9  GTP E 501 "
           pdb=" O4' GTP E 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -36.98  141.57     1      2.00e+01 2.50e-03 4.28e+01
  ... (remaining 8420 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.109: 1948
       0.109 -    0.217: 121
       0.217 -    0.326: 4
       0.326 -    0.435: 0
       0.435 -    0.543: 1
  Chirality restraints: 2074
  Sorted by residual:
  chirality pdb=" C18 TA1 B 502 "
            pdb=" C10 TA1 B 502 "
            pdb=" C17 TA1 B 502 "
            pdb=" C20 TA1 B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -3.16   -2.62   -0.54 2.00e-01 2.50e+01 7.38e+00
  chirality pdb=" C02 TA1 B 502 "
            pdb=" C01 TA1 B 502 "
            pdb=" C10 TA1 B 502 "
            pdb=" O02 TA1 B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.56    2.82   -0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CA  ARG B  62 "
            pdb=" N   ARG B  62 "
            pdb=" C   ARG B  62 "
            pdb=" CB  ARG B  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 2071 not shown)

  Planarity restraints: 2452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY E 416 "    0.024 2.00e-02 2.50e+03   4.97e-02 2.47e+01
        pdb=" C   GLY E 416 "   -0.086 2.00e-02 2.50e+03
        pdb=" O   GLY E 416 "    0.033 2.00e-02 2.50e+03
        pdb=" N   GLU E 417 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN K  39 "   -0.078 5.00e-02 4.00e+02   1.16e-01 2.16e+01
        pdb=" N   PRO K  40 "    0.201 5.00e-02 4.00e+02
        pdb=" CA  PRO K  40 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO K  40 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  57 "   -0.019 2.00e-02 2.50e+03   3.71e-02 1.38e+01
        pdb=" C   ASN B  57 "    0.064 2.00e-02 2.50e+03
        pdb=" O   ASN B  57 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   LYS B  58 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 2449 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.55: 87
        2.55 -     3.14: 10456
        3.14 -     3.73: 19816
        3.73 -     4.31: 27673
        4.31 -     4.90: 47970
  Nonbonded interactions: 106002
  Sorted by model distance:
  nonbonded pdb=" O1B GTP E 501 "
            pdb="MG    MG E 502 "
     model   vdw
     1.969 2.170
  nonbonded pdb=" O1G GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     1.989 2.170
  nonbonded pdb=" O3B GTP E 501 "
            pdb="MG    MG E 502 "
     model   vdw
     2.013 2.170
  nonbonded pdb=" O1G GTP E 501 "
            pdb="MG    MG E 502 "
     model   vdw
     2.071 2.170
  nonbonded pdb=" O1B GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     2.085 2.170
  ... (remaining 105997 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 'A'
  selection = (chain 'E' and (resid 1 through 440 or resid 501 through 502))
}

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=0.48 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.090
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
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      :  0.006   0.092  13903  Z= 0.327
  Angle     :  0.966  12.919  18876  Z= 0.554
  Chirality :  0.055   0.543   2074
  Planarity :  0.008   0.116   2452
  Dihedral  : 18.777 157.110   5243
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.70 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 19.11 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.20), residues: 1705
  helix:  0.74 (0.20), residues: 704
  sheet: -0.46 (0.29), residues: 310
  loop : -1.18 (0.22), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG E 339 
 TYR   0.035   0.002   TYR B  50 
 PHE   0.040   0.002   PHE K  52 
 TRP   0.021   0.002   TRP A 346 
 HIS   0.013   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00584 (13903)
  covalent geometry    : angle       0.96578 (18876)
  hydrogen bonds       : bond        0.17535 (  647)
  hydrogen bonds       : angle       6.52422 ( 1947)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 277
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
REVERT: K  107 MET cc_start: 0.8167 (mmt) cc_final: 0.7887 (mmm)
REVERT: K  179 GLU cc_start: 0.8132 (tt0) cc_final: 0.7870 (tt0)
REVERT: K  192 ILE cc_start: 0.7898 (tt) cc_final: 0.7602 (pp)
REVERT: K  248 ASP cc_start: 0.7111 (t0) cc_final: 0.6802 (t0)
REVERT: K  354 ILE cc_start: 0.8083 (mt) cc_final: 0.7818 (mm)
REVERT: A   24 TYR cc_start: 0.8233 (m-80) cc_final: 0.7707 (m-80)
REVERT: A  302 MET cc_start: 0.7880 (mmm) cc_final: 0.6475 (mtm)
REVERT: B    1 MET cc_start: 0.5365 (tpt) cc_final: 0.5128 (tpt)
REVERT: B  415 MET cc_start: 0.8478 (ttm) cc_final: 0.8276 (ttp)
REVERT: E   26 LEU cc_start: 0.8463 (mm) cc_final: 0.8191 (tp)
REVERT: E  203 MET cc_start: 0.8550 (mtp) cc_final: 0.8276 (mtm)
REVERT: E  297 GLU cc_start: 0.7814 (tp30) cc_final: 0.7439 (tp30)
REVERT: E  302 MET cc_start: 0.8423 (mmm) cc_final: 0.7912 (mtm)
REVERT: E  322 ASP cc_start: 0.8460 (t0) cc_final: 0.8044 (t0)
  outliers start: 21
  outliers final: 11
  residues processed: 294
  average time/residue: 0.5918
  time to fit residues: 190.9305
Evaluate side-chains
  263 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 252
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   13 ARG
Chi-restraints excluded: chain K residue  215 SER
Chi-restraints excluded: chain K residue  258 THR
Chi-restraints excluded: chain K residue  300 LYS
Chi-restraints excluded: chain K residue  309 SER
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain B residue  404 ASP
Chi-restraints excluded: chain E residue  132 LEU
Chi-restraints excluded: chain E residue  178 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.3980
   chunk 149 optimal weight:    3.9990
   overall best weight:    1.8788

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

Flipped N/Q/H residues before XYZ refinement:
** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 121 GLN
** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 107 HIS
B   8 GLN
B 204 ASN
B 298 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.132138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.101423 restraints weight = 18771.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 1.98
r_work: 0.3268 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3127
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3127
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  13903  Z= 0.247
  Angle     :  0.675  11.817  18876  Z= 0.345
  Chirality :  0.047   0.186   2074
  Planarity :  0.005   0.076   2452
  Dihedral  : 12.735 154.935   2063
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.12 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 16.31 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.20), residues: 1705
  helix:  1.23 (0.20), residues: 717
  sheet:  0.01 (0.30), residues: 300
  loop : -1.16 (0.22), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 241 
 TYR   0.016   0.002   TYR A  24 
 PHE   0.017   0.002   PHE B 367 
 TRP   0.013   0.002   TRP B 344 
 HIS   0.010   0.002   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 (13903)
  covalent geometry    : angle       0.67465 (18876)
  hydrogen bonds       : bond        0.06240 (  647)
  hydrogen bonds       : angle       4.59533 ( 1947)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  333 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 276
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
REVERT: K  105 TYR cc_start: 0.7861 (t80) cc_final: 0.6910 (t80)
REVERT: K  107 MET cc_start: 0.8152 (mmt) cc_final: 0.7921 (mmm)
REVERT: K  179 GLU cc_start: 0.8252 (tt0) cc_final: 0.8043 (tt0)
REVERT: K  192 ILE cc_start: 0.7749 (tt) cc_final: 0.7377 (pp)
REVERT: K  248 ASP cc_start: 0.7282 (t0) cc_final: 0.6972 (t0)
REVERT: K  287 GLU cc_start: 0.7770 (tp30) cc_final: 0.7496 (tp30)
REVERT: K  338 TYR cc_start: 0.6471 (t80) cc_final: 0.6257 (t80)
REVERT: B   57 ASN cc_start: 0.7736 (t0) cc_final: 0.7224 (t0)
REVERT: B   94 GLN cc_start: 0.8148 (mp10) cc_final: 0.7944 (mm-40)
REVERT: B  164 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7761 (ttt)
REVERT: B  291 GLN cc_start: 0.8253 (tt0) cc_final: 0.7995 (mt0)
REVERT: B  316 ILE cc_start: 0.8601 (mm) cc_final: 0.8367 (mt)
REVERT: E   26 LEU cc_start: 0.8627 (mm) cc_final: 0.8367 (tp)
REVERT: E  322 ASP cc_start: 0.8678 (t0) cc_final: 0.8335 (t0)
REVERT: E  392 ASP cc_start: 0.8250 (t0) cc_final: 0.7941 (m-30)
  outliers start: 57
  outliers final: 23
  residues processed: 308
  average time/residue: 0.5919
  time to fit residues: 199.9470
Evaluate side-chains
  289 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 265
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   28 ILE
Chi-restraints excluded: chain K residue   51 SER
Chi-restraints excluded: chain K residue  270 ASN
Chi-restraints excluded: chain K residue  281 VAL
Chi-restraints excluded: chain K residue  282 ILE
Chi-restraints excluded: chain K residue  283 SER
Chi-restraints excluded: chain K residue  305 LEU
Chi-restraints excluded: chain K residue  339 ASP
Chi-restraints excluded: chain K residue  343 SER
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain E residue  132 LEU
Chi-restraints excluded: chain E residue  198 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 119 optimal weight:    0.8980
   chunk 29 optimal weight:   10.0000
   chunk 137 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
K  72 GLN
K  90 ASN
** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.134665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.103977 restraints weight = 18989.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.00
r_work: 0.3312 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13903  Z= 0.139
  Angle     :  0.563   6.981  18876  Z= 0.288
  Chirality :  0.044   0.410   2074
  Planarity :  0.005   0.070   2452
  Dihedral  : 10.218 156.957   2048
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.12 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 18.43 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.20), residues: 1705
  helix:  1.56 (0.20), residues: 718
  sheet:  0.29 (0.30), residues: 295
  loop : -1.13 (0.22), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 339 
 TYR   0.015   0.001   TYR A  24 
 PHE   0.014   0.001   PHE B 367 
 TRP   0.014   0.001   TRP B 344 
 HIS   0.004   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (13903)
  covalent geometry    : angle       0.56255 (18876)
  hydrogen bonds       : bond        0.04660 (  647)
  hydrogen bonds       : angle       4.23140 ( 1947)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 281
  time to evaluate  : 0.529 
Fit side-chains
REVERT: K   19 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7824 (mt-10)
REVERT: K  192 ILE cc_start: 0.7787 (tt) cc_final: 0.7375 (pp)
REVERT: K  248 ASP cc_start: 0.7300 (t0) cc_final: 0.7050 (t0)
REVERT: K  287 GLU cc_start: 0.7789 (tp30) cc_final: 0.7584 (tp30)
REVERT: A  332 ILE cc_start: 0.8469 (mm) cc_final: 0.8251 (mt)
REVERT: A  371 VAL cc_start: 0.9105 (p) cc_final: 0.8887 (m)
REVERT: A  392 ASP cc_start: 0.8272 (m-30) cc_final: 0.8071 (m-30)
REVERT: B    1 MET cc_start: 0.5028 (tpt) cc_final: 0.4813 (tpt)
REVERT: B   57 ASN cc_start: 0.7743 (t0) cc_final: 0.7213 (t0)
REVERT: B  164 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7741 (ttt)
REVERT: B  213 ARG cc_start: 0.8434 (mtm180) cc_final: 0.8081 (mtm-85)
REVERT: B  219 THR cc_start: 0.8875 (m) cc_final: 0.8639 (p)
REVERT: B  257 MET cc_start: 0.8175 (mmp) cc_final: 0.7801 (mmm)
REVERT: B  316 ILE cc_start: 0.8586 (mm) cc_final: 0.8338 (mt)
REVERT: E   26 LEU cc_start: 0.8587 (mm) cc_final: 0.8329 (tp)
REVERT: E  170 SER cc_start: 0.8452 (m) cc_final: 0.8189 (m)
REVERT: E  322 ASP cc_start: 0.8581 (t0) cc_final: 0.8282 (t0)
REVERT: E  392 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7883 (m-30)
  outliers start: 42
  outliers final: 15
  residues processed: 301
  average time/residue: 0.5708
  time to fit residues: 188.5178
Evaluate side-chains
  278 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 261
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   28 ILE
Chi-restraints excluded: chain K residue  281 VAL
Chi-restraints excluded: chain K residue  282 ILE
Chi-restraints excluded: chain K residue  283 SER
Chi-restraints excluded: chain K residue  305 LEU
Chi-restraints excluded: chain K residue  343 SER
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain B residue  123 GLU
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain E residue  132 LEU
Chi-restraints excluded: chain E residue  392 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 168 optimal weight:    0.9980
   chunk 29 optimal weight:   20.0000
   chunk 27 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   chunk 128 optimal weight:    0.6980
   chunk 10 optimal weight:   10.0000
   chunk 92 optimal weight:    3.9990
   chunk 23 optimal weight:    8.9990
   chunk 130 optimal weight:    2.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 293 ASN
B 165 ASN
B 195 ASN
E 139 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.129221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.098259 restraints weight = 21284.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.12
r_work: 0.3220 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.061  13903  Z= 0.311
  Angle     :  0.670   7.472  18876  Z= 0.345
  Chirality :  0.049   0.318   2074
  Planarity :  0.005   0.068   2452
  Dihedral  : 10.331 161.951   2046
  Min Nonbonded Distance : 1.817

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.76 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 17.95 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.20), residues: 1705
  helix:  1.41 (0.20), residues: 716
  sheet:  0.22 (0.29), residues: 300
  loop : -1.30 (0.22), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG K 129 
 TYR   0.020   0.002   TYR A 319 
 PHE   0.022   0.002   PHE A 141 
 TRP   0.015   0.002   TRP B 344 
 HIS   0.013   0.002   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00776 (13903)
  covalent geometry    : angle       0.66991 (18876)
  hydrogen bonds       : bond        0.06563 (  647)
  hydrogen bonds       : angle       4.39430 ( 1947)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 280
  time to evaluate  : 0.555 
Fit side-chains
REVERT: K    7 LYS cc_start: 0.8163 (mptt) cc_final: 0.7776 (tmmt)
REVERT: K   19 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7701 (mt-10)
REVERT: K  105 TYR cc_start: 0.7669 (t80) cc_final: 0.7229 (t80)
REVERT: K  192 ILE cc_start: 0.7844 (tt) cc_final: 0.7436 (pp)
REVERT: K  248 ASP cc_start: 0.7342 (t0) cc_final: 0.7063 (t0)
REVERT: K  287 GLU cc_start: 0.7836 (tp30) cc_final: 0.7612 (tp30)
REVERT: K  341 THR cc_start: 0.8817 (m) cc_final: 0.8554 (p)
REVERT: A  320 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8299 (mtp180)
REVERT: B   57 ASN cc_start: 0.7993 (t0) cc_final: 0.7495 (t0)
REVERT: B  131 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8224 (tp40)
REVERT: B  164 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7797 (ttt)
REVERT: E   26 LEU cc_start: 0.8747 (mm) cc_final: 0.8506 (tp)
REVERT: E  265 ILE cc_start: 0.8384 (pt) cc_final: 0.7971 (mt)
REVERT: E  322 ASP cc_start: 0.8655 (t0) cc_final: 0.8323 (t0)
REVERT: E  392 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8006 (m-30)
  outliers start: 64
  outliers final: 33
  residues processed: 314
  average time/residue: 0.5860
  time to fit residues: 202.5454
Evaluate side-chains
  308 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 271
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   28 ILE
Chi-restraints excluded: chain K residue   51 SER
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  226 THR
Chi-restraints excluded: chain K residue  247 VAL
Chi-restraints excluded: chain K residue  270 ASN
Chi-restraints excluded: chain K residue  281 VAL
Chi-restraints excluded: chain K residue  282 ILE
Chi-restraints excluded: chain K residue  283 SER
Chi-restraints excluded: chain K residue  305 LEU
Chi-restraints excluded: chain K residue  339 ASP
Chi-restraints excluded: chain K residue  343 SER
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain A residue  120 ASP
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  320 ARG
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  379 SER
Chi-restraints excluded: chain A residue  424 ASP
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  135 LEU
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain E residue  132 LEU
Chi-restraints excluded: chain E residue  154 MET
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  367 ASP
Chi-restraints excluded: chain E residue  379 SER
Chi-restraints excluded: chain E residue  392 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 141 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 165 optimal weight:    0.9980
   chunk 125 optimal weight:    0.8980
   chunk 41 optimal weight:    0.1980
   chunk 85 optimal weight:    0.0970
   chunk 144 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 88 optimal weight:    0.5980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
K  70 GLN
** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  11 GLN
B 165 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.134007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.103352 restraints weight = 18847.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.01
r_work: 0.3315 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3176
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3176
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13903  Z= 0.117
  Angle     :  0.542   7.620  18876  Z= 0.276
  Chirality :  0.043   0.238   2074
  Planarity :  0.004   0.067   2452
  Dihedral  :  9.831 160.859   2046
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.06 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 20.75 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.20), residues: 1705
  helix:  1.72 (0.20), residues: 713
  sheet:  0.41 (0.30), residues: 298
  loop : -1.22 (0.22), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 339 
 TYR   0.017   0.001   TYR A  24 
 PHE   0.013   0.001   PHE B 367 
 TRP   0.012   0.001   TRP B 344 
 HIS   0.003   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (13903)
  covalent geometry    : angle       0.54152 (18876)
  hydrogen bonds       : bond        0.04111 (  647)
  hydrogen bonds       : angle       4.06754 ( 1947)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 280
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
REVERT: K    7 LYS cc_start: 0.8125 (mptt) cc_final: 0.7621 (tmtp)
REVERT: K   19 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7687 (mt-10)
REVERT: K  105 TYR cc_start: 0.7572 (t80) cc_final: 0.6834 (t80)
REVERT: K  116 GLN cc_start: 0.5354 (mm-40) cc_final: 0.5053 (mm-40)
REVERT: K  136 ASP cc_start: 0.5689 (m-30) cc_final: 0.5452 (t0)
REVERT: K  192 ILE cc_start: 0.7864 (tt) cc_final: 0.7413 (pp)
REVERT: K  248 ASP cc_start: 0.7387 (t0) cc_final: 0.7164 (t0)
REVERT: K  287 GLU cc_start: 0.7814 (tp30) cc_final: 0.7603 (tp30)
REVERT: K  338 TYR cc_start: 0.6168 (t80) cc_final: 0.5673 (t80)
REVERT: K  341 THR cc_start: 0.8780 (m) cc_final: 0.8565 (p)
REVERT: K  342 LEU cc_start: 0.8843 (tt) cc_final: 0.8575 (tm)
REVERT: K  353 GLN cc_start: 0.7781 (mp10) cc_final: 0.7419 (mp10)
REVERT: A  332 ILE cc_start: 0.8402 (mm) cc_final: 0.8193 (mt)
REVERT: A  371 VAL cc_start: 0.9103 (p) cc_final: 0.8887 (m)
REVERT: A  437 VAL cc_start: 0.9052 (p) cc_final: 0.8692 (m)
REVERT: B   57 ASN cc_start: 0.7827 (t0) cc_final: 0.7355 (t0)
REVERT: B  131 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8070 (tp40)
REVERT: B  164 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7752 (ttt)
REVERT: B  213 ARG cc_start: 0.8461 (mtm180) cc_final: 0.8132 (mtm-85)
REVERT: B  282 ARG cc_start: 0.8511 (ttm110) cc_final: 0.8147 (mtp85)
REVERT: B  316 ILE cc_start: 0.8539 (mm) cc_final: 0.8247 (mt)
REVERT: E   26 LEU cc_start: 0.8634 (mm) cc_final: 0.8390 (tp)
REVERT: E  181 VAL cc_start: 0.8646 (p) cc_final: 0.8343 (t)
REVERT: E  302 MET cc_start: 0.8381 (mmm) cc_final: 0.7900 (mtm)
REVERT: E  392 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7842 (m-30)
REVERT: E  449 GLU cc_start: -0.1508 (OUTLIER) cc_final: -0.1842 (pm20)
  outliers start: 46
  outliers final: 28
  residues processed: 308
  average time/residue: 0.5959
  time to fit residues: 201.1215
Evaluate side-chains
  292 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 260
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   28 ILE
Chi-restraints excluded: chain K residue   51 SER
Chi-restraints excluded: chain K residue   70 GLN
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  270 ASN
Chi-restraints excluded: chain K residue  281 VAL
Chi-restraints excluded: chain K residue  282 ILE
Chi-restraints excluded: chain K residue  283 SER
Chi-restraints excluded: chain K residue  305 LEU
Chi-restraints excluded: chain K residue  339 ASP
Chi-restraints excluded: chain K residue  343 SER
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  135 LEU
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain E residue  132 LEU
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  220 GLU
Chi-restraints excluded: chain E residue  392 ASP
Chi-restraints excluded: chain E residue  449 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0060
   chunk 131 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 136 optimal weight:    0.7980
   chunk 162 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0980
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
K  70 GLN
** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 165 ASN
B 195 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.134288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.103286 restraints weight = 21710.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.17
r_work: 0.3317 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3156
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3156
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13903  Z= 0.114
  Angle     :  0.549   8.184  18876  Z= 0.277
  Chirality :  0.043   0.225   2074
  Planarity :  0.004   0.064   2452
  Dihedral  :  9.603 160.464   2046
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 21.23 %
    Favored  : 75.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.21), residues: 1705
  helix:  1.86 (0.20), residues: 716
  sheet:  0.48 (0.30), residues: 298
  loop : -1.18 (0.22), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 339 
 TYR   0.014   0.001   TYR A  24 
 PHE   0.012   0.001   PHE B 367 
 TRP   0.013   0.001   TRP B 344 
 HIS   0.003   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (13903)
  covalent geometry    : angle       0.54942 (18876)
  hydrogen bonds       : bond        0.03987 (  647)
  hydrogen bonds       : angle       3.99068 ( 1947)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 266
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
REVERT: K    7 LYS cc_start: 0.8136 (mptt) cc_final: 0.7625 (tmtp)
REVERT: K   19 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7743 (mt-10)
REVERT: K   98 GLN cc_start: 0.8337 (pt0) cc_final: 0.8126 (tt0)
REVERT: K  105 TYR cc_start: 0.7586 (t80) cc_final: 0.6804 (t80)
REVERT: K  116 GLN cc_start: 0.5321 (mm-40) cc_final: 0.5077 (mm-40)
REVERT: K  136 ASP cc_start: 0.5738 (m-30) cc_final: 0.5487 (t0)
REVERT: K  192 ILE cc_start: 0.7863 (tt) cc_final: 0.7401 (pp)
REVERT: K  246 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7616 (mt)
REVERT: K  248 ASP cc_start: 0.7438 (t0) cc_final: 0.7208 (t0)
REVERT: K  287 GLU cc_start: 0.7798 (tp30) cc_final: 0.7591 (tp30)
REVERT: K  342 LEU cc_start: 0.8819 (tt) cc_final: 0.8498 (tm)
REVERT: K  353 GLN cc_start: 0.7791 (mp10) cc_final: 0.7403 (mp10)
REVERT: A  254 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7353 (mt-10)
REVERT: A  332 ILE cc_start: 0.8389 (mm) cc_final: 0.8165 (mt)
REVERT: A  371 VAL cc_start: 0.9093 (p) cc_final: 0.8879 (m)
REVERT: A  437 VAL cc_start: 0.9029 (p) cc_final: 0.8673 (m)
REVERT: B    1 MET cc_start: 0.6228 (mmm) cc_final: 0.5064 (ttm)
REVERT: B   57 ASN cc_start: 0.7848 (t0) cc_final: 0.7369 (t0)
REVERT: B  188 SER cc_start: 0.8559 (t) cc_final: 0.8197 (p)
REVERT: B  213 ARG cc_start: 0.8516 (mtm180) cc_final: 0.8182 (mtm-85)
REVERT: B  282 ARG cc_start: 0.8516 (ttm110) cc_final: 0.8148 (mtp85)
REVERT: B  316 ILE cc_start: 0.8506 (mm) cc_final: 0.8211 (mt)
REVERT: E   26 LEU cc_start: 0.8610 (mm) cc_final: 0.8347 (tp)
REVERT: E  181 VAL cc_start: 0.8641 (p) cc_final: 0.8352 (t)
REVERT: E  392 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7852 (m-30)
REVERT: E  449 GLU cc_start: -0.1465 (OUTLIER) cc_final: -0.1742 (pm20)
  outliers start: 44
  outliers final: 30
  residues processed: 289
  average time/residue: 0.5892
  time to fit residues: 186.6193
Evaluate side-chains
  288 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 254
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   28 ILE
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   51 SER
Chi-restraints excluded: chain K residue   70 GLN
Chi-restraints excluded: chain K residue   93 ILE
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  246 LEU
Chi-restraints excluded: chain K residue  258 THR
Chi-restraints excluded: chain K residue  270 ASN
Chi-restraints excluded: chain K residue  281 VAL
Chi-restraints excluded: chain K residue  282 ILE
Chi-restraints excluded: chain K residue  305 LEU
Chi-restraints excluded: chain K residue  339 ASP
Chi-restraints excluded: chain K residue  360 ILE
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain B residue  135 LEU
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain E residue  132 LEU
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  220 GLU
Chi-restraints excluded: chain E residue  392 ASP
Chi-restraints excluded: chain E residue  449 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9980
   chunk 12 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 121 optimal weight:    2.9990
   chunk 36 optimal weight:   30.0000
   chunk 115 optimal weight:    0.0870
   chunk 118 optimal weight:    3.9990
   chunk 111 optimal weight:    0.4980
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.3162

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

Flipped N/Q/H residues before XYZ refinement:
K  70 GLN
** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  11 GLN
B 165 ASN
B 195 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.132005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.101242 restraints weight = 21629.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 2.08
r_work: 0.3265 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3129
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3129 r_free = 0.3129    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3129 r_free = 0.3129    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3129
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13903  Z= 0.179
  Angle     :  0.586   8.748  18876  Z= 0.298
  Chirality :  0.045   0.234   2074
  Planarity :  0.005   0.062   2452
  Dihedral  :  9.670 162.256   2046
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 21.09 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.20), residues: 1705
  helix:  1.84 (0.20), residues: 712
  sheet:  0.58 (0.30), residues: 293
  loop : -1.24 (0.22), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 339 
 TYR   0.019   0.001   TYR K  96 
 PHE   0.017   0.002   PHE B 367 
 TRP   0.014   0.001   TRP B 344 
 HIS   0.007   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (13903)
  covalent geometry    : angle       0.58578 (18876)
  hydrogen bonds       : bond        0.04867 (  647)
  hydrogen bonds       : angle       4.06559 ( 1947)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 252
  time to evaluate  : 0.522 
Fit side-chains
REVERT: K    7 LYS cc_start: 0.8125 (mptt) cc_final: 0.7689 (tmtp)
REVERT: K   19 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7749 (mt-10)
REVERT: K   42 GLN cc_start: 0.5610 (OUTLIER) cc_final: 0.4858 (mp10)
REVERT: K  136 ASP cc_start: 0.5583 (m-30) cc_final: 0.5349 (t0)
REVERT: K  183 LYS cc_start: 0.8161 (tttt) cc_final: 0.7729 (tmtp)
REVERT: K  224 ILE cc_start: 0.8063 (mm) cc_final: 0.7853 (mt)
REVERT: K  248 ASP cc_start: 0.7414 (t0) cc_final: 0.7181 (t0)
REVERT: K  287 GLU cc_start: 0.7849 (tp30) cc_final: 0.7637 (tp30)
REVERT: K  342 LEU cc_start: 0.8838 (tt) cc_final: 0.8507 (tm)
REVERT: K  354 ILE cc_start: 0.8268 (mt) cc_final: 0.7727 (mm)
REVERT: A  254 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7415 (mt-10)
REVERT: A  332 ILE cc_start: 0.8430 (mm) cc_final: 0.8170 (mt)
REVERT: A  371 VAL cc_start: 0.9102 (p) cc_final: 0.8881 (m)
REVERT: A  437 VAL cc_start: 0.9061 (p) cc_final: 0.8728 (m)
REVERT: B    1 MET cc_start: 0.6294 (mmm) cc_final: 0.5129 (ttm)
REVERT: B   43 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8501 (mt0)
REVERT: B   57 ASN cc_start: 0.7902 (t0) cc_final: 0.7429 (t0)
REVERT: B  179 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8271 (t)
REVERT: B  213 ARG cc_start: 0.8514 (mtm180) cc_final: 0.8110 (mtm-85)
REVERT: B  282 ARG cc_start: 0.8541 (ttm110) cc_final: 0.8145 (mtp85)
REVERT: B  316 ILE cc_start: 0.8580 (mm) cc_final: 0.8293 (mt)
REVERT: E   26 LEU cc_start: 0.8705 (mm) cc_final: 0.8434 (tp)
REVERT: E  181 VAL cc_start: 0.8682 (p) cc_final: 0.8384 (t)
REVERT: E  302 MET cc_start: 0.8441 (mmm) cc_final: 0.7965 (mtm)
REVERT: E  392 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7873 (m-30)
REVERT: E  449 GLU cc_start: -0.1484 (OUTLIER) cc_final: -0.1748 (pm20)
  outliers start: 52
  outliers final: 32
  residues processed: 280
  average time/residue: 0.5602
  time to fit residues: 172.0390
Evaluate side-chains
  287 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 249
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   42 GLN
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   51 SER
Chi-restraints excluded: chain K residue   93 ILE
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  192 ILE
Chi-restraints excluded: chain K residue  258 THR
Chi-restraints excluded: chain K residue  270 ASN
Chi-restraints excluded: chain K residue  281 VAL
Chi-restraints excluded: chain K residue  305 LEU
Chi-restraints excluded: chain K residue  339 ASP
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain B residue   43 GLN
Chi-restraints excluded: chain B residue  135 LEU
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain E residue  132 LEU
Chi-restraints excluded: chain E residue  178 SER
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  198 SER
Chi-restraints excluded: chain E residue  220 GLU
Chi-restraints excluded: chain E residue  334 THR
Chi-restraints excluded: chain E residue  367 ASP
Chi-restraints excluded: chain E residue  379 SER
Chi-restraints excluded: chain E residue  392 ASP
Chi-restraints excluded: chain E residue  449 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 134 optimal weight:    3.9990
   chunk 108 optimal weight:    0.8980
   chunk 121 optimal weight:    1.9990
   chunk 139 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   chunk 106 optimal weight:    0.7980
   chunk 154 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 36 optimal weight:   30.0000
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  11 GLN
B 165 ASN
B 195 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.132348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.101439 restraints weight = 21066.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 2.15
r_work: 0.3267 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  13903  Z= 0.161
  Angle     :  0.575   9.706  18876  Z= 0.293
  Chirality :  0.044   0.225   2074
  Planarity :  0.004   0.061   2452
  Dihedral  :  9.635 162.895   2046
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.37 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.20), residues: 1705
  helix:  1.82 (0.20), residues: 712
  sheet:  0.57 (0.30), residues: 293
  loop : -1.24 (0.22), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 339 
 TYR   0.022   0.001   TYR K  96 
 PHE   0.016   0.001   PHE B 367 
 TRP   0.012   0.001   TRP B 344 
 HIS   0.005   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (13903)
  covalent geometry    : angle       0.57473 (18876)
  hydrogen bonds       : bond        0.04673 (  647)
  hydrogen bonds       : angle       4.05715 ( 1947)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 263
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
REVERT: K    7 LYS cc_start: 0.8143 (mptt) cc_final: 0.7608 (tmtp)
REVERT: K   19 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7758 (mt-10)
REVERT: K   42 GLN cc_start: 0.5481 (OUTLIER) cc_final: 0.4755 (mp10)
REVERT: K   98 GLN cc_start: 0.8333 (pt0) cc_final: 0.8118 (tt0)
REVERT: K  183 LYS cc_start: 0.8147 (tttt) cc_final: 0.7811 (tmtp)
REVERT: K  224 ILE cc_start: 0.8063 (mm) cc_final: 0.7849 (mt)
REVERT: K  248 ASP cc_start: 0.7426 (t0) cc_final: 0.7211 (t0)
REVERT: K  287 GLU cc_start: 0.7844 (tp30) cc_final: 0.7628 (tp30)
REVERT: K  342 LEU cc_start: 0.8815 (tt) cc_final: 0.8501 (tm)
REVERT: K  353 GLN cc_start: 0.7838 (mp10) cc_final: 0.7418 (mp10)
REVERT: K  354 ILE cc_start: 0.8276 (mt) cc_final: 0.7730 (mm)
REVERT: A  187 SER cc_start: 0.8859 (t) cc_final: 0.8585 (p)
REVERT: A  254 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7417 (mt-10)
REVERT: A  302 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7559 (mtm)
REVERT: A  332 ILE cc_start: 0.8417 (mm) cc_final: 0.8151 (mt)
REVERT: A  371 VAL cc_start: 0.9095 (p) cc_final: 0.8880 (m)
REVERT: A  437 VAL cc_start: 0.9048 (p) cc_final: 0.8735 (m)
REVERT: B    1 MET cc_start: 0.6345 (mmm) cc_final: 0.5191 (ttm)
REVERT: B   43 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8511 (mt0)
REVERT: B   57 ASN cc_start: 0.7899 (t0) cc_final: 0.7423 (t0)
REVERT: B  164 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7771 (ttp)
REVERT: B  179 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8266 (t)
REVERT: B  213 ARG cc_start: 0.8525 (mtm180) cc_final: 0.8138 (mtm-85)
REVERT: B  282 ARG cc_start: 0.8554 (ttm110) cc_final: 0.8160 (mtp85)
REVERT: B  291 GLN cc_start: 0.8287 (tt0) cc_final: 0.8068 (tt0)
REVERT: B  304 ASP cc_start: 0.8479 (t0) cc_final: 0.8277 (t70)
REVERT: B  316 ILE cc_start: 0.8582 (mm) cc_final: 0.8303 (mt)
REVERT: E   26 LEU cc_start: 0.8684 (mm) cc_final: 0.8423 (tp)
REVERT: E   69 ASP cc_start: 0.8206 (t70) cc_final: 0.8001 (t70)
REVERT: E  181 VAL cc_start: 0.8679 (p) cc_final: 0.8378 (t)
REVERT: E  302 MET cc_start: 0.8432 (mmm) cc_final: 0.7968 (mtm)
REVERT: E  392 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7908 (m-30)
REVERT: E  449 GLU cc_start: -0.1534 (OUTLIER) cc_final: -0.1787 (pm20)
  outliers start: 47
  outliers final: 30
  residues processed: 287
  average time/residue: 0.5740
  time to fit residues: 180.2423
Evaluate side-chains
  293 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 255
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   42 GLN
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   51 SER
Chi-restraints excluded: chain K residue   93 ILE
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  152 GLU
Chi-restraints excluded: chain K residue  192 ILE
Chi-restraints excluded: chain K residue  258 THR
Chi-restraints excluded: chain K residue  270 ASN
Chi-restraints excluded: chain K residue  281 VAL
Chi-restraints excluded: chain K residue  305 LEU
Chi-restraints excluded: chain K residue  339 ASP
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain B residue   43 GLN
Chi-restraints excluded: chain B residue  135 LEU
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  280 GLN
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain E residue  132 LEU
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  198 SER
Chi-restraints excluded: chain E residue  334 THR
Chi-restraints excluded: chain E residue  392 ASP
Chi-restraints excluded: chain E residue  434 GLU
Chi-restraints excluded: chain E residue  449 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 139 optimal weight:    1.9990
   chunk 126 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 125 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 100 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  11 GLN
B 165 ASN
B 195 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.130431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.100246 restraints weight = 18841.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 1.91
r_work: 0.3261 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3125
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3125
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  13903  Z= 0.223
  Angle     :  0.619  10.315  18876  Z= 0.316
  Chirality :  0.046   0.238   2074
  Planarity :  0.005   0.061   2452
  Dihedral  :  9.764 163.406   2046
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 21.71 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.20), residues: 1705
  helix:  1.72 (0.20), residues: 711
  sheet:  0.37 (0.29), residues: 300
  loop : -1.30 (0.22), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 339 
 TYR   0.024   0.002   TYR K  96 
 PHE   0.016   0.002   PHE B 367 
 TRP   0.013   0.002   TRP B 344 
 HIS   0.009   0.002   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00553 (13903)
  covalent geometry    : angle       0.61892 (18876)
  hydrogen bonds       : bond        0.05478 (  647)
  hydrogen bonds       : angle       4.15929 ( 1947)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 251
  time to evaluate  : 0.451 
Fit side-chains
REVERT: K    7 LYS cc_start: 0.8169 (mptt) cc_final: 0.7656 (tmtt)
REVERT: K   19 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7788 (mt-10)
REVERT: K   42 GLN cc_start: 0.5640 (OUTLIER) cc_final: 0.4859 (mp10)
REVERT: K  248 ASP cc_start: 0.7371 (t0) cc_final: 0.7142 (t0)
REVERT: K  287 GLU cc_start: 0.7852 (tp30) cc_final: 0.7639 (tp30)
REVERT: K  342 LEU cc_start: 0.8818 (tt) cc_final: 0.8508 (tm)
REVERT: K  354 ILE cc_start: 0.8316 (mt) cc_final: 0.7772 (mm)
REVERT: A  187 SER cc_start: 0.8854 (t) cc_final: 0.8558 (p)
REVERT: A  254 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7429 (mt-10)
REVERT: A  332 ILE cc_start: 0.8425 (mm) cc_final: 0.8172 (mt)
REVERT: A  437 VAL cc_start: 0.9058 (p) cc_final: 0.8765 (m)
REVERT: B   43 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8539 (mt0)
REVERT: B   57 ASN cc_start: 0.7908 (t0) cc_final: 0.7430 (t0)
REVERT: B  179 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8278 (t)
REVERT: B  193 VAL cc_start: 0.8629 (p) cc_final: 0.8384 (t)
REVERT: B  282 ARG cc_start: 0.8553 (ttm110) cc_final: 0.8154 (mtp85)
REVERT: B  291 GLN cc_start: 0.8230 (tt0) cc_final: 0.8007 (tt0)
REVERT: B  316 ILE cc_start: 0.8582 (mm) cc_final: 0.8316 (mt)
REVERT: B  415 MET cc_start: 0.8145 (ttm) cc_final: 0.7802 (ttp)
REVERT: E   26 LEU cc_start: 0.8720 (mm) cc_final: 0.8463 (tp)
REVERT: E  108 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.6389 (p90)
REVERT: E  181 VAL cc_start: 0.8733 (p) cc_final: 0.8416 (t)
REVERT: E  302 MET cc_start: 0.8456 (mmm) cc_final: 0.7980 (mtm)
REVERT: E  322 ASP cc_start: 0.8590 (t0) cc_final: 0.8354 (t0)
REVERT: E  392 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7856 (m-30)
REVERT: E  449 GLU cc_start: -0.1525 (OUTLIER) cc_final: -0.1762 (pm20)
  outliers start: 46
  outliers final: 32
  residues processed: 276
  average time/residue: 0.5450
  time to fit residues: 165.9034
Evaluate side-chains
  290 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 251
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   37 ILE
Chi-restraints excluded: chain K residue   42 GLN
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   51 SER
Chi-restraints excluded: chain K residue   93 ILE
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  152 GLU
Chi-restraints excluded: chain K residue  192 ILE
Chi-restraints excluded: chain K residue  258 THR
Chi-restraints excluded: chain K residue  270 ASN
Chi-restraints excluded: chain K residue  281 VAL
Chi-restraints excluded: chain K residue  305 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain B residue   43 GLN
Chi-restraints excluded: chain B residue  135 LEU
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  280 GLN
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain E residue  108 TYR
Chi-restraints excluded: chain E residue  132 LEU
Chi-restraints excluded: chain E residue  178 SER
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  198 SER
Chi-restraints excluded: chain E residue  334 THR
Chi-restraints excluded: chain E residue  379 SER
Chi-restraints excluded: chain E residue  392 ASP
Chi-restraints excluded: chain E residue  434 GLU
Chi-restraints excluded: chain E residue  449 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   chunk 87 optimal weight:    0.6980
   chunk 129 optimal weight:    0.4980
   chunk 45 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 119 optimal weight:    0.7980
   chunk 2 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9990
   chunk 154 optimal weight:    0.3980
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  11 GLN
B 165 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.134150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.103384 restraints weight = 21153.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 2.08
r_work: 0.3305 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3165
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3165
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13903  Z= 0.123
  Angle     :  0.560  10.940  18876  Z= 0.285
  Chirality :  0.043   0.205   2074
  Planarity :  0.004   0.061   2452
  Dihedral  :  9.508 162.163   2046
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 22.66 %
    Favored  : 75.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.20), residues: 1705
  helix:  1.85 (0.20), residues: 714
  sheet:  0.50 (0.30), residues: 296
  loop : -1.23 (0.22), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 339 
 TYR   0.025   0.001   TYR K  96 
 PHE   0.013   0.001   PHE B 367 
 TRP   0.012   0.001   TRP E 388 
 HIS   0.003   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (13903)
  covalent geometry    : angle       0.56020 (18876)
  hydrogen bonds       : bond        0.04047 (  647)
  hydrogen bonds       : angle       4.00788 ( 1947)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 255
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K    7 LYS cc_start: 0.8173 (mptt) cc_final: 0.7648 (tmtp)
REVERT: K   19 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7753 (mt-10)
REVERT: K   42 GLN cc_start: 0.5500 (OUTLIER) cc_final: 0.4766 (mp10)
REVERT: K  183 LYS cc_start: 0.8181 (tptt) cc_final: 0.7898 (tptm)
REVERT: K  287 GLU cc_start: 0.7869 (tp30) cc_final: 0.7654 (tp30)
REVERT: K  353 GLN cc_start: 0.7827 (mp10) cc_final: 0.7433 (mp10)
REVERT: K  354 ILE cc_start: 0.8305 (mt) cc_final: 0.7758 (mm)
REVERT: A  187 SER cc_start: 0.8817 (t) cc_final: 0.8574 (p)
REVERT: A  254 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7425 (mt-10)
REVERT: A  332 ILE cc_start: 0.8416 (mm) cc_final: 0.8195 (mt)
REVERT: A  371 VAL cc_start: 0.9109 (p) cc_final: 0.8895 (m)
REVERT: A  437 VAL cc_start: 0.9029 (p) cc_final: 0.8747 (m)
REVERT: B   43 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8532 (mt0)
REVERT: B   57 ASN cc_start: 0.7868 (t0) cc_final: 0.7397 (t0)
REVERT: B  164 MET cc_start: 0.8049 (ttp) cc_final: 0.7834 (ttt)
REVERT: B  179 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8213 (t)
REVERT: B  188 SER cc_start: 0.8479 (t) cc_final: 0.8175 (p)
REVERT: B  193 VAL cc_start: 0.8619 (p) cc_final: 0.8365 (t)
REVERT: B  196 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8598 (m)
REVERT: B  213 ARG cc_start: 0.8518 (mtm180) cc_final: 0.8166 (mtm-85)
REVERT: B  282 ARG cc_start: 0.8561 (ttm110) cc_final: 0.8160 (mtp85)
REVERT: B  291 GLN cc_start: 0.8247 (tt0) cc_final: 0.8000 (tt0)
REVERT: B  316 ILE cc_start: 0.8561 (mm) cc_final: 0.8290 (mt)
REVERT: E   26 LEU cc_start: 0.8656 (mm) cc_final: 0.8395 (tp)
REVERT: E  181 VAL cc_start: 0.8681 (p) cc_final: 0.8380 (t)
REVERT: E  302 MET cc_start: 0.8394 (mmm) cc_final: 0.7922 (mtm)
REVERT: E  392 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7686 (m-30)
REVERT: E  449 GLU cc_start: -0.1556 (OUTLIER) cc_final: -0.1790 (pm20)
  outliers start: 33
  outliers final: 22
  residues processed: 275
  average time/residue: 0.5595
  time to fit residues: 168.0755
Evaluate side-chains
  280 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 251
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   37 ILE
Chi-restraints excluded: chain K residue   42 GLN
Chi-restraints excluded: chain K residue   46 THR
Chi-restraints excluded: chain K residue   51 SER
Chi-restraints excluded: chain K residue   93 ILE
Chi-restraints excluded: chain K residue  133 THR
Chi-restraints excluded: chain K residue  152 GLU
Chi-restraints excluded: chain K residue  192 ILE
Chi-restraints excluded: chain K residue  270 ASN
Chi-restraints excluded: chain K residue  305 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  254 GLU
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain B residue   43 GLN
Chi-restraints excluded: chain B residue  135 LEU
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  280 GLN
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain E residue  132 LEU
Chi-restraints excluded: chain E residue  178 SER
Chi-restraints excluded: chain E residue  191 THR
Chi-restraints excluded: chain E residue  334 THR
Chi-restraints excluded: chain E residue  392 ASP
Chi-restraints excluded: chain E residue  449 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 36 optimal weight:   30.0000
   chunk 125 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 118 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 117 optimal weight:    0.6980
   chunk 121 optimal weight:    0.3980
   chunk 151 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0870
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 195 ASN
B 298 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.134592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.104172 restraints weight = 18871.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.94
r_work: 0.3321 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3188
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3188
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13903  Z= 0.118
  Angle     :  0.555  10.829  18876  Z= 0.281
  Chirality :  0.043   0.207   2074
  Planarity :  0.004   0.061   2452
  Dihedral  :  9.361 161.585   2046
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 23.21 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.21), residues: 1705
  helix:  1.93 (0.20), residues: 714
  sheet:  0.39 (0.29), residues: 302
  loop : -1.13 (0.22), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 339 
 TYR   0.023   0.001   TYR K  96 
 PHE   0.012   0.001   PHE B 367 
 TRP   0.012   0.001   TRP B 344 
 HIS   0.003   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (13903)
  covalent geometry    : angle       0.55468 (18876)
  hydrogen bonds       : bond        0.03955 (  647)
  hydrogen bonds       : angle       3.96214 ( 1947)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6073.90 seconds
wall clock time: 104 minutes 4.71 seconds (6244.71 seconds total)