Starting phenix.real_space_refine
on Wed Aug  5 13:42:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8s82_19790/08_2026/8s82_19790.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8s82_19790/08_2026/8s82_19790.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8s82_19790/08_2026/8s82_19790.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8s82_19790/08_2026/8s82_19790.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8s82_19790/08_2026/8s82_19790.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8s82_19790/08_2026/8s82_19790.cif"
  }
  resolution = 2.92
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.021
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: 5
    Type Number    sf(0)   Gaussians
     P      40      5.49       5
     S      40      5.16       5
     C    6306      2.51       5
     N    1688      2.21       5
     O    2054      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10128
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "K"
      Number of atoms: 4616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 557, 4616
          Classifications: {'peptide': 557}
          Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 534}
    Chain: "L"
      Number of atoms: 4657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4657
          Classifications: {'peptide': 587}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 559}
    Chain: "D"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 441
          Classifications: {'DNA': 21}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 20}
    Chain: "C"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 414
          Classifications: {'DNA': 21}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 20}
  Time building chain proxies: 1.53, per 1000 atoms: 0.15
  Number of scatterers: 10128
  At special positions: 0
  Unit cell: (95.265, 109.719, 141.912, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     P      40     15.00
     O    2054      8.00
     N    1688      7.00
     C    6306      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: 0.72
  Conformation dependent library (CDL) restraints added in 373.8 milliseconds
  

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2202

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 7 sheets defined
      36.4% alpha, 19.9% beta
      19 base pairs and 29 stacking pairs defined.
    Time for finding SS restraints: 1.33
  Creating SS restraints...
    Processing helix  chain 'K' and resid 12 through 17
      removed outlier: 3.608A  pdb=" N   PHE K  16 " --> pdb=" O   SER K  12 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LYS K  17 " --> pdb=" O   GLU K  13 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 12 through 17'
    Processing helix  chain 'K' and resid 26 through 43
    Processing helix  chain 'K' and resid 77 through 93
    Processing helix  chain 'K' and resid 97 through 102
    Processing helix  chain 'K' and resid 114 through 128
      removed outlier: 3.580A  pdb=" N   PHE K 126 " --> pdb=" O   MET K 122 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 150 through 154
      removed outlier: 3.573A  pdb=" N   GLN K 154 " --> pdb=" O   GLN K 151 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 156 through 172
    Processing helix  chain 'K' and resid 190 through 198
      removed outlier: 3.570A  pdb=" N   GLN K 198 " --> pdb=" O   SER K 194 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 225 through 232
      removed outlier: 3.687A  pdb=" N   ARG K 232 " --> pdb=" O   SER K 228 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 267 through 270
      removed outlier: 3.806A  pdb=" N   VAL K 270 " --> pdb=" O   LYS K 267 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 267 through 270'
    Processing helix  chain 'K' and resid 318 through 328
      removed outlier: 3.788A  pdb=" N   ILE K 324 " --> pdb=" O   SER K 320 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ALA K 328 " --> pdb=" O   ILE K 324 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 369 through 384
    Processing helix  chain 'K' and resid 443 through 461
      removed outlier: 4.028A  pdb=" N   TYR K 460 " --> pdb=" O   SER K 456 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   PHE K 461 " --> pdb=" O   ILE K 457 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 468 through 472
    Processing helix  chain 'K' and resid 474 through 490
    Processing helix  chain 'K' and resid 500 through 512
      removed outlier: 3.589A  pdb=" N   LYS K 505 " --> pdb=" O   PRO K 501 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 513 through 529
      removed outlier: 3.748A  pdb=" N   LYS K 517 " --> pdb=" O   ASP K 513 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 537 through 555
      removed outlier: 3.827A  pdb=" N   LYS K 541 " --> pdb=" O   GLN K 537 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   VAL K 543 " --> pdb=" O   LEU K 539 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   PHE K 553 " --> pdb=" O   PHE K 549 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ASP K 555 " --> pdb=" O   LYS K 551 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 12 through 18
      removed outlier: 3.766A  pdb=" N   ASN L  18 " --> pdb=" O   SER L  14 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 19 through 39
      removed outlier: 4.080A  pdb=" N   LYS L  38 " --> pdb=" O   ASN L  34 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 75 through 93
    Processing helix  chain 'L' and resid 104 through 121
      removed outlier: 3.724A  pdb=" N   CYS L 108 " --> pdb=" O   SER L 104 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU L 109 " --> pdb=" O   MET L 105 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LEU L 110 " --> pdb=" O   ILE L 106 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL L 111 " --> pdb=" O   GLN L 107 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   PHE L 120 " --> pdb=" O   ILE L 116 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 142 through 153
      removed outlier: 4.147A  pdb=" N   ASP L 147 " --> pdb=" O   ASP L 143 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU L 148 " --> pdb=" O   GLU L 144 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 174 through 182
    Processing helix  chain 'L' and resid 190 through 199
      removed outlier: 3.585A  pdb=" N   THR L 198 " --> pdb=" O   LEU L 194 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 220 through 225
    Processing helix  chain 'L' and resid 308 through 310
      No H-bonds generated for 'chain 'L' and resid 308 through 310'
    Processing helix  chain 'L' and resid 326 through 334
      removed outlier: 3.806A  pdb=" N   VAL L 334 " --> pdb=" O   VAL L 330 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 353 through 357
      removed outlier: 3.587A  pdb=" N   LEU L 357 " --> pdb=" O   ARG L 354 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 372 through 389
    Processing helix  chain 'L' and resid 467 through 480
    Processing helix  chain 'L' and resid 498 through 501
    Processing helix  chain 'L' and resid 512 through 516
      removed outlier: 3.615A  pdb=" N   GLU L 516 " --> pdb=" O   LYS L 513 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 527 through 545
    Processing helix  chain 'L' and resid 558 through 564
      removed outlier: 3.999A  pdb=" N   LYS L 564 " --> pdb=" O   SER L 560 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 576 through 583
    Processing sheet with id=AA1, first strand: chain 'K' and resid 68 through 75
      removed outlier: 6.373A  pdb=" N   CYS K  53 " --> pdb=" O   LEU K  70 " (cutoff:3.500A)
      removed outlier: 5.265A  pdb=" N   ILE K  51 " --> pdb=" O   PRO K  72 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   ARG K  74 " --> pdb=" O   THR K  49 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   THR K  49 " --> pdb=" O   ARG K  74 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   LYS K 139 " --> pdb=" O   ASN K 175 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   ALA K 177 " --> pdb=" O   LYS K 139 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   VAL K 141 " --> pdb=" O   ALA K 177 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   PHE K 179 " --> pdb=" O   VAL K 141 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   LEU K 143 " --> pdb=" O   PHE K 179 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ILE K 181 " --> pdb=" O   LEU K 143 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   THR K 145 " --> pdb=" O   ILE K 181 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ILE K 221 " --> pdb=" O   THR K 178 " (cutoff:3.500A)
      removed outlier: 5.818A  pdb=" N   PHE K 180 " --> pdb=" O   ILE K 221 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 239 through 248
      removed outlier: 7.718A  pdb=" N   MET K 240 " --> pdb=" O   THR K 261 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   THR K 261 " --> pdb=" O   MET K 240 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   GLN K 242 " --> pdb=" O   GLY K 259 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   GLY K 259 " --> pdb=" O   GLN K 242 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   VAL K 257 " --> pdb=" O   PRO K 244 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   ILE K 246 " --> pdb=" O   VAL K 255 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   VAL K 255 " --> pdb=" O   ILE K 246 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   LYS K 386 " --> pdb=" O   PRO K 407 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   TRP K 391 " --> pdb=" O   ILE K 338 " (cutoff:3.500A)
      removed outlier: 5.478A  pdb=" N   ILE K 338 " --> pdb=" O   TRP K 391 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   LYS K 393 " --> pdb=" O   LEU K 336 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   LEU K 336 " --> pdb=" O   LYS K 393 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   ASP K 248 " --> pdb=" O   ILE K 338 " (cutoff:3.500A)
      removed outlier: 12.377A  pdb=" N   GLY K 340 " --> pdb=" O   ASP K 248 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 302 through 307
      removed outlier: 3.968A  pdb=" N   TYR L 281 " --> pdb=" O   ILE L 307 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   HIS L 284 " --> pdb=" O   GLU K 284 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   GLU K 284 " --> pdb=" O   HIS L 284 " (cutoff:3.500A)
      removed outlier: 10.188A  pdb=" N   GLU L 286 " --> pdb=" O   ARG K 282 " (cutoff:3.500A)
      removed outlier: 13.070A  pdb=" N   ARG K 282 " --> pdb=" O   GLU L 286 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   LEU K 274 " --> pdb=" O   ALA K 285 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'K' and resid 314 through 315
    Processing sheet with id=AA5, first strand: chain 'K' and resid 430 through 431
    Processing sheet with id=AA6, first strand: chain 'L' and resid 64 through 71
      removed outlier: 6.610A  pdb=" N   CYS L  47 " --> pdb=" O   ILE L  67 " (cutoff:3.500A)
      removed outlier: 5.364A  pdb=" N   SER L  69 " --> pdb=" O   ILE L  45 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   ILE L  45 " --> pdb=" O   SER L  69 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   LEU L  71 " --> pdb=" O   ASP L  43 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   ASP L  43 " --> pdb=" O   LEU L  71 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   GLU L   3 " --> pdb=" O   TRP L  44 " (cutoff:3.500A)
      removed outlier: 8.848A  pdb=" N   SER L  46 " --> pdb=" O   GLU L   3 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   THR L   5 " --> pdb=" O   SER L  46 " (cutoff:3.500A)
      removed outlier: 8.280A  pdb=" N   TYR L  48 " --> pdb=" O   THR L   5 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   PHE L   7 " --> pdb=" O   TYR L  48 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   ALA L  50 " --> pdb=" O   PHE L   7 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL L   9 " --> pdb=" O   ALA L  50 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   SER L   4 " --> pdb=" O   GLN L 128 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   VAL L 130 " --> pdb=" O   SER L   4 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   THR L   6 " --> pdb=" O   VAL L 130 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   PHE L 132 " --> pdb=" O   THR L   6 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   ILE L   8 " --> pdb=" O   PHE L 132 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   ILE L 129 " --> pdb=" O   ILE L 158 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   ILE L 160 " --> pdb=" O   ILE L 129 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   VAL L 131 " --> pdb=" O   ILE L 160 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 211 through 217
      removed outlier: 3.537A  pdb=" N   PHE L 211 " --> pdb=" O   ALA L 245 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   ALA L 366 " --> pdb=" O   LYS L 428 " (cutoff:3.500A)
      removed outlier: 9.526A  pdb=" N   LYS L 428 " --> pdb=" O   ALA L 366 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   MET L 407 " --> pdb=" O   LEU L 435 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   LYS L 391 " --> pdb=" O   PRO L 412 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   ILE L 392 " --> pdb=" O   PHE L 346 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   PHE L 346 " --> pdb=" O   ILE L 392 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL L 394 " --> pdb=" O   ARG L 344 " (cutoff:3.500A)
      removed outlier: 8.250A  pdb=" N   LEU L 341 " --> pdb=" O   SER L 212 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   GLU L 214 " --> pdb=" O   LEU L 341 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   LEU L 343 " --> pdb=" O   GLU L 214 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   ARG L 216 " --> pdb=" O   LEU L 343 " (cutoff:3.500A)
      removed outlier: 8.344A  pdb=" N   GLY L 345 " --> pdb=" O   ARG L 216 " (cutoff:3.500A)

    365 hydrogen bonds defined for protein.
    1032 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      50 hydrogen bonds
      100 hydrogen bond angles
      0 basepair planarities
      19 basepair parallelities
      29 stacking parallelities
  Total time for adding SS restraints: 1.31

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3056
        1.34 -     1.46: 1779
        1.46 -     1.57: 5428
        1.57 -     1.69: 80
        1.69 -     1.81: 65
  Bond restraints: 10408
  Sorted by residual:
  bond pdb=" C3'  DG D   6 "
       pdb=" C2'  DG D   6 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.13e+01
  bond pdb=" C3'  DT D   9 "
       pdb=" C2'  DT D   9 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.96e+00
  bond pdb=" C3'  DC C  11 "
       pdb=" C2'  DC C  11 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.30e+00
  bond pdb=" C3'  DT D   7 "
       pdb=" C2'  DT D   7 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.42e+00
  bond pdb=" C3'  DC C   6 "
       pdb=" C2'  DC C   6 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.32e+00
  ... (remaining 10403 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 13825
        1.72 -     3.45: 380
        3.45 -     5.17: 23
        5.17 -     6.90: 4
        6.90 -     8.62: 3
  Bond angle restraints: 14235
  Sorted by residual:
  angle pdb=" C   LYS K 288 "
        pdb=" N   ARG K 289 "
        pdb=" CA  ARG K 289 "
      ideal   model   delta    sigma   weight residual
     121.70  130.32   -8.62 1.80e+00 3.09e-01 2.29e+01
  angle pdb=" C   VAL L 208 "
        pdb=" N   ARG L 209 "
        pdb=" CA  ARG L 209 "
      ideal   model   delta    sigma   weight residual
     121.54  129.76   -8.22 1.91e+00 2.74e-01 1.85e+01
  angle pdb=" N3   DT D   9 "
        pdb=" C4   DT D   9 "
        pdb=" O4   DT D   9 "
      ideal   model   delta    sigma   weight residual
     119.90  122.36   -2.46 6.00e-01 2.78e+00 1.68e+01
  angle pdb=" N3   DT D  21 "
        pdb=" C4   DT D  21 "
        pdb=" O4   DT D  21 "
      ideal   model   delta    sigma   weight residual
     119.90  122.36   -2.46 6.00e-01 2.78e+00 1.68e+01
  angle pdb=" N3   DT D   7 "
        pdb=" C4   DT D   7 "
        pdb=" O4   DT D   7 "
      ideal   model   delta    sigma   weight residual
     119.90  122.33   -2.43 6.00e-01 2.78e+00 1.64e+01
  ... (remaining 14230 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 5592
       17.88 -    35.75: 449
       35.75 -    53.63: 176
       53.63 -    71.51: 51
       71.51 -    89.39: 4
  Dihedral angle restraints: 6272
    sinusoidal: 2876
      harmonic: 3396
  Sorted by residual:
  dihedral pdb=" N   ARG K 289 "
           pdb=" C   ARG K 289 "
           pdb=" CA  ARG K 289 "
           pdb=" CB  ARG K 289 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  137.48  -14.68     0      2.50e+00 1.60e-01 3.45e+01
  dihedral pdb=" C   ARG K 289 "
           pdb=" N   ARG K 289 "
           pdb=" CA  ARG K 289 "
           pdb=" CB  ARG K 289 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.22   13.62     0      2.50e+00 1.60e-01 2.97e+01
  dihedral pdb=" CA  TYR K 286 "
           pdb=" C   TYR K 286 "
           pdb=" N   SER K 287 "
           pdb=" CA  SER K 287 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.36  -19.64     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 6269 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.114: 1580
       0.114 -    0.229: 17
       0.229 -    0.343: 0
       0.343 -    0.457: 0
       0.457 -    0.571: 1
  Chirality restraints: 1598
  Sorted by residual:
  chirality pdb=" CA  ARG K 289 "
            pdb=" N   ARG K 289 "
            pdb=" C   ARG K 289 "
            pdb=" CB  ARG K 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.94    0.57 2.00e-01 2.50e+01 8.16e+00
  chirality pdb=" CA  ILE L 364 "
            pdb=" N   ILE L 364 "
            pdb=" C   ILE L 364 "
            pdb=" CB  ILE L 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.27e-01
  chirality pdb=" CA  ILE K  96 "
            pdb=" N   ILE K  96 "
            pdb=" C   ILE K  96 "
            pdb=" CB  ILE K  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.86e-01
  ... (remaining 1595 not shown)

  Planarity restraints: 1681
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE L 246 "   -0.024 5.00e-02 4.00e+02   3.62e-02 2.09e+00
        pdb=" N   PRO L 247 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO L 247 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO L 247 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS K 243 "   -0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO K 244 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO K 244 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO K 244 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN L 228 "    0.020 5.00e-02 4.00e+02   3.05e-02 1.49e+00
        pdb=" N   PRO L 229 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO L 229 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO L 229 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1678 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 136
        2.64 -     3.20: 8896
        3.20 -     3.77: 15442
        3.77 -     4.33: 21603
        4.33 -     4.90: 34919
  Nonbonded interactions: 80996
  Sorted by model distance:
  nonbonded pdb=" OH  TYR K 467 "
            pdb=" O   PRO L 436 "
     model   vdw
     2.070 3.040
  nonbonded pdb=" O   THR L 358 "
            pdb=" OG1 THR L 358 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" O   VAL L 179 "
            pdb=" OG  SER L 185 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" O   TYR K 367 "
            pdb=" OG  SER K 370 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OE2 GLU L   3 "
            pdb=" OG1 THR L 505 "
     model   vdw
     2.229 3.040
  ... (remaining 80991 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             12.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.500
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10408  Z= 0.272
  Angle     :  0.663   8.620  14235  Z= 0.454
  Chirality :  0.044   0.571   1598
  Planarity :  0.004   0.036   1681
  Dihedral  : 15.567  89.386   4070
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.95 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  :  9.59 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.23), residues: 1140
  helix:  1.07 (0.27), residues: 363
  sheet:  0.14 (0.39), residues: 161
  loop : -1.41 (0.22), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 354 
 TYR   0.013   0.001   TYR K 550 
 PHE   0.015   0.001   PHE K  71 
 TRP   0.007   0.002   TRP K 391 
 HIS   0.003   0.001   HIS L 417 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00400 /  0.27 (10408)
  covalent geometry    : angle       0.66280 /  0.45 (14235)
  hydrogen bonds       : bond        0.14974 /  9.77 (  415)
  hydrogen bonds       : angle       6.04587 /  4.41 ( 1132)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 172
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: K   18 GLU cc_start: 0.8251 (mp0) cc_final: 0.7496 (tm-30)
REVERT: K   46 ARG cc_start: 0.7578 (tpp-160) cc_final: 0.7154 (mmm-85)
REVERT: K  114 ARG cc_start: 0.7877 (mtm110) cc_final: 0.7547 (mmp80)
REVERT: K  152 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6949 (mp0)
REVERT: K  154 GLN cc_start: 0.5888 (mm110) cc_final: 0.5673 (mm110)
REVERT: K  218 THR cc_start: 0.8621 (p) cc_final: 0.8329 (m)
REVERT: K  219 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7637 (tptt)
REVERT: K  238 ARG cc_start: 0.7648 (ttp80) cc_final: 0.7336 (ttm-80)
REVERT: K  289 ARG cc_start: 0.4528 (OUTLIER) cc_final: 0.1126 (mmm-85)
REVERT: K  356 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7727 (mtmt)
REVERT: K  446 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6908 (t0)
REVERT: K  513 ASP cc_start: 0.7837 (t0) cc_final: 0.7144 (m-30)
REVERT: L   23 LYS cc_start: 0.8067 (mttt) cc_final: 0.7837 (mtmt)
REVERT: L   88 GLN cc_start: 0.8627 (tt0) cc_final: 0.8417 (tt0)
REVERT: L  164 LYS cc_start: 0.5800 (OUTLIER) cc_final: 0.5240 (mptm)
REVERT: L  184 ASN cc_start: 0.7164 (m-40) cc_final: 0.6263 (t0)
REVERT: L  243 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7858 (t)
REVERT: L  303 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.6288 (pp)
REVERT: L  344 ARG cc_start: 0.5984 (mtm110) cc_final: 0.5678 (mtp85)
REVERT: L  401 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6479 (ttpt)
REVERT: L  445 ASP cc_start: 0.7642 (m-30) cc_final: 0.7421 (m-30)
  outliers start: 69
  outliers final: 28
  residues processed: 229
  average time/residue: 0.4347
  time to fit residues: 107.3083
Evaluate side-chains
  150 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 113
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   38 LEU
Chi-restraints excluded: chain K residue   43 VAL
Chi-restraints excluded: chain K residue   79 THR
Chi-restraints excluded: chain K residue  130 ILE
Chi-restraints excluded: chain K residue  134 LYS
Chi-restraints excluded: chain K residue  152 GLU
Chi-restraints excluded: chain K residue  204 ASN
Chi-restraints excluded: chain K residue  219 LYS
Chi-restraints excluded: chain K residue  254 ILE
Chi-restraints excluded: chain K residue  257 VAL
Chi-restraints excluded: chain K residue  289 ARG
Chi-restraints excluded: chain K residue  356 LYS
Chi-restraints excluded: chain K residue  446 ASP
Chi-restraints excluded: chain K residue  454 THR
Chi-restraints excluded: chain K residue  506 ASP
Chi-restraints excluded: chain K residue  544 LYS
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue    9 VAL
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain L residue  111 VAL
Chi-restraints excluded: chain L residue  164 LYS
Chi-restraints excluded: chain L residue  243 VAL
Chi-restraints excluded: chain L residue  283 ILE
Chi-restraints excluded: chain L residue  292 VAL
Chi-restraints excluded: chain L residue  303 ILE
Chi-restraints excluded: chain L residue  328 VAL
Chi-restraints excluded: chain L residue  333 THR
Chi-restraints excluded: chain L residue  354 ARG
Chi-restraints excluded: chain L residue  358 THR
Chi-restraints excluded: chain L residue  401 LYS
Chi-restraints excluded: chain L residue  467 HIS
Chi-restraints excluded: chain L residue  482 THR
Chi-restraints excluded: chain L residue  487 GLU
Chi-restraints excluded: chain L residue  497 ILE
Chi-restraints excluded: chain L residue  500 VAL
Chi-restraints excluded: chain L residue  546 ILE
Chi-restraints excluded: chain L residue  578 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.3980
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K 133 GLN
K 204 ASN
K 316 ASN
K 455 GLN
** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 547 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.234625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.189214 restraints weight = 10753.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.4213 rms_B_bonded: 2.45
r_work: 0.3919 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10408  Z= 0.191
  Angle     :  0.626  10.898  14235  Z= 0.343
  Chirality :  0.043   0.176   1598
  Planarity :  0.005   0.047   1681
  Dihedral  : 17.435  83.800   1767
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.68 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  6.77 %
    Allowed  : 16.82 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.23), residues: 1140
  helix:  1.30 (0.27), residues: 367
  sheet:  0.19 (0.40), residues: 148
  loop : -1.37 (0.22), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L 186 
 TYR   0.017   0.002   TYR K 403 
 PHE   0.016   0.002   PHE L 476 
 TRP   0.007   0.002   TRP L  44 
 HIS   0.009   0.001   HIS L 284 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00428 /  0.19 (10408)
  covalent geometry    : angle       0.62598 /  0.34 (14235)
  hydrogen bonds       : bond        0.05104 /  3.48 (  415)
  hydrogen bonds       : angle       4.97775 /  3.56 ( 1132)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 111
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: K   18 GLU cc_start: 0.8220 (mp0) cc_final: 0.7469 (tm-30)
REVERT: K   46 ARG cc_start: 0.7791 (tpp-160) cc_final: 0.7187 (mmm-85)
REVERT: K   82 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.6526 (ttmm)
REVERT: K  114 ARG cc_start: 0.7984 (mtm110) cc_final: 0.7578 (mmp80)
REVERT: K  152 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7080 (mp0)
REVERT: K  155 ASP cc_start: 0.6805 (t70) cc_final: 0.6501 (t0)
REVERT: K  218 THR cc_start: 0.8618 (p) cc_final: 0.8309 (m)
REVERT: K  219 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7656 (mptt)
REVERT: K  238 ARG cc_start: 0.7707 (ttp80) cc_final: 0.7209 (ttp-110)
REVERT: K  289 ARG cc_start: 0.3576 (OUTLIER) cc_final: 0.1121 (mmm-85)
REVERT: K  291 PHE cc_start: 0.4670 (OUTLIER) cc_final: 0.3879 (p90)
REVERT: K  312 ASP cc_start: 0.7331 (p0) cc_final: 0.7088 (p0)
REVERT: K  356 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7656 (mtmt)
REVERT: K  446 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6874 (t0)
REVERT: K  513 ASP cc_start: 0.7818 (t0) cc_final: 0.7043 (m-30)
REVERT: K  548 MET cc_start: 0.6183 (mmm) cc_final: 0.5845 (mpt)
REVERT: L   23 LYS cc_start: 0.7982 (mttt) cc_final: 0.7639 (mtmm)
REVERT: L   88 GLN cc_start: 0.8608 (tt0) cc_final: 0.8392 (tt0)
REVERT: L  164 LYS cc_start: 0.5847 (OUTLIER) cc_final: 0.5206 (mptt)
REVERT: L  184 ASN cc_start: 0.6861 (m-40) cc_final: 0.5984 (t0)
REVERT: L  195 VAL cc_start: 0.8214 (p) cc_final: 0.7946 (m)
REVERT: L  243 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7846 (t)
REVERT: L  302 TYR cc_start: 0.6143 (OUTLIER) cc_final: 0.5047 (p90)
REVERT: L  303 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.6230 (pp)
REVERT: L  401 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6423 (ttpt)
REVERT: L  521 ASP cc_start: 0.6512 (OUTLIER) cc_final: 0.6018 (t0)
  outliers start: 72
  outliers final: 34
  residues processed: 169
  average time/residue: 0.4501
  time to fit residues: 82.1379
Evaluate side-chains
  153 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 106
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   13 GLU
Chi-restraints excluded: chain K residue   14 THR
Chi-restraints excluded: chain K residue   79 THR
Chi-restraints excluded: chain K residue   82 LYS
Chi-restraints excluded: chain K residue   91 LEU
Chi-restraints excluded: chain K residue  100 ASP
Chi-restraints excluded: chain K residue  130 ILE
Chi-restraints excluded: chain K residue  134 LYS
Chi-restraints excluded: chain K residue  152 GLU
Chi-restraints excluded: chain K residue  204 ASN
Chi-restraints excluded: chain K residue  219 LYS
Chi-restraints excluded: chain K residue  252 ASN
Chi-restraints excluded: chain K residue  254 ILE
Chi-restraints excluded: chain K residue  257 VAL
Chi-restraints excluded: chain K residue  289 ARG
Chi-restraints excluded: chain K residue  291 PHE
Chi-restraints excluded: chain K residue  356 LYS
Chi-restraints excluded: chain K residue  446 ASP
Chi-restraints excluded: chain K residue  506 ASP
Chi-restraints excluded: chain K residue  544 LYS
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue    9 VAL
Chi-restraints excluded: chain L residue   64 VAL
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain L residue  111 VAL
Chi-restraints excluded: chain L residue  164 LYS
Chi-restraints excluded: chain L residue  222 LEU
Chi-restraints excluded: chain L residue  243 VAL
Chi-restraints excluded: chain L residue  283 ILE
Chi-restraints excluded: chain L residue  292 VAL
Chi-restraints excluded: chain L residue  302 TYR
Chi-restraints excluded: chain L residue  303 ILE
Chi-restraints excluded: chain L residue  323 VAL
Chi-restraints excluded: chain L residue  328 VAL
Chi-restraints excluded: chain L residue  333 THR
Chi-restraints excluded: chain L residue  354 ARG
Chi-restraints excluded: chain L residue  358 THR
Chi-restraints excluded: chain L residue  401 LYS
Chi-restraints excluded: chain L residue  413 VAL
Chi-restraints excluded: chain L residue  467 HIS
Chi-restraints excluded: chain L residue  487 GLU
Chi-restraints excluded: chain L residue  497 ILE
Chi-restraints excluded: chain L residue  500 VAL
Chi-restraints excluded: chain L residue  503 ASP
Chi-restraints excluded: chain L residue  521 ASP
Chi-restraints excluded: chain L residue  546 ILE
Chi-restraints excluded: chain L residue  578 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 91 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9990
   chunk 99 optimal weight:    0.3980
   chunk 38 optimal weight:    0.5980
   chunk 83 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K  77 ASN
K 455 GLN
** L  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 535 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 = 0.4707 r_free = 0.4707 target = 0.241012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.196848 restraints weight = 10614.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.4351 rms_B_bonded: 2.19
r_work: 0.4018 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10408  Z= 0.147
  Angle     :  0.577  10.356  14235  Z= 0.318
  Chirality :  0.042   0.162   1598
  Planarity :  0.004   0.049   1681
  Dihedral  : 17.556  83.690   1762
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.86 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 16.35 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.24), residues: 1140
  helix:  1.40 (0.27), residues: 366
  sheet: -0.10 (0.39), residues: 158
  loop : -1.26 (0.23), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 186 
 TYR   0.012   0.002   TYR K 403 
 PHE   0.016   0.001   PHE L 476 
 TRP   0.006   0.001   TRP L  44 
 HIS   0.003   0.001   HIS L 417 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.15 (10408)
  covalent geometry    : angle       0.57705 /  0.32 (14235)
  hydrogen bonds       : bond        0.04416 /  3.00 (  415)
  hydrogen bonds       : angle       4.73199 /  3.37 ( 1132)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 109
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: K   18 GLU cc_start: 0.8315 (mp0) cc_final: 0.7588 (tm-30)
REVERT: K   46 ARG cc_start: 0.7809 (tpp-160) cc_final: 0.7322 (mmm-85)
REVERT: K   82 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.6518 (ttmm)
REVERT: K  114 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7567 (mmp80)
REVERT: K  155 ASP cc_start: 0.6819 (t70) cc_final: 0.6533 (t0)
REVERT: K  218 THR cc_start: 0.8677 (p) cc_final: 0.8394 (m)
REVERT: K  219 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7708 (mptt)
REVERT: K  238 ARG cc_start: 0.7754 (ttp80) cc_final: 0.7526 (ttt-90)
REVERT: K  289 ARG cc_start: 0.3741 (OUTLIER) cc_final: 0.0957 (mmm-85)
REVERT: K  312 ASP cc_start: 0.7345 (p0) cc_final: 0.7108 (p0)
REVERT: K  323 GLN cc_start: 0.7801 (mm110) cc_final: 0.7175 (mm110)
REVERT: K  356 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7683 (mtmt)
REVERT: K  513 ASP cc_start: 0.7690 (t0) cc_final: 0.7062 (m-30)
REVERT: L   10 ASP cc_start: 0.6825 (OUTLIER) cc_final: 0.6597 (m-30)
REVERT: L   23 LYS cc_start: 0.7965 (mttt) cc_final: 0.7669 (mtmm)
REVERT: L   87 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7813 (mtpp)
REVERT: L   88 GLN cc_start: 0.8600 (tt0) cc_final: 0.8386 (tt0)
REVERT: L  156 ARG cc_start: 0.7449 (ptm160) cc_final: 0.6428 (ptp-170)
REVERT: L  164 LYS cc_start: 0.5842 (OUTLIER) cc_final: 0.5201 (mptt)
REVERT: L  184 ASN cc_start: 0.6870 (m-40) cc_final: 0.5839 (t0)
REVERT: L  195 VAL cc_start: 0.8352 (p) cc_final: 0.8097 (m)
REVERT: L  243 VAL cc_start: 0.7985 (OUTLIER) cc_final: 0.7733 (t)
REVERT: L  302 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.4941 (p90)
REVERT: L  303 ILE cc_start: 0.6574 (OUTLIER) cc_final: 0.6295 (pp)
REVERT: L  401 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6528 (ttpt)
REVERT: L  445 ASP cc_start: 0.7907 (m-30) cc_final: 0.7659 (m-30)
REVERT: L  521 ASP cc_start: 0.6342 (OUTLIER) cc_final: 0.5883 (t0)
  outliers start: 76
  outliers final: 33
  residues processed: 175
  average time/residue: 0.4334
  time to fit residues: 82.4240
Evaluate side-chains
  143 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 98
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   13 GLU
Chi-restraints excluded: chain K residue   14 THR
Chi-restraints excluded: chain K residue   79 THR
Chi-restraints excluded: chain K residue   82 LYS
Chi-restraints excluded: chain K residue   91 LEU
Chi-restraints excluded: chain K residue  100 ASP
Chi-restraints excluded: chain K residue  130 ILE
Chi-restraints excluded: chain K residue  134 LYS
Chi-restraints excluded: chain K residue  204 ASN
Chi-restraints excluded: chain K residue  219 LYS
Chi-restraints excluded: chain K residue  254 ILE
Chi-restraints excluded: chain K residue  257 VAL
Chi-restraints excluded: chain K residue  275 VAL
Chi-restraints excluded: chain K residue  289 ARG
Chi-restraints excluded: chain K residue  356 LYS
Chi-restraints excluded: chain K residue  506 ASP
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue    9 VAL
Chi-restraints excluded: chain L residue   10 ASP
Chi-restraints excluded: chain L residue   46 SER
Chi-restraints excluded: chain L residue   64 VAL
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain L residue   87 LYS
Chi-restraints excluded: chain L residue  111 VAL
Chi-restraints excluded: chain L residue  164 LYS
Chi-restraints excluded: chain L residue  243 VAL
Chi-restraints excluded: chain L residue  292 VAL
Chi-restraints excluded: chain L residue  302 TYR
Chi-restraints excluded: chain L residue  303 ILE
Chi-restraints excluded: chain L residue  323 VAL
Chi-restraints excluded: chain L residue  328 VAL
Chi-restraints excluded: chain L residue  333 THR
Chi-restraints excluded: chain L residue  341 LEU
Chi-restraints excluded: chain L residue  354 ARG
Chi-restraints excluded: chain L residue  401 LYS
Chi-restraints excluded: chain L residue  413 VAL
Chi-restraints excluded: chain L residue  467 HIS
Chi-restraints excluded: chain L residue  487 GLU
Chi-restraints excluded: chain L residue  497 ILE
Chi-restraints excluded: chain L residue  500 VAL
Chi-restraints excluded: chain L residue  503 ASP
Chi-restraints excluded: chain L residue  521 ASP
Chi-restraints excluded: chain L residue  546 ILE
Chi-restraints excluded: chain L residue  578 LEU
Chi-restraints excluded: chain L residue  579 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 104 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9980
   chunk 109 optimal weight:    0.1980
   chunk 112 optimal weight:    4.9990
   chunk 68 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** L  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.237843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.194444 restraints weight = 10595.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.4326 rms_B_bonded: 2.11
r_work: 0.4004 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10408  Z= 0.157
  Angle     :  0.581  10.371  14235  Z= 0.316
  Chirality :  0.042   0.164   1598
  Planarity :  0.004   0.052   1681
  Dihedral  : 17.542  83.739   1750
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.60 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  7.05 %
    Allowed  : 17.20 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.24), residues: 1140
  helix:  1.39 (0.27), residues: 366
  sheet: -0.14 (0.38), residues: 159
  loop : -1.25 (0.23), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 186 
 TYR   0.020   0.002   TYR L 531 
 PHE   0.017   0.001   PHE L 476 
 TRP   0.007   0.001   TRP L  44 
 HIS   0.003   0.001   HIS L 417 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.16 (10408)
  covalent geometry    : angle       0.58110 /  0.32 (14235)
  hydrogen bonds       : bond        0.04308 /  2.94 (  415)
  hydrogen bonds       : angle       4.67223 /  3.33 ( 1132)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 100
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: K   46 ARG cc_start: 0.7776 (tpp-160) cc_final: 0.7332 (mmm-85)
REVERT: K   82 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.6533 (ttmm)
REVERT: K  114 ARG cc_start: 0.7746 (mtm110) cc_final: 0.7535 (mmp80)
REVERT: K  155 ASP cc_start: 0.6806 (t70) cc_final: 0.6522 (t0)
REVERT: K  218 THR cc_start: 0.8698 (p) cc_final: 0.8433 (m)
REVERT: K  219 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7727 (mptt)
REVERT: K  289 ARG cc_start: 0.3866 (OUTLIER) cc_final: 0.1038 (mmm-85)
REVERT: K  291 PHE cc_start: 0.4865 (OUTLIER) cc_final: 0.4092 (p90)
REVERT: K  323 GLN cc_start: 0.7800 (mm110) cc_final: 0.7183 (mm110)
REVERT: K  356 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7659 (mtmt)
REVERT: K  513 ASP cc_start: 0.7698 (t0) cc_final: 0.7056 (m-30)
REVERT: K  536 ILE cc_start: 0.8007 (mt) cc_final: 0.7764 (mm)
REVERT: L   87 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7849 (mtpp)
REVERT: L   88 GLN cc_start: 0.8601 (tt0) cc_final: 0.8365 (tt0)
REVERT: L  156 ARG cc_start: 0.7394 (ptm160) cc_final: 0.6403 (ptp-170)
REVERT: L  164 LYS cc_start: 0.5851 (OUTLIER) cc_final: 0.5222 (mptt)
REVERT: L  184 ASN cc_start: 0.6910 (m-40) cc_final: 0.5807 (t0)
REVERT: L  195 VAL cc_start: 0.8333 (p) cc_final: 0.8100 (m)
REVERT: L  243 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7768 (t)
REVERT: L  303 ILE cc_start: 0.6534 (OUTLIER) cc_final: 0.6226 (pp)
REVERT: L  401 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6535 (ttpt)
REVERT: L  469 ILE cc_start: 0.3261 (OUTLIER) cc_final: 0.2790 (tp)
REVERT: L  521 ASP cc_start: 0.6351 (OUTLIER) cc_final: 0.5885 (t0)
  outliers start: 75
  outliers final: 35
  residues processed: 159
  average time/residue: 0.4138
  time to fit residues: 71.6294
Evaluate side-chains
  147 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 100
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   14 THR
Chi-restraints excluded: chain K residue   79 THR
Chi-restraints excluded: chain K residue   82 LYS
Chi-restraints excluded: chain K residue   91 LEU
Chi-restraints excluded: chain K residue  100 ASP
Chi-restraints excluded: chain K residue  130 ILE
Chi-restraints excluded: chain K residue  134 LYS
Chi-restraints excluded: chain K residue  219 LYS
Chi-restraints excluded: chain K residue  254 ILE
Chi-restraints excluded: chain K residue  257 VAL
Chi-restraints excluded: chain K residue  275 VAL
Chi-restraints excluded: chain K residue  289 ARG
Chi-restraints excluded: chain K residue  291 PHE
Chi-restraints excluded: chain K residue  344 SER
Chi-restraints excluded: chain K residue  356 LYS
Chi-restraints excluded: chain K residue  506 ASP
Chi-restraints excluded: chain K residue  544 LYS
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue    9 VAL
Chi-restraints excluded: chain L residue   46 SER
Chi-restraints excluded: chain L residue   64 VAL
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain L residue   87 LYS
Chi-restraints excluded: chain L residue  111 VAL
Chi-restraints excluded: chain L residue  164 LYS
Chi-restraints excluded: chain L residue  222 LEU
Chi-restraints excluded: chain L residue  243 VAL
Chi-restraints excluded: chain L residue  283 ILE
Chi-restraints excluded: chain L residue  292 VAL
Chi-restraints excluded: chain L residue  303 ILE
Chi-restraints excluded: chain L residue  323 VAL
Chi-restraints excluded: chain L residue  328 VAL
Chi-restraints excluded: chain L residue  333 THR
Chi-restraints excluded: chain L residue  341 LEU
Chi-restraints excluded: chain L residue  354 ARG
Chi-restraints excluded: chain L residue  401 LYS
Chi-restraints excluded: chain L residue  413 VAL
Chi-restraints excluded: chain L residue  467 HIS
Chi-restraints excluded: chain L residue  469 ILE
Chi-restraints excluded: chain L residue  487 GLU
Chi-restraints excluded: chain L residue  497 ILE
Chi-restraints excluded: chain L residue  500 VAL
Chi-restraints excluded: chain L residue  503 ASP
Chi-restraints excluded: chain L residue  521 ASP
Chi-restraints excluded: chain L residue  546 ILE
Chi-restraints excluded: chain L residue  578 LEU
Chi-restraints excluded: chain L residue  579 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 78 optimal weight:    0.2980
   chunk 41 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K  77 ASN
** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4715 r_free = 0.4715 target = 0.241792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.193268 restraints weight = 10801.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.4312 rms_B_bonded: 2.72
r_work: 0.3997 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10408  Z= 0.194
  Angle     :  0.605  10.451  14235  Z= 0.327
  Chirality :  0.043   0.166   1598
  Planarity :  0.004   0.055   1681
  Dihedral  : 17.606  83.378   1748
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.56 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  7.42 %
    Allowed  : 17.76 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.41 (0.24), residues: 1140
  helix:  1.30 (0.27), residues: 366
  sheet: -0.18 (0.40), residues: 154
  loop : -1.30 (0.23), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 186 
 TYR   0.018   0.002   TYR L 531 
 PHE   0.020   0.002   PHE L 476 
 TRP   0.009   0.002   TRP L  44 
 HIS   0.004   0.001   HIS L 417 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00449 /  0.19 (10408)
  covalent geometry    : angle       0.60467 /  0.33 (14235)
  hydrogen bonds       : bond        0.04534 /  3.10 (  415)
  hydrogen bonds       : angle       4.74331 /  3.37 ( 1132)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 99
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: K   18 GLU cc_start: 0.8340 (mp0) cc_final: 0.7618 (tm-30)
REVERT: K   46 ARG cc_start: 0.7786 (tpp-160) cc_final: 0.7330 (mmm-85)
REVERT: K   82 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.6650 (ttmm)
REVERT: K  155 ASP cc_start: 0.6820 (t70) cc_final: 0.6495 (t0)
REVERT: K  218 THR cc_start: 0.8720 (p) cc_final: 0.8457 (m)
REVERT: K  219 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7732 (mptt)
REVERT: K  289 ARG cc_start: 0.3924 (OUTLIER) cc_final: 0.1188 (mmm-85)
REVERT: K  291 PHE cc_start: 0.4863 (OUTLIER) cc_final: 0.4107 (p90)
REVERT: K  446 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6872 (t0)
REVERT: K  513 ASP cc_start: 0.7735 (t0) cc_final: 0.7211 (m-30)
REVERT: K  536 ILE cc_start: 0.8130 (mt) cc_final: 0.7882 (mm)
REVERT: L   87 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7848 (mtpp)
REVERT: L   88 GLN cc_start: 0.8606 (tt0) cc_final: 0.8388 (tt0)
REVERT: L  105 MET cc_start: 0.6560 (tmt) cc_final: 0.5670 (tmm)
REVERT: L  156 ARG cc_start: 0.7408 (ptm160) cc_final: 0.6489 (ptp-170)
REVERT: L  164 LYS cc_start: 0.5904 (OUTLIER) cc_final: 0.5254 (mptt)
REVERT: L  184 ASN cc_start: 0.6918 (m-40) cc_final: 0.6197 (t160)
REVERT: L  195 VAL cc_start: 0.8421 (p) cc_final: 0.8204 (m)
REVERT: L  243 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7877 (t)
REVERT: L  262 GLU cc_start: 0.7428 (pm20) cc_final: 0.6547 (mt-10)
REVERT: L  303 ILE cc_start: 0.6604 (OUTLIER) cc_final: 0.6280 (pp)
REVERT: L  401 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6704 (ttpt)
REVERT: L  469 ILE cc_start: 0.3284 (OUTLIER) cc_final: 0.2821 (tp)
REVERT: L  474 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6054 (tm-30)
REVERT: L  521 ASP cc_start: 0.6526 (OUTLIER) cc_final: 0.5994 (t0)
  outliers start: 79
  outliers final: 41
  residues processed: 162
  average time/residue: 0.4017
  time to fit residues: 71.2730
Evaluate side-chains
  151 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 97
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   14 THR
Chi-restraints excluded: chain K residue   43 VAL
Chi-restraints excluded: chain K residue   61 GLU
Chi-restraints excluded: chain K residue   79 THR
Chi-restraints excluded: chain K residue   82 LYS
Chi-restraints excluded: chain K residue   91 LEU
Chi-restraints excluded: chain K residue  100 ASP
Chi-restraints excluded: chain K residue  130 ILE
Chi-restraints excluded: chain K residue  134 LYS
Chi-restraints excluded: chain K residue  219 LYS
Chi-restraints excluded: chain K residue  254 ILE
Chi-restraints excluded: chain K residue  257 VAL
Chi-restraints excluded: chain K residue  275 VAL
Chi-restraints excluded: chain K residue  289 ARG
Chi-restraints excluded: chain K residue  291 PHE
Chi-restraints excluded: chain K residue  344 SER
Chi-restraints excluded: chain K residue  404 THR
Chi-restraints excluded: chain K residue  446 ASP
Chi-restraints excluded: chain K residue  506 ASP
Chi-restraints excluded: chain K residue  544 LYS
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue    9 VAL
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   46 SER
Chi-restraints excluded: chain L residue   64 VAL
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain L residue   87 LYS
Chi-restraints excluded: chain L residue  102 LEU
Chi-restraints excluded: chain L residue  111 VAL
Chi-restraints excluded: chain L residue  162 CYS
Chi-restraints excluded: chain L residue  164 LYS
Chi-restraints excluded: chain L residue  222 LEU
Chi-restraints excluded: chain L residue  243 VAL
Chi-restraints excluded: chain L residue  283 ILE
Chi-restraints excluded: chain L residue  292 VAL
Chi-restraints excluded: chain L residue  303 ILE
Chi-restraints excluded: chain L residue  323 VAL
Chi-restraints excluded: chain L residue  328 VAL
Chi-restraints excluded: chain L residue  333 THR
Chi-restraints excluded: chain L residue  341 LEU
Chi-restraints excluded: chain L residue  354 ARG
Chi-restraints excluded: chain L residue  401 LYS
Chi-restraints excluded: chain L residue  413 VAL
Chi-restraints excluded: chain L residue  467 HIS
Chi-restraints excluded: chain L residue  469 ILE
Chi-restraints excluded: chain L residue  474 GLU
Chi-restraints excluded: chain L residue  487 GLU
Chi-restraints excluded: chain L residue  497 ILE
Chi-restraints excluded: chain L residue  500 VAL
Chi-restraints excluded: chain L residue  503 ASP
Chi-restraints excluded: chain L residue  521 ASP
Chi-restraints excluded: chain L residue  546 ILE
Chi-restraints excluded: chain L residue  578 LEU
Chi-restraints excluded: chain L residue  579 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 113 optimal weight:   10.0000
   chunk 28 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 97 optimal weight:    0.1980
   chunk 80 optimal weight:    0.3980
   chunk 25 optimal weight:    0.8980
   chunk 104 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4730 r_free = 0.4730 target = 0.243737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.196371 restraints weight = 10989.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.4331 rms_B_bonded: 2.61
r_work: 0.4014 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10408  Z= 0.146
  Angle     :  0.576  10.198  14235  Z= 0.314
  Chirality :  0.041   0.162   1598
  Planarity :  0.004   0.056   1681
  Dihedral  : 17.535  83.690   1744
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.60 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  6.77 %
    Allowed  : 19.08 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.24), residues: 1140
  helix:  1.43 (0.27), residues: 366
  sheet: -0.27 (0.39), residues: 165
  loop : -1.23 (0.23), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K 114 
 TYR   0.018   0.001   TYR L 531 
 PHE   0.017   0.001   PHE L 476 
 TRP   0.006   0.001   TRP L  44 
 HIS   0.003   0.001   HIS L 417 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.15 (10408)
  covalent geometry    : angle       0.57642 /  0.31 (14235)
  hydrogen bonds       : bond        0.04176 /  2.87 (  415)
  hydrogen bonds       : angle       4.64362 /  3.30 ( 1132)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 100
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: K   46 ARG cc_start: 0.7770 (tpp-160) cc_final: 0.7306 (mmm-85)
REVERT: K   82 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.6628 (ttmm)
REVERT: K  152 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.5773 (mm-30)
REVERT: K  155 ASP cc_start: 0.6775 (t70) cc_final: 0.6445 (t0)
REVERT: K  218 THR cc_start: 0.8706 (p) cc_final: 0.8451 (m)
REVERT: K  219 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7724 (mptt)
REVERT: K  289 ARG cc_start: 0.3895 (OUTLIER) cc_final: 0.1167 (mmm-85)
REVERT: K  323 GLN cc_start: 0.7746 (mm110) cc_final: 0.6942 (mm-40)
REVERT: K  446 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6871 (t0)
REVERT: K  506 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6798 (m-30)
REVERT: K  513 ASP cc_start: 0.7738 (t0) cc_final: 0.7214 (m-30)
REVERT: K  536 ILE cc_start: 0.8145 (mt) cc_final: 0.7885 (mm)
REVERT: L   87 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7824 (mtpp)
REVERT: L   88 GLN cc_start: 0.8582 (tt0) cc_final: 0.8353 (tt0)
REVERT: L  141 ILE cc_start: 0.5018 (OUTLIER) cc_final: 0.4530 (mp)
REVERT: L  156 ARG cc_start: 0.7411 (ptm160) cc_final: 0.6697 (ptp-170)
REVERT: L  164 LYS cc_start: 0.5923 (OUTLIER) cc_final: 0.5319 (mptt)
REVERT: L  195 VAL cc_start: 0.8349 (p) cc_final: 0.8134 (m)
REVERT: L  243 VAL cc_start: 0.8056 (OUTLIER) cc_final: 0.7816 (t)
REVERT: L  303 ILE cc_start: 0.6619 (OUTLIER) cc_final: 0.6297 (pp)
REVERT: L  401 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6497 (ttpt)
REVERT: L  469 ILE cc_start: 0.3286 (OUTLIER) cc_final: 0.2808 (tp)
REVERT: L  521 ASP cc_start: 0.6437 (OUTLIER) cc_final: 0.5973 (t0)
  outliers start: 72
  outliers final: 38
  residues processed: 157
  average time/residue: 0.4313
  time to fit residues: 73.9286
Evaluate side-chains
  148 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 96
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   43 VAL
Chi-restraints excluded: chain K residue   61 GLU
Chi-restraints excluded: chain K residue   79 THR
Chi-restraints excluded: chain K residue   82 LYS
Chi-restraints excluded: chain K residue   91 LEU
Chi-restraints excluded: chain K residue  100 ASP
Chi-restraints excluded: chain K residue  130 ILE
Chi-restraints excluded: chain K residue  134 LYS
Chi-restraints excluded: chain K residue  152 GLU
Chi-restraints excluded: chain K residue  219 LYS
Chi-restraints excluded: chain K residue  254 ILE
Chi-restraints excluded: chain K residue  257 VAL
Chi-restraints excluded: chain K residue  275 VAL
Chi-restraints excluded: chain K residue  289 ARG
Chi-restraints excluded: chain K residue  344 SER
Chi-restraints excluded: chain K residue  446 ASP
Chi-restraints excluded: chain K residue  506 ASP
Chi-restraints excluded: chain K residue  539 LEU
Chi-restraints excluded: chain K residue  544 LYS
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue    9 VAL
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   64 VAL
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain L residue   87 LYS
Chi-restraints excluded: chain L residue  102 LEU
Chi-restraints excluded: chain L residue  111 VAL
Chi-restraints excluded: chain L residue  141 ILE
Chi-restraints excluded: chain L residue  162 CYS
Chi-restraints excluded: chain L residue  164 LYS
Chi-restraints excluded: chain L residue  243 VAL
Chi-restraints excluded: chain L residue  283 ILE
Chi-restraints excluded: chain L residue  292 VAL
Chi-restraints excluded: chain L residue  303 ILE
Chi-restraints excluded: chain L residue  323 VAL
Chi-restraints excluded: chain L residue  328 VAL
Chi-restraints excluded: chain L residue  333 THR
Chi-restraints excluded: chain L residue  341 LEU
Chi-restraints excluded: chain L residue  354 ARG
Chi-restraints excluded: chain L residue  401 LYS
Chi-restraints excluded: chain L residue  405 VAL
Chi-restraints excluded: chain L residue  413 VAL
Chi-restraints excluded: chain L residue  467 HIS
Chi-restraints excluded: chain L residue  469 ILE
Chi-restraints excluded: chain L residue  480 MET
Chi-restraints excluded: chain L residue  487 GLU
Chi-restraints excluded: chain L residue  497 ILE
Chi-restraints excluded: chain L residue  500 VAL
Chi-restraints excluded: chain L residue  521 ASP
Chi-restraints excluded: chain L residue  546 ILE
Chi-restraints excluded: chain L residue  578 LEU
Chi-restraints excluded: chain L residue  579 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 93 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 101 optimal weight:    9.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 406 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4700 r_free = 0.4700 target = 0.239066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.196392 restraints weight = 10724.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.4358 rms_B_bonded: 2.14
r_work: 0.4024 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.109  10408  Z= 0.164
  Angle     :  0.596  10.234  14235  Z= 0.321
  Chirality :  0.042   0.188   1598
  Planarity :  0.004   0.059   1681
  Dihedral  : 17.561  83.772   1744
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.30 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  6.86 %
    Allowed  : 19.55 %
    Favored  : 73.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.24), residues: 1140
  helix:  1.40 (0.27), residues: 364
  sheet: -0.32 (0.38), residues: 170
  loop : -1.24 (0.23), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 186 
 TYR   0.020   0.002   TYR L 531 
 PHE   0.017   0.001   PHE L 476 
 TRP   0.015   0.002   TRP K 391 
 HIS   0.003   0.001   HIS L 417 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.16 (10408)
  covalent geometry    : angle       0.59588 /  0.32 (14235)
  hydrogen bonds       : bond        0.04277 /  2.93 (  415)
  hydrogen bonds       : angle       4.66502 /  3.30 ( 1132)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 97
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: K   18 GLU cc_start: 0.8386 (mp0) cc_final: 0.7595 (tm-30)
REVERT: K   46 ARG cc_start: 0.7750 (tpp-160) cc_final: 0.7287 (mmm-85)
REVERT: K   82 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.6645 (ttmm)
REVERT: K  114 ARG cc_start: 0.7683 (mtp85) cc_final: 0.7212 (mmp80)
REVERT: K  152 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6468 (mm-30)
REVERT: K  155 ASP cc_start: 0.6726 (t70) cc_final: 0.6372 (t0)
REVERT: K  218 THR cc_start: 0.8697 (p) cc_final: 0.8451 (m)
REVERT: K  219 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7709 (mptt)
REVERT: K  289 ARG cc_start: 0.3707 (OUTLIER) cc_final: 0.1097 (mmm-85)
REVERT: K  291 PHE cc_start: 0.4770 (OUTLIER) cc_final: 0.4029 (p90)
REVERT: K  323 GLN cc_start: 0.7778 (mm110) cc_final: 0.7053 (mm-40)
REVERT: K  356 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7652 (mtmt)
REVERT: K  446 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6868 (t0)
REVERT: K  506 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6835 (m-30)
REVERT: K  513 ASP cc_start: 0.7741 (t0) cc_final: 0.7241 (m-30)
REVERT: K  536 ILE cc_start: 0.8133 (mt) cc_final: 0.7883 (mm)
REVERT: L   87 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7771 (mtpp)
REVERT: L   88 GLN cc_start: 0.8558 (tt0) cc_final: 0.8313 (tt0)
REVERT: L  141 ILE cc_start: 0.4931 (OUTLIER) cc_final: 0.4482 (mp)
REVERT: L  156 ARG cc_start: 0.7405 (ptm160) cc_final: 0.6684 (ptp-170)
REVERT: L  164 LYS cc_start: 0.5936 (OUTLIER) cc_final: 0.5311 (mptt)
REVERT: L  195 VAL cc_start: 0.8329 (p) cc_final: 0.8112 (m)
REVERT: L  243 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7841 (t)
REVERT: L  262 GLU cc_start: 0.7187 (pm20) cc_final: 0.6284 (mt-10)
REVERT: L  303 ILE cc_start: 0.6554 (OUTLIER) cc_final: 0.6216 (pp)
REVERT: L  401 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6496 (ttpt)
REVERT: L  469 ILE cc_start: 0.3274 (OUTLIER) cc_final: 0.2831 (tp)
REVERT: L  474 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.5951 (tm-30)
REVERT: L  521 ASP cc_start: 0.6462 (OUTLIER) cc_final: 0.5983 (t0)
  outliers start: 73
  outliers final: 38
  residues processed: 154
  average time/residue: 0.4508
  time to fit residues: 75.5849
Evaluate side-chains
  148 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 93
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   14 THR
Chi-restraints excluded: chain K residue   43 VAL
Chi-restraints excluded: chain K residue   61 GLU
Chi-restraints excluded: chain K residue   79 THR
Chi-restraints excluded: chain K residue   82 LYS
Chi-restraints excluded: chain K residue   91 LEU
Chi-restraints excluded: chain K residue  100 ASP
Chi-restraints excluded: chain K residue  130 ILE
Chi-restraints excluded: chain K residue  134 LYS
Chi-restraints excluded: chain K residue  152 GLU
Chi-restraints excluded: chain K residue  219 LYS
Chi-restraints excluded: chain K residue  254 ILE
Chi-restraints excluded: chain K residue  257 VAL
Chi-restraints excluded: chain K residue  275 VAL
Chi-restraints excluded: chain K residue  289 ARG
Chi-restraints excluded: chain K residue  291 PHE
Chi-restraints excluded: chain K residue  344 SER
Chi-restraints excluded: chain K residue  356 LYS
Chi-restraints excluded: chain K residue  404 THR
Chi-restraints excluded: chain K residue  446 ASP
Chi-restraints excluded: chain K residue  506 ASP
Chi-restraints excluded: chain K residue  544 LYS
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue    9 VAL
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   64 VAL
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain L residue   87 LYS
Chi-restraints excluded: chain L residue  111 VAL
Chi-restraints excluded: chain L residue  141 ILE
Chi-restraints excluded: chain L residue  162 CYS
Chi-restraints excluded: chain L residue  164 LYS
Chi-restraints excluded: chain L residue  243 VAL
Chi-restraints excluded: chain L residue  283 ILE
Chi-restraints excluded: chain L residue  292 VAL
Chi-restraints excluded: chain L residue  303 ILE
Chi-restraints excluded: chain L residue  323 VAL
Chi-restraints excluded: chain L residue  328 VAL
Chi-restraints excluded: chain L residue  333 THR
Chi-restraints excluded: chain L residue  341 LEU
Chi-restraints excluded: chain L residue  354 ARG
Chi-restraints excluded: chain L residue  401 LYS
Chi-restraints excluded: chain L residue  405 VAL
Chi-restraints excluded: chain L residue  413 VAL
Chi-restraints excluded: chain L residue  467 HIS
Chi-restraints excluded: chain L residue  469 ILE
Chi-restraints excluded: chain L residue  474 GLU
Chi-restraints excluded: chain L residue  487 GLU
Chi-restraints excluded: chain L residue  497 ILE
Chi-restraints excluded: chain L residue  500 VAL
Chi-restraints excluded: chain L residue  503 ASP
Chi-restraints excluded: chain L residue  521 ASP
Chi-restraints excluded: chain L residue  546 ILE
Chi-restraints excluded: chain L residue  578 LEU
Chi-restraints excluded: chain L residue  579 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 106 optimal weight:    0.0970
   chunk 80 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 102 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 107 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0040
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.4790

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.239234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.195580 restraints weight = 10510.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.4356 rms_B_bonded: 2.10
r_work: 0.4043 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.088  10408  Z= 0.135
  Angle     :  0.575   9.949  14235  Z= 0.310
  Chirality :  0.041   0.176   1598
  Planarity :  0.004   0.060   1681
  Dihedral  : 17.526  84.212   1744
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.60 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 20.58 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.24), residues: 1140
  helix:  1.44 (0.28), residues: 365
  sheet: -0.23 (0.39), residues: 164
  loop : -1.18 (0.24), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 452 
 TYR   0.019   0.001   TYR L 531 
 PHE   0.016   0.001   PHE L 476 
 TRP   0.014   0.002   TRP K 391 
 HIS   0.003   0.001   HIS K 485 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.14 (10408)
  covalent geometry    : angle       0.57475 /  0.31 (14235)
  hydrogen bonds       : bond        0.04023 /  2.76 (  415)
  hydrogen bonds       : angle       4.58606 /  3.24 ( 1132)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 101
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: K   46 ARG cc_start: 0.7747 (tpp-160) cc_final: 0.7302 (mmm-85)
REVERT: K   82 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.6555 (ttmm)
REVERT: K  114 ARG cc_start: 0.7705 (mtp85) cc_final: 0.6963 (mmp-170)
REVERT: K  152 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6517 (mm-30)
REVERT: K  155 ASP cc_start: 0.6682 (t70) cc_final: 0.6344 (t0)
REVERT: K  218 THR cc_start: 0.8696 (p) cc_final: 0.8455 (m)
REVERT: K  219 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7697 (mptt)
REVERT: K  289 ARG cc_start: 0.3676 (OUTLIER) cc_final: 0.2577 (mmm-85)
REVERT: K  323 GLN cc_start: 0.7797 (mm110) cc_final: 0.7079 (mm-40)
REVERT: K  356 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7641 (mtmt)
REVERT: K  506 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6830 (m-30)
REVERT: K  513 ASP cc_start: 0.7741 (t0) cc_final: 0.7242 (m-30)
REVERT: K  536 ILE cc_start: 0.8100 (mt) cc_final: 0.7853 (mm)
REVERT: K  544 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7669 (tptt)
REVERT: L   88 GLN cc_start: 0.8530 (tt0) cc_final: 0.8305 (tt0)
REVERT: L  141 ILE cc_start: 0.4843 (OUTLIER) cc_final: 0.4419 (mp)
REVERT: L  156 ARG cc_start: 0.7425 (ptm160) cc_final: 0.6712 (ptp-170)
REVERT: L  164 LYS cc_start: 0.5928 (OUTLIER) cc_final: 0.5311 (mptt)
REVERT: L  195 VAL cc_start: 0.8299 (p) cc_final: 0.8096 (m)
REVERT: L  243 VAL cc_start: 0.8007 (OUTLIER) cc_final: 0.7769 (t)
REVERT: L  262 GLU cc_start: 0.7250 (pm20) cc_final: 0.6227 (mt-10)
REVERT: L  303 ILE cc_start: 0.6528 (OUTLIER) cc_final: 0.6199 (pp)
REVERT: L  307 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8114 (tp)
REVERT: L  401 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6551 (ttpt)
REVERT: L  474 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.5941 (tm-30)
REVERT: L  521 ASP cc_start: 0.6433 (OUTLIER) cc_final: 0.5890 (t0)
  outliers start: 65
  outliers final: 36
  residues processed: 153
  average time/residue: 0.4246
  time to fit residues: 70.9935
Evaluate side-chains
  149 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 99
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   43 VAL
Chi-restraints excluded: chain K residue   61 GLU
Chi-restraints excluded: chain K residue   79 THR
Chi-restraints excluded: chain K residue   82 LYS
Chi-restraints excluded: chain K residue   91 LEU
Chi-restraints excluded: chain K residue  100 ASP
Chi-restraints excluded: chain K residue  130 ILE
Chi-restraints excluded: chain K residue  134 LYS
Chi-restraints excluded: chain K residue  152 GLU
Chi-restraints excluded: chain K residue  254 ILE
Chi-restraints excluded: chain K residue  257 VAL
Chi-restraints excluded: chain K residue  275 VAL
Chi-restraints excluded: chain K residue  289 ARG
Chi-restraints excluded: chain K residue  356 LYS
Chi-restraints excluded: chain K residue  506 ASP
Chi-restraints excluded: chain K residue  539 LEU
Chi-restraints excluded: chain K residue  544 LYS
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue    9 VAL
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   64 VAL
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain L residue  102 LEU
Chi-restraints excluded: chain L residue  111 VAL
Chi-restraints excluded: chain L residue  141 ILE
Chi-restraints excluded: chain L residue  162 CYS
Chi-restraints excluded: chain L residue  164 LYS
Chi-restraints excluded: chain L residue  243 VAL
Chi-restraints excluded: chain L residue  292 VAL
Chi-restraints excluded: chain L residue  303 ILE
Chi-restraints excluded: chain L residue  307 ILE
Chi-restraints excluded: chain L residue  323 VAL
Chi-restraints excluded: chain L residue  328 VAL
Chi-restraints excluded: chain L residue  333 THR
Chi-restraints excluded: chain L residue  341 LEU
Chi-restraints excluded: chain L residue  354 ARG
Chi-restraints excluded: chain L residue  401 LYS
Chi-restraints excluded: chain L residue  405 VAL
Chi-restraints excluded: chain L residue  413 VAL
Chi-restraints excluded: chain L residue  467 HIS
Chi-restraints excluded: chain L residue  474 GLU
Chi-restraints excluded: chain L residue  480 MET
Chi-restraints excluded: chain L residue  487 GLU
Chi-restraints excluded: chain L residue  497 ILE
Chi-restraints excluded: chain L residue  500 VAL
Chi-restraints excluded: chain L residue  503 ASP
Chi-restraints excluded: chain L residue  521 ASP
Chi-restraints excluded: chain L residue  546 ILE
Chi-restraints excluded: chain L residue  578 LEU
Chi-restraints excluded: chain L residue  579 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 56 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 20 optimal weight:    0.2980
   chunk 91 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 110 optimal weight:    0.4980
   chunk 106 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 112 optimal weight:    0.0020
   overall best weight:    0.4788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.239596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.196214 restraints weight = 10566.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.4361 rms_B_bonded: 2.07
r_work: 0.4046 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  10408  Z= 0.136
  Angle     :  0.576   9.927  14235  Z= 0.310
  Chirality :  0.041   0.166   1598
  Planarity :  0.004   0.061   1681
  Dihedral  : 17.498  84.513   1740
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.95 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 20.96 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.24), residues: 1140
  helix:  1.40 (0.28), residues: 365
  sheet: -0.19 (0.39), residues: 164
  loop : -1.15 (0.24), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 550 
 TYR   0.019   0.001   TYR L 531 
 PHE   0.015   0.001   PHE L 476 
 TRP   0.010   0.002   TRP K 391 
 HIS   0.003   0.001   HIS K 485 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.14 (10408)
  covalent geometry    : angle       0.57582 /  0.31 (14235)
  hydrogen bonds       : bond        0.04002 /  2.75 (  415)
  hydrogen bonds       : angle       4.59304 /  3.25 ( 1132)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 103
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: K   18 GLU cc_start: 0.8405 (mp0) cc_final: 0.7625 (tm-30)
REVERT: K   46 ARG cc_start: 0.7755 (tpp-160) cc_final: 0.7316 (mmm-85)
REVERT: K   82 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.6563 (ttmm)
REVERT: K  114 ARG cc_start: 0.7676 (mtp85) cc_final: 0.6942 (mmp-170)
REVERT: K  152 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6524 (mm-30)
REVERT: K  155 ASP cc_start: 0.6648 (t70) cc_final: 0.6319 (t0)
REVERT: K  218 THR cc_start: 0.8700 (p) cc_final: 0.8458 (m)
REVERT: K  219 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7685 (mptt)
REVERT: K  289 ARG cc_start: 0.3610 (OUTLIER) cc_final: 0.2447 (mmm-85)
REVERT: K  291 PHE cc_start: 0.4726 (OUTLIER) cc_final: 0.3970 (p90)
REVERT: K  323 GLN cc_start: 0.7800 (mm110) cc_final: 0.6976 (mm-40)
REVERT: K  356 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7616 (mtmt)
REVERT: K  506 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6843 (m-30)
REVERT: K  509 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6586 (mmt)
REVERT: K  513 ASP cc_start: 0.7750 (t0) cc_final: 0.7249 (m-30)
REVERT: K  536 ILE cc_start: 0.8125 (mt) cc_final: 0.7867 (mm)
REVERT: K  544 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7646 (tptt)
REVERT: K  548 MET cc_start: 0.6191 (mpp) cc_final: 0.5753 (OUTLIER)
REVERT: L   87 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7920 (mtpp)
REVERT: L   88 GLN cc_start: 0.8531 (tt0) cc_final: 0.8318 (tt0)
REVERT: L  156 ARG cc_start: 0.7400 (ptm160) cc_final: 0.6695 (ptp90)
REVERT: L  164 LYS cc_start: 0.5941 (OUTLIER) cc_final: 0.5322 (mptt)
REVERT: L  195 VAL cc_start: 0.8299 (p) cc_final: 0.8094 (m)
REVERT: L  243 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7764 (t)
REVERT: L  303 ILE cc_start: 0.6506 (OUTLIER) cc_final: 0.6181 (pp)
REVERT: L  307 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8155 (tp)
REVERT: L  401 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6565 (ttpt)
REVERT: L  474 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.5911 (tm-30)
REVERT: L  521 ASP cc_start: 0.6366 (OUTLIER) cc_final: 0.5782 (t0)
  outliers start: 61
  outliers final: 38
  residues processed: 153
  average time/residue: 0.4708
  time to fit residues: 78.3349
Evaluate side-chains
  151 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 98
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   38 LEU
Chi-restraints excluded: chain K residue   43 VAL
Chi-restraints excluded: chain K residue   61 GLU
Chi-restraints excluded: chain K residue   79 THR
Chi-restraints excluded: chain K residue   82 LYS
Chi-restraints excluded: chain K residue   91 LEU
Chi-restraints excluded: chain K residue  100 ASP
Chi-restraints excluded: chain K residue  130 ILE
Chi-restraints excluded: chain K residue  134 LYS
Chi-restraints excluded: chain K residue  152 GLU
Chi-restraints excluded: chain K residue  254 ILE
Chi-restraints excluded: chain K residue  257 VAL
Chi-restraints excluded: chain K residue  275 VAL
Chi-restraints excluded: chain K residue  289 ARG
Chi-restraints excluded: chain K residue  291 PHE
Chi-restraints excluded: chain K residue  356 LYS
Chi-restraints excluded: chain K residue  500 THR
Chi-restraints excluded: chain K residue  506 ASP
Chi-restraints excluded: chain K residue  509 MET
Chi-restraints excluded: chain K residue  539 LEU
Chi-restraints excluded: chain K residue  544 LYS
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue    9 VAL
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain L residue   87 LYS
Chi-restraints excluded: chain L residue  102 LEU
Chi-restraints excluded: chain L residue  111 VAL
Chi-restraints excluded: chain L residue  164 LYS
Chi-restraints excluded: chain L residue  190 MET
Chi-restraints excluded: chain L residue  243 VAL
Chi-restraints excluded: chain L residue  292 VAL
Chi-restraints excluded: chain L residue  303 ILE
Chi-restraints excluded: chain L residue  307 ILE
Chi-restraints excluded: chain L residue  323 VAL
Chi-restraints excluded: chain L residue  328 VAL
Chi-restraints excluded: chain L residue  333 THR
Chi-restraints excluded: chain L residue  341 LEU
Chi-restraints excluded: chain L residue  354 ARG
Chi-restraints excluded: chain L residue  401 LYS
Chi-restraints excluded: chain L residue  405 VAL
Chi-restraints excluded: chain L residue  413 VAL
Chi-restraints excluded: chain L residue  467 HIS
Chi-restraints excluded: chain L residue  474 GLU
Chi-restraints excluded: chain L residue  480 MET
Chi-restraints excluded: chain L residue  487 GLU
Chi-restraints excluded: chain L residue  497 ILE
Chi-restraints excluded: chain L residue  500 VAL
Chi-restraints excluded: chain L residue  503 ASP
Chi-restraints excluded: chain L residue  521 ASP
Chi-restraints excluded: chain L residue  546 ILE
Chi-restraints excluded: chain L residue  578 LEU
Chi-restraints excluded: chain L residue  579 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9980
   chunk 81 optimal weight:    0.2980
   chunk 16 optimal weight:    5.9990
   chunk 38 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 43 optimal weight:    0.3980
   chunk 1 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K 449 ASN
** L  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4707 r_free = 0.4707 target = 0.239991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.196159 restraints weight = 10403.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.4354 rms_B_bonded: 2.11
r_work: 0.4027 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  10408  Z= 0.140
  Angle     :  0.580  10.008  14235  Z= 0.311
  Chirality :  0.041   0.163   1598
  Planarity :  0.004   0.059   1681
  Dihedral  : 17.498  84.720   1740
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.33 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 21.05 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.24), residues: 1140
  helix:  1.40 (0.27), residues: 365
  sheet: -0.20 (0.39), residues: 164
  loop : -1.14 (0.24), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 550 
 TYR   0.017   0.001   TYR L 531 
 PHE   0.016   0.001   PHE L 476 
 TRP   0.008   0.002   TRP K 391 
 HIS   0.003   0.001   HIS L 417 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.14 (10408)
  covalent geometry    : angle       0.58009 /  0.31 (14235)
  hydrogen bonds       : bond        0.04020 /  2.77 (  415)
  hydrogen bonds       : angle       4.55812 /  3.23 ( 1132)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 98
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: K   18 GLU cc_start: 0.8435 (mp0) cc_final: 0.7611 (tm-30)
REVERT: K   46 ARG cc_start: 0.7784 (tpp-160) cc_final: 0.7336 (mmm-85)
REVERT: K   82 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.6596 (ttmm)
REVERT: K  114 ARG cc_start: 0.7735 (mtp85) cc_final: 0.6965 (mmp-170)
REVERT: K  152 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6562 (mm-30)
REVERT: K  155 ASP cc_start: 0.6666 (t70) cc_final: 0.6278 (t0)
REVERT: K  218 THR cc_start: 0.8695 (p) cc_final: 0.8452 (m)
REVERT: K  219 LYS cc_start: 0.8162 (mtmm) cc_final: 0.7686 (mptt)
REVERT: K  289 ARG cc_start: 0.3559 (OUTLIER) cc_final: 0.2243 (mmm-85)
REVERT: K  323 GLN cc_start: 0.7696 (mm110) cc_final: 0.6968 (mm110)
REVERT: K  356 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7624 (mtmt)
REVERT: K  506 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6818 (m-30)
REVERT: K  509 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6617 (mmt)
REVERT: K  513 ASP cc_start: 0.7751 (t0) cc_final: 0.7247 (m-30)
REVERT: K  536 ILE cc_start: 0.8134 (mt) cc_final: 0.7881 (mm)
REVERT: K  544 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7762 (tptt)
REVERT: L   87 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7985 (mtpp)
REVERT: L   88 GLN cc_start: 0.8508 (tt0) cc_final: 0.8291 (tt0)
REVERT: L  156 ARG cc_start: 0.7433 (ptm160) cc_final: 0.6719 (ptp90)
REVERT: L  164 LYS cc_start: 0.5969 (OUTLIER) cc_final: 0.5338 (mptt)
REVERT: L  195 VAL cc_start: 0.8288 (p) cc_final: 0.8080 (m)
REVERT: L  243 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7783 (t)
REVERT: L  262 GLU cc_start: 0.7378 (pm20) cc_final: 0.6489 (mt-10)
REVERT: L  303 ILE cc_start: 0.6552 (OUTLIER) cc_final: 0.6222 (pp)
REVERT: L  307 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8024 (tp)
REVERT: L  401 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6550 (ttpt)
REVERT: L  474 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.5904 (tm-30)
  outliers start: 63
  outliers final: 38
  residues processed: 150
  average time/residue: 0.4665
  time to fit residues: 76.0886
Evaluate side-chains
  151 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 99
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   38 LEU
Chi-restraints excluded: chain K residue   43 VAL
Chi-restraints excluded: chain K residue   61 GLU
Chi-restraints excluded: chain K residue   79 THR
Chi-restraints excluded: chain K residue   82 LYS
Chi-restraints excluded: chain K residue   91 LEU
Chi-restraints excluded: chain K residue  100 ASP
Chi-restraints excluded: chain K residue  130 ILE
Chi-restraints excluded: chain K residue  134 LYS
Chi-restraints excluded: chain K residue  152 GLU
Chi-restraints excluded: chain K residue  254 ILE
Chi-restraints excluded: chain K residue  257 VAL
Chi-restraints excluded: chain K residue  275 VAL
Chi-restraints excluded: chain K residue  289 ARG
Chi-restraints excluded: chain K residue  356 LYS
Chi-restraints excluded: chain K residue  404 THR
Chi-restraints excluded: chain K residue  500 THR
Chi-restraints excluded: chain K residue  506 ASP
Chi-restraints excluded: chain K residue  509 MET
Chi-restraints excluded: chain K residue  539 LEU
Chi-restraints excluded: chain K residue  544 LYS
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue    9 VAL
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   64 VAL
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain L residue   87 LYS
Chi-restraints excluded: chain L residue  102 LEU
Chi-restraints excluded: chain L residue  111 VAL
Chi-restraints excluded: chain L residue  164 LYS
Chi-restraints excluded: chain L residue  243 VAL
Chi-restraints excluded: chain L residue  292 VAL
Chi-restraints excluded: chain L residue  303 ILE
Chi-restraints excluded: chain L residue  307 ILE
Chi-restraints excluded: chain L residue  323 VAL
Chi-restraints excluded: chain L residue  328 VAL
Chi-restraints excluded: chain L residue  333 THR
Chi-restraints excluded: chain L residue  341 LEU
Chi-restraints excluded: chain L residue  354 ARG
Chi-restraints excluded: chain L residue  401 LYS
Chi-restraints excluded: chain L residue  405 VAL
Chi-restraints excluded: chain L residue  413 VAL
Chi-restraints excluded: chain L residue  467 HIS
Chi-restraints excluded: chain L residue  474 GLU
Chi-restraints excluded: chain L residue  480 MET
Chi-restraints excluded: chain L residue  487 GLU
Chi-restraints excluded: chain L residue  497 ILE
Chi-restraints excluded: chain L residue  500 VAL
Chi-restraints excluded: chain L residue  503 ASP
Chi-restraints excluded: chain L residue  546 ILE
Chi-restraints excluded: chain L residue  578 LEU
Chi-restraints excluded: chain L residue  579 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 105 optimal weight:    0.3980
   chunk 75 optimal weight:    0.4980
   chunk 21 optimal weight:    0.0370
   chunk 90 optimal weight:    0.9990
   chunk 20 optimal weight:    7.9990
   chunk 67 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 94 optimal weight:    0.6980
   chunk 114 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   chunk 99 optimal weight:    0.6980
   overall best weight:    0.4658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** L  20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.240714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.196638 restraints weight = 10563.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.4336 rms_B_bonded: 2.15
r_work: 0.4015 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  10408  Z= 0.131
  Angle     :  0.570   9.881  14235  Z= 0.306
  Chirality :  0.041   0.161   1598
  Planarity :  0.004   0.060   1681
  Dihedral  : 17.474  85.029   1740
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.77 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 21.33 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.24), residues: 1140
  helix:  1.41 (0.28), residues: 367
  sheet: -0.17 (0.39), residues: 164
  loop : -1.15 (0.23), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 550 
 TYR   0.017   0.001   TYR L 531 
 PHE   0.015   0.001   PHE L 476 
 TRP   0.007   0.001   TRP K 391 
 HIS   0.003   0.001   HIS K 485 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 (10408)
  covalent geometry    : angle       0.56992 /  0.31 (14235)
  hydrogen bonds       : bond        0.03931 /  2.69 (  415)
  hydrogen bonds       : angle       4.53115 /  3.22 ( 1132)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3280.12 seconds
wall clock time: 56 minutes 40.95 seconds (3400.95 seconds total)