Starting phenix.real_space_refine
on Sun Jun  8 06:46:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ca1_16515/06_2025/8ca1_16515.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ca1_16515/06_2025/8ca1_16515.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ca1_16515/06_2025/8ca1_16515.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ca1_16515/06_2025/8ca1_16515.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ca1_16515/06_2025/8ca1_16515.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ca1_16515/06_2025/8ca1_16515.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.254
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       4      5.49       5
     S      50      5.16       5
     C    5708      2.51       5
     N    1566      2.21       5
     O    1708      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9036
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 4465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 589, 4465
          Classifications: {'peptide': 589}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 570}
    Chain: "A"
      Number of atoms: 4465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 589, 4465
          Classifications: {'peptide': 589}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 570}
    Chain: "B"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.73, per 1000 atoms: 0.86
  Number of scatterers: 9036
  At special positions: 0
  Unit cell: (85.176, 112.216, 86.528, 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      50     16.00
     P       4     15.00
     O    1708      8.00
     N    1566      7.00
     C    5708      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: 2.64
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2112

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 6 sheets defined
      67.1% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'B' and resid 73 through 80
    Processing helix  chain 'B' and resid 84 through 88
      removed outlier: 3.965A  pdb=" N   GLN B  87 " --> pdb=" O   THR B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 117
      removed outlier: 4.036A  pdb=" N   GLY B 108 " --> pdb=" O   LYS B 104 " (cutoff:3.500A)
      Proline residue:  B 109  - end of helix
    Processing helix  chain 'B' and resid 119 through 127
    Processing helix  chain 'B' and resid 130 through 140
      removed outlier: 3.878A  pdb=" N   GLY B 136 " --> pdb=" O   ASP B 132 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU B 137 " --> pdb=" O   THR B 133 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LYS B 138 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLU B 139 " --> pdb=" O   GLN B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 145
      removed outlier: 4.130A  pdb=" N   LEU B 145 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 152
    Processing helix  chain 'B' and resid 157 through 170
    Processing helix  chain 'B' and resid 172 through 185
      removed outlier: 3.934A  pdb=" N   ILE B 185 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 193
      removed outlier: 3.743A  pdb=" N   LEU B 191 " --> pdb=" O   PHE B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 208
      Proline residue:  B 204  - end of helix
      removed outlier: 3.766A  pdb=" N   SER B 208 " --> pdb=" O   PRO B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 229
    Processing helix  chain 'B' and resid 288 through 290
      No H-bonds generated for 'chain 'B' and resid 288 through 290'
    Processing helix  chain 'B' and resid 329 through 367
      removed outlier: 4.677A  pdb=" N   PHE B 343 " --> pdb=" O   ASN B 339 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   GLY B 344 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   MET B 345 " --> pdb=" O   GLY B 341 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA B 346 " --> pdb=" O   ARG B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 408
      removed outlier: 3.754A  pdb=" N   MET B 400 " --> pdb=" O   SER B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 444
      removed outlier: 3.681A  pdb=" N   TRP B 428 " --> pdb=" O   SER B 424 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   GLY B 440 " --> pdb=" O   GLN B 436 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   MET B 441 " --> pdb=" O   ILE B 437 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   MET B 444 " --> pdb=" O   GLY B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 457
    Processing helix  chain 'B' and resid 458 through 461
    Processing helix  chain 'B' and resid 465 through 493
      removed outlier: 4.856A  pdb=" N   ASP B 480 " --> pdb=" O   GLN B 476 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   LYS B 481 " --> pdb=" O   GLY B 477 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLY B 482 " --> pdb=" O   CYS B 478 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLY B 489 " --> pdb=" O   LEU B 485 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LYS B 493 " --> pdb=" O   GLY B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 513
    Processing helix  chain 'B' and resid 527 through 529
      No H-bonds generated for 'chain 'B' and resid 527 through 529'
    Processing helix  chain 'B' and resid 530 through 556
      removed outlier: 3.598A  pdb=" N   ALA B 537 " --> pdb=" O   SER B 533 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL B 538 " --> pdb=" O   GLY B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 561
      removed outlier: 3.771A  pdb=" N   VAL B 560 " --> pdb=" O   LYS B 557 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 562 through 593
      removed outlier: 3.505A  pdb=" N   ARG B 568 " --> pdb=" O   PHE B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 596 through 624
      removed outlier: 3.690A  pdb=" N   SER B 624 " --> pdb=" O   ALA B 620 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 625 through 646
    Processing helix  chain 'A' and resid 73 through 80
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.972A  pdb=" N   GLN A  87 " --> pdb=" O   THR A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 117
      removed outlier: 4.027A  pdb=" N   GLY A 108 " --> pdb=" O   LYS A 104 " (cutoff:3.500A)
      Proline residue:  A 109  - end of helix
    Processing helix  chain 'A' and resid 119 through 127
    Processing helix  chain 'A' and resid 130 through 140
      removed outlier: 3.880A  pdb=" N   GLY A 136 " --> pdb=" O   ASP A 132 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU A 137 " --> pdb=" O   THR A 133 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LYS A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLU A 139 " --> pdb=" O   GLN A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 145
      removed outlier: 4.126A  pdb=" N   LEU A 145 " --> pdb=" O   ALA A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 152
    Processing helix  chain 'A' and resid 157 through 170
    Processing helix  chain 'A' and resid 172 through 185
      removed outlier: 3.933A  pdb=" N   ILE A 185 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 193
      removed outlier: 3.743A  pdb=" N   LEU A 191 " --> pdb=" O   PHE A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 208
      Proline residue:  A 204  - end of helix
      removed outlier: 3.766A  pdb=" N   SER A 208 " --> pdb=" O   PRO A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 229
    Processing helix  chain 'A' and resid 288 through 290
      No H-bonds generated for 'chain 'A' and resid 288 through 290'
    Processing helix  chain 'A' and resid 329 through 367
      removed outlier: 4.677A  pdb=" N   PHE A 343 " --> pdb=" O   ASN A 339 " (cutoff:3.500A)
      removed outlier: 5.901A  pdb=" N   GLY A 344 " --> pdb=" O   ASN A 340 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   MET A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA A 346 " --> pdb=" O   ARG A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 408
      removed outlier: 3.739A  pdb=" N   MET A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 444
      removed outlier: 3.685A  pdb=" N   TRP A 428 " --> pdb=" O   SER A 424 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   GLY A 440 " --> pdb=" O   GLN A 436 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   MET A 441 " --> pdb=" O   ILE A 437 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   MET A 444 " --> pdb=" O   GLY A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 457
    Processing helix  chain 'A' and resid 458 through 461
    Processing helix  chain 'A' and resid 465 through 493
      removed outlier: 4.881A  pdb=" N   ASP A 480 " --> pdb=" O   GLN A 476 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   LYS A 481 " --> pdb=" O   GLY A 477 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLY A 482 " --> pdb=" O   CYS A 478 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLY A 489 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LYS A 493 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 513
    Processing helix  chain 'A' and resid 527 through 529
      No H-bonds generated for 'chain 'A' and resid 527 through 529'
    Processing helix  chain 'A' and resid 530 through 556
      removed outlier: 3.507A  pdb=" N   LEU A 536 " --> pdb=" O   ARG A 532 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA A 537 " --> pdb=" O   SER A 533 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   VAL A 538 " --> pdb=" O   GLY A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 561
      removed outlier: 3.776A  pdb=" N   VAL A 560 " --> pdb=" O   LYS A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 593
      removed outlier: 3.506A  pdb=" N   ARG A 568 " --> pdb=" O   PHE A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 624
      removed outlier: 3.687A  pdb=" N   SER A 624 " --> pdb=" O   ALA A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 646
    Processing sheet with id=AA1, first strand: chain 'B' and resid 213 through 216
      removed outlier: 5.718A  pdb=" N   ALA B 214 " --> pdb=" O   THR B 261 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   PHE B 263 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   CYS B 216 " --> pdb=" O   PHE B 263 " (cutoff:3.500A)
      removed outlier: 9.259A  pdb=" N   LYS B 265 " --> pdb=" O   CYS B 216 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   ALA B 282 " --> pdb=" O   LEU B 324 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 232 through 235
      removed outlier: 6.208A  pdb=" N   TYR B 241 " --> pdb=" O   PRO B 319 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   THR B 243 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   LYS B 317 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   ASN B 245 " --> pdb=" O   GLY B 315 " (cutoff:3.500A)
      removed outlier: 7.120A  pdb=" N   GLY B 315 " --> pdb=" O   ASN B 245 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   SER B 247 " --> pdb=" O   PHE B 313 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   PHE B 313 " --> pdb=" O   SER B 247 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   ILE B 249 " --> pdb=" O   VAL B 311 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   VAL B 311 " --> pdb=" O   ILE B 249 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 369
    Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 216
      removed outlier: 5.722A  pdb=" N   ALA A 214 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   PHE A 263 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   CYS A 216 " --> pdb=" O   PHE A 263 " (cutoff:3.500A)
      removed outlier: 9.244A  pdb=" N   LYS A 265 " --> pdb=" O   CYS A 216 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   ALA A 282 " --> pdb=" O   LEU A 324 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 235
      removed outlier: 6.210A  pdb=" N   TYR A 241 " --> pdb=" O   PRO A 319 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   THR A 243 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   LYS A 317 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ASN A 245 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   GLY A 315 " --> pdb=" O   ASN A 245 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   SER A 247 " --> pdb=" O   PHE A 313 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   PHE A 313 " --> pdb=" O   SER A 247 " (cutoff:3.500A)
      removed outlier: 5.359A  pdb=" N   ILE A 249 " --> pdb=" O   VAL A 311 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   VAL A 311 " --> pdb=" O   ILE A 249 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 368 through 369

    569 hydrogen bonds defined for protein.
    1647 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.00

  Time building geometry restraints manager: 3.10 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: 3002
        1.34 -     1.46: 1931
        1.46 -     1.58: 4172
        1.58 -     1.70: 1
        1.70 -     1.82: 86
  Bond restraints: 9192
  Sorted by residual:
  bond pdb=" O5B FAD B 701 "
       pdb=" PA  FAD B 701 "
    ideal  model  delta    sigma   weight residual
    1.634  1.528  0.106 2.00e-02 2.50e+03 2.79e+01
  bond pdb=" O3P FAD B 701 "
       pdb=" P   FAD B 701 "
    ideal  model  delta    sigma   weight residual
    1.660  1.557  0.103 2.00e-02 2.50e+03 2.63e+01
  bond pdb=" O3P FAD A 701 "
       pdb=" P   FAD A 701 "
    ideal  model  delta    sigma   weight residual
    1.660  1.566  0.094 2.00e-02 2.50e+03 2.23e+01
  bond pdb=" O5B FAD A 701 "
       pdb=" PA  FAD A 701 "
    ideal  model  delta    sigma   weight residual
    1.634  1.541  0.093 2.00e-02 2.50e+03 2.18e+01
  bond pdb=" O5' FAD B 701 "
       pdb=" P   FAD B 701 "
    ideal  model  delta    sigma   weight residual
    1.637  1.570  0.067 2.00e-02 2.50e+03 1.12e+01
  ... (remaining 9187 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 12176
        2.75 -     5.51: 210
        5.51 -     8.26: 10
        8.26 -    11.02: 3
       11.02 -    13.77: 1
  Bond angle restraints: 12400
  Sorted by residual:
  angle pdb=" CB  MET B 301 "
        pdb=" CG  MET B 301 "
        pdb=" SD  MET B 301 "
      ideal   model   delta    sigma   weight residual
     112.70  126.47  -13.77 3.00e+00 1.11e-01 2.11e+01
  angle pdb=" N   GLU B 450 "
        pdb=" CA  GLU B 450 "
        pdb=" CB  GLU B 450 "
      ideal   model   delta    sigma   weight residual
     110.12  104.63    5.49 1.47e+00 4.63e-01 1.39e+01
  angle pdb=" N   GLU A 450 "
        pdb=" CA  GLU A 450 "
        pdb=" CB  GLU A 450 "
      ideal   model   delta    sigma   weight residual
     110.12  104.94    5.18 1.47e+00 4.63e-01 1.24e+01
  angle pdb=" C   MET A 301 "
        pdb=" CA  MET A 301 "
        pdb=" CB  MET A 301 "
      ideal   model   delta    sigma   weight residual
     110.32  103.14    7.18 2.11e+00 2.25e-01 1.16e+01
  angle pdb=" CA  GLU A 450 "
        pdb=" CB  GLU A 450 "
        pdb=" CG  GLU A 450 "
      ideal   model   delta    sigma   weight residual
     114.10  120.60   -6.50 2.00e+00 2.50e-01 1.06e+01
  ... (remaining 12395 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.11: 5199
       22.11 -    44.21: 310
       44.21 -    66.32: 38
       66.32 -    88.43: 15
       88.43 -   110.53: 4
  Dihedral angle restraints: 5566
    sinusoidal: 2256
      harmonic: 3310
  Sorted by residual:
  dihedral pdb=" CA  LYS B 493 "
           pdb=" C   LYS B 493 "
           pdb=" N   ASN B 494 "
           pdb=" CA  ASN B 494 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.20   27.80     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  LYS A 493 "
           pdb=" C   LYS A 493 "
           pdb=" N   ASN A 494 "
           pdb=" CA  ASN A 494 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.22   27.78     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  THR B 368 "
           pdb=" C   THR B 368 "
           pdb=" N   GLN B 369 "
           pdb=" CA  GLN B 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.15   26.85     0      5.00e+00 4.00e-02 2.88e+01
  ... (remaining 5563 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1060
       0.052 -    0.104: 262
       0.104 -    0.156: 48
       0.156 -    0.208: 14
       0.208 -    0.259: 4
  Chirality restraints: 1388
  Sorted by residual:
  chirality pdb=" CA  PHE B 496 "
            pdb=" N   PHE B 496 "
            pdb=" C   PHE B 496 "
            pdb=" CB  PHE B 496 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  PHE A 496 "
            pdb=" N   PHE A 496 "
            pdb=" C   PHE A 496 "
            pdb=" CB  PHE A 496 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  ILE A 303 "
            pdb=" N   ILE A 303 "
            pdb=" C   ILE A 303 "
            pdb=" CB  ILE A 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 1385 not shown)

  Planarity restraints: 1596
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 549 "   -0.020 2.00e-02 2.50e+03   3.99e-02 1.59e+01
        pdb=" C   GLU B 549 "    0.069 2.00e-02 2.50e+03
        pdb=" O   GLU B 549 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   ALA B 550 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 549 "   -0.020 2.00e-02 2.50e+03   3.98e-02 1.59e+01
        pdb=" C   GLU A 549 "    0.069 2.00e-02 2.50e+03
        pdb=" O   GLU A 549 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   ALA A 550 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 548 "    0.015 2.00e-02 2.50e+03   3.05e-02 9.30e+00
        pdb=" C   VAL B 548 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   VAL B 548 "    0.020 2.00e-02 2.50e+03
        pdb=" N   GLU B 549 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1593 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 135
        2.61 -     3.18: 9451
        3.18 -     3.76: 14198
        3.76 -     4.33: 20206
        4.33 -     4.90: 31744
  Nonbonded interactions: 75734
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 222 "
            pdb=" OE1 GLN A 369 "
     model   vdw
     2.041 3.040
  nonbonded pdb=" OD2 ASP A 467 "
            pdb=" O2B FAD A 701 "
     model   vdw
     2.061 3.040
  nonbonded pdb=" OH  TYR A 202 "
            pdb=" OD1 ASN A 322 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" OH  TYR B 202 "
            pdb=" OD1 ASN B 322 "
     model   vdw
     2.133 3.040
  nonbonded pdb=" NZ  LYS A 420 "
            pdb=" OD1 ASN A 466 "
     model   vdw
     2.154 3.120
  ... (remaining 75729 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.680
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.110   9192  Z= 0.289
  Angle     :  0.892  13.771  12400  Z= 0.505
  Chirality :  0.050   0.259   1388
  Planarity :  0.011   0.088   1596
  Dihedral  : 14.977 110.531   3454
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.45 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.23), residues: 1174
  helix: -1.38 (0.17), residues: 668
  sheet: -1.29 (0.54), residues: 72
  loop : -0.76 (0.32), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.005   TRP A 250 
 HIS   0.014   0.003   HIS A 182 
 PHE   0.046   0.004   PHE A 496 
 TYR   0.016   0.005   TYR A 577 
 ARG   0.024   0.004   ARG B 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16595 (  569)
  hydrogen bonds       : angle       7.48130 ( 1647)
  covalent geometry    : bond        0.00582 ( 9192)
  covalent geometry    : angle       0.89246 (12400)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  192 LEU cc_start: 0.9019 (mm) cc_final: 0.8812 (mt)
REVERT: A  382 GLU cc_start: 0.8364 (pp20) cc_final: 0.8022 (pp20)
REVERT: A  410 LYS cc_start: 0.7663 (mmtt) cc_final: 0.7324 (tptt)
REVERT: A  438 MET cc_start: 0.8767 (mmm) cc_final: 0.8060 (mmm)
REVERT: A  479 MET cc_start: 0.8531 (mmp) cc_final: 0.8112 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1917
  time to fit residues: 26.6436
Evaluate side-chains
  68 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 87 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 46 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 55 optimal weight:   10.0000
   chunk 67 optimal weight:    8.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
B  87 GLN
B 183 GLN
B 369 GLN
B 599 HIS
A  87 GLN
A 183 GLN
A 599 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.074453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.065420 restraints weight = 31886.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.067370 restraints weight = 16467.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.068712 restraints weight = 10136.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9192  Z= 0.181
  Angle     :  0.668   8.271  12400  Z= 0.351
  Chirality :  0.044   0.159   1388
  Planarity :  0.004   0.036   1596
  Dihedral  :  9.094  77.624   1346
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.36 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  7.01 %
    Favored  : 91.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.24), residues: 1174
  helix:  0.91 (0.19), residues: 688
  sheet: -0.12 (0.59), residues: 56
  loop : -0.40 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 250 
 HIS   0.006   0.002   HIS A 182 
 PHE   0.012   0.002   PHE A 422 
 TYR   0.014   0.001   TYR A 202 
 ARG   0.006   0.001   ARG A 568 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05575 (  569)
  hydrogen bonds       : angle       4.84668 ( 1647)
  covalent geometry    : bond        0.00392 ( 9192)
  covalent geometry    : angle       0.66816 (12400)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  138 LYS cc_start: 0.8457 (mptt) cc_final: 0.8252 (mptt)
REVERT: B  382 GLU cc_start: 0.8726 (pt0) cc_final: 0.8193 (pp20)
REVERT: B  438 MET cc_start: 0.8963 (mmm) cc_final: 0.8294 (mmm)
REVERT: B  503 MET cc_start: 0.5398 (mmt) cc_final: 0.2882 (tmm)
REVERT: A  382 GLU cc_start: 0.8670 (pp20) cc_final: 0.8456 (pp20)
REVERT: A  438 MET cc_start: 0.9080 (mmm) cc_final: 0.8210 (mmm)
REVERT: A  479 MET cc_start: 0.8482 (mmp) cc_final: 0.8083 (mmt)
  outliers start: 11
  outliers final: 7
  residues processed: 95
  average time/residue: 0.1832
  time to fit residues: 25.7816
Evaluate side-chains
  77 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  345 MET
Chi-restraints excluded: chain B residue  369 GLN
Chi-restraints excluded: chain B residue  397 MET
Chi-restraints excluded: chain A residue   78 MET
Chi-restraints excluded: chain A residue  138 LYS
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 21 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   chunk 19 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 106 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B 369 GLN
** A  87 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 = 0.3289 r_free = 0.3289 target = 0.076474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.067270 restraints weight = 32038.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.069404 restraints weight = 16471.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.070796 restraints weight = 9906.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9192  Z= 0.123
  Angle     :  0.574  13.853  12400  Z= 0.294
  Chirality :  0.039   0.146   1388
  Planarity :  0.004   0.034   1596
  Dihedral  :  8.616  60.418   1346
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.96 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  9.66 %
    Favored  : 88.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.25), residues: 1174
  helix:  1.61 (0.19), residues: 690
  sheet:  0.35 (0.59), residues: 56
  loop :  0.06 (0.33), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 250 
 HIS   0.006   0.001   HIS A 182 
 PHE   0.011   0.001   PHE A 422 
 TYR   0.009   0.001   TYR B 202 
 ARG   0.003   0.000   ARG B 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04722 (  569)
  hydrogen bonds       : angle       4.20027 ( 1647)
  covalent geometry    : bond        0.00257 ( 9192)
  covalent geometry    : angle       0.57425 (12400)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  138 LYS cc_start: 0.8424 (mptt) cc_final: 0.8187 (mptt)
REVERT: B  382 GLU cc_start: 0.8663 (pt0) cc_final: 0.8108 (pp20)
REVERT: B  438 MET cc_start: 0.8909 (mmm) cc_final: 0.8503 (mmm)
REVERT: B  503 MET cc_start: 0.5609 (mmt) cc_final: 0.3889 (tmm)
REVERT: A  382 GLU cc_start: 0.8677 (pp20) cc_final: 0.8372 (pp20)
REVERT: A  438 MET cc_start: 0.9038 (mmm) cc_final: 0.8185 (mmm)
REVERT: A  479 MET cc_start: 0.8476 (mmp) cc_final: 0.8047 (mmt)
  outliers start: 13
  outliers final: 7
  residues processed: 102
  average time/residue: 0.2342
  time to fit residues: 35.7855
Evaluate side-chains
  84 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  397 MET
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain A residue  138 LYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 79 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 2 optimal weight:    5.9990
   chunk 49 optimal weight:    7.9990
   chunk 14 optimal weight:   20.0000
   chunk 67 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    3.7986

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

Flipped N/Q/H residues before XYZ refinement:
** B  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 369 GLN
B 375 HIS
B 618 ASN
** A  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 363 HIS
A 369 GLN
A 375 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.073310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.064039 restraints weight = 32422.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.066017 restraints weight = 16710.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.067406 restraints weight = 10284.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.3020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9192  Z= 0.212
  Angle     :  0.649  13.126  12400  Z= 0.333
  Chirality :  0.042   0.204   1388
  Planarity :  0.004   0.033   1596
  Dihedral  :  8.393  55.347   1346
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.39 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 10.62 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.25), residues: 1174
  helix:  1.66 (0.20), residues: 678
  sheet:  0.36 (0.56), residues: 60
  loop : -0.10 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 250 
 HIS   0.011   0.002   HIS A 182 
 PHE   0.013   0.002   PHE A 422 
 TYR   0.011   0.002   TYR A 161 
 ARG   0.003   0.001   ARG B 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05101 (  569)
  hydrogen bonds       : angle       4.36190 ( 1647)
  covalent geometry    : bond        0.00472 ( 9192)
  covalent geometry    : angle       0.64872 (12400)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  138 LYS cc_start: 0.8447 (mptt) cc_final: 0.8188 (mptt)
REVERT: B  218 THR cc_start: 0.8868 (m) cc_final: 0.8107 (p)
REVERT: B  382 GLU cc_start: 0.8783 (pt0) cc_final: 0.7990 (pp20)
REVERT: B  503 MET cc_start: 0.5676 (mmt) cc_final: 0.3805 (tmm)
REVERT: A  218 THR cc_start: 0.8910 (m) cc_final: 0.8149 (p)
REVERT: A  382 GLU cc_start: 0.8688 (pp20) cc_final: 0.8481 (pp20)
REVERT: A  438 MET cc_start: 0.9017 (mmm) cc_final: 0.8389 (mmm)
REVERT: A  479 MET cc_start: 0.8382 (mmp) cc_final: 0.8031 (mmt)
  outliers start: 23
  outliers final: 12
  residues processed: 98
  average time/residue: 0.1924
  time to fit residues: 28.1992
Evaluate side-chains
  88 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  345 MET
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 101 optimal weight:    0.0770
   chunk 29 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 108 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 78 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.7338

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

Flipped N/Q/H residues before XYZ refinement:
B 369 GLN
A  87 GLN
A 363 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.077358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.068063 restraints weight = 31869.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.070160 restraints weight = 16418.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.071531 restraints weight = 9970.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9192  Z= 0.108
  Angle     :  0.544  12.370  12400  Z= 0.274
  Chirality :  0.039   0.230   1388
  Planarity :  0.003   0.031   1596
  Dihedral  :  8.070  56.408   1346
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 11.25 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.26), residues: 1174
  helix:  1.95 (0.20), residues: 692
  sheet: -0.55 (0.56), residues: 78
  loop :  0.39 (0.35), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 607 
 HIS   0.006   0.001   HIS B 182 
 PHE   0.009   0.001   PHE A 422 
 TYR   0.007   0.001   TYR A 202 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04195 (  569)
  hydrogen bonds       : angle       3.88847 ( 1647)
  covalent geometry    : bond        0.00223 ( 9192)
  covalent geometry    : angle       0.54442 (12400)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  138 LYS cc_start: 0.8400 (mptt) cc_final: 0.8188 (mptt)
REVERT: B  218 THR cc_start: 0.8726 (m) cc_final: 0.7993 (p)
REVERT: B  380 ILE cc_start: 0.9487 (mp) cc_final: 0.9249 (mt)
REVERT: B  382 GLU cc_start: 0.8734 (pt0) cc_final: 0.7929 (pp20)
REVERT: B  467 ASP cc_start: 0.8415 (m-30) cc_final: 0.7952 (p0)
REVERT: B  503 MET cc_start: 0.5395 (mmt) cc_final: 0.4557 (tmm)
REVERT: B  583 LEU cc_start: 0.8973 (mt) cc_final: 0.8600 (tt)
REVERT: A  218 THR cc_start: 0.8757 (m) cc_final: 0.8007 (p)
REVERT: A  382 GLU cc_start: 0.8704 (pp20) cc_final: 0.8412 (pp20)
REVERT: A  438 MET cc_start: 0.8953 (mmm) cc_final: 0.8447 (mmm)
REVERT: A  467 ASP cc_start: 0.8368 (m-30) cc_final: 0.8147 (p0)
REVERT: A  479 MET cc_start: 0.8340 (mmp) cc_final: 0.7969 (mmt)
  outliers start: 22
  outliers final: 9
  residues processed: 102
  average time/residue: 0.1798
  time to fit residues: 27.6738
Evaluate side-chains
  88 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  345 MET
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  405 MET
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9980
   chunk 80 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 54 optimal weight:    7.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 369 GLN
B 498 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.075712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.066398 restraints weight = 32219.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.068399 restraints weight = 16828.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.069745 restraints weight = 10410.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.3701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9192  Z= 0.137
  Angle     :  0.565  11.267  12400  Z= 0.287
  Chirality :  0.040   0.199   1388
  Planarity :  0.003   0.031   1596
  Dihedral  :  7.865  57.382   1346
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 12.74 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.26), residues: 1174
  helix:  2.00 (0.20), residues: 694
  sheet: -0.45 (0.59), residues: 74
  loop :  0.38 (0.35), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 607 
 HIS   0.008   0.002   HIS B 182 
 PHE   0.011   0.001   PHE B 422 
 TYR   0.007   0.001   TYR A 399 
 ARG   0.002   0.000   ARG A 532 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04329 (  569)
  hydrogen bonds       : angle       3.95980 ( 1647)
  covalent geometry    : bond        0.00303 ( 9192)
  covalent geometry    : angle       0.56542 (12400)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  138 LYS cc_start: 0.8405 (mptt) cc_final: 0.8184 (mptt)
REVERT: B  218 THR cc_start: 0.8753 (m) cc_final: 0.8021 (p)
REVERT: B  382 GLU cc_start: 0.8745 (pt0) cc_final: 0.8091 (pp20)
REVERT: B  503 MET cc_start: 0.5423 (mmt) cc_final: 0.4245 (tmm)
REVERT: A  218 THR cc_start: 0.8806 (m) cc_final: 0.8061 (p)
REVERT: A  353 MET cc_start: 0.8903 (mmm) cc_final: 0.8663 (mmm)
REVERT: A  382 GLU cc_start: 0.8844 (pp20) cc_final: 0.8553 (pp20)
REVERT: A  438 MET cc_start: 0.9023 (mmm) cc_final: 0.8401 (mmm)
REVERT: A  479 MET cc_start: 0.8329 (mmp) cc_final: 0.7985 (mmt)
  outliers start: 22
  outliers final: 13
  residues processed: 94
  average time/residue: 0.1787
  time to fit residues: 25.5878
Evaluate side-chains
  84 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  345 MET
Chi-restraints excluded: chain B residue  369 GLN
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 87 optimal weight:    6.9990
   chunk 114 optimal weight:    8.9990
   chunk 46 optimal weight:    9.9990
   chunk 51 optimal weight:   10.0000
   chunk 72 optimal weight:    9.9990
   chunk 74 optimal weight:    7.9990
   chunk 80 optimal weight:    9.9990
   chunk 52 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 158 ASN
B 363 HIS
B 369 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.072113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.062866 restraints weight = 33048.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.064860 restraints weight = 17184.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.066200 restraints weight = 10551.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   9192  Z= 0.281
  Angle     :  0.732  10.548  12400  Z= 0.373
  Chirality :  0.044   0.170   1388
  Planarity :  0.004   0.042   1596
  Dihedral  :  8.166  62.932   1346
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 12.53 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.25), residues: 1174
  helix:  1.65 (0.19), residues: 678
  sheet: -0.11 (0.62), residues: 62
  loop : -0.20 (0.32), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 250 
 HIS   0.014   0.002   HIS A 182 
 PHE   0.015   0.002   PHE B 422 
 TYR   0.015   0.002   TYR A 161 
 ARG   0.004   0.001   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05289 (  569)
  hydrogen bonds       : angle       4.48580 ( 1647)
  covalent geometry    : bond        0.00616 ( 9192)
  covalent geometry    : angle       0.73220 (12400)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
REVERT: B  218 THR cc_start: 0.9033 (m) cc_final: 0.8245 (p)
REVERT: B  301 MET cc_start: 0.8434 (mmm) cc_final: 0.8104 (mmm)
REVERT: B  380 ILE cc_start: 0.9536 (mp) cc_final: 0.9239 (mt)
REVERT: B  382 GLU cc_start: 0.8800 (pt0) cc_final: 0.8109 (pp20)
REVERT: B  450 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8239 (pt0)
REVERT: A  218 THR cc_start: 0.9037 (m) cc_final: 0.8264 (p)
REVERT: A  301 MET cc_start: 0.8304 (mmm) cc_final: 0.8092 (mmm)
REVERT: A  382 GLU cc_start: 0.8760 (pp20) cc_final: 0.8539 (pp20)
REVERT: A  438 MET cc_start: 0.9093 (mmm) cc_final: 0.8358 (mmm)
REVERT: A  450 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8332 (pt0)
REVERT: A  479 MET cc_start: 0.8399 (mmp) cc_final: 0.8119 (mmt)
  outliers start: 24
  outliers final: 20
  residues processed: 90
  average time/residue: 0.1723
  time to fit residues: 24.1326
Evaluate side-chains
  93 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  345 MET
Chi-restraints excluded: chain B residue  353 MET
Chi-restraints excluded: chain B residue  369 GLN
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain B residue  559 ILE
Chi-restraints excluded: chain B residue  648 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  559 ILE
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  648 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 112 optimal weight:    1.9990
   chunk 100 optimal weight:    5.9990
   chunk 107 optimal weight:    4.9990
   chunk 2 optimal weight:    0.2980
   chunk 25 optimal weight:    0.4980
   chunk 109 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
B 369 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.077241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.067882 restraints weight = 32510.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.070006 restraints weight = 16625.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.071511 restraints weight = 10081.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9192  Z= 0.111
  Angle     :  0.570  10.651  12400  Z= 0.284
  Chirality :  0.039   0.164   1388
  Planarity :  0.003   0.032   1596
  Dihedral  :  7.856  59.986   1346
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 13.80 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.26), residues: 1174
  helix:  2.00 (0.20), residues: 692
  sheet: -0.31 (0.62), residues: 72
  loop :  0.27 (0.35), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 607 
 HIS   0.006   0.001   HIS A 182 
 PHE   0.012   0.001   PHE B 422 
 TYR   0.009   0.001   TYR A 202 
 ARG   0.003   0.000   ARG B 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04164 (  569)
  hydrogen bonds       : angle       3.93102 ( 1647)
  covalent geometry    : bond        0.00232 ( 9192)
  covalent geometry    : angle       0.56969 (12400)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  218 THR cc_start: 0.8745 (m) cc_final: 0.8037 (p)
REVERT: B  380 ILE cc_start: 0.9446 (mp) cc_final: 0.9044 (mt)
REVERT: B  382 GLU cc_start: 0.8697 (pt0) cc_final: 0.7947 (pp20)
REVERT: B  503 MET cc_start: 0.5387 (mmt) cc_final: 0.4570 (tmm)
REVERT: A  218 THR cc_start: 0.8811 (m) cc_final: 0.8098 (p)
REVERT: A  382 GLU cc_start: 0.8796 (pp20) cc_final: 0.8529 (pp20)
REVERT: A  438 MET cc_start: 0.8944 (mmm) cc_final: 0.8309 (mmm)
REVERT: A  479 MET cc_start: 0.8308 (mmp) cc_final: 0.7935 (mmt)
  outliers start: 17
  outliers final: 14
  residues processed: 98
  average time/residue: 0.1818
  time to fit residues: 27.6095
Evaluate side-chains
  90 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  353 MET
Chi-restraints excluded: chain B residue  405 MET
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  648 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  648 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 99 optimal weight:   10.0000
   chunk 24 optimal weight:    6.9990
   chunk 114 optimal weight:    7.9990
   chunk 58 optimal weight:   20.0000
   chunk 115 optimal weight:    4.9990
   chunk 95 optimal weight:    0.8980
   chunk 41 optimal weight:    7.9990
   chunk 28 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    3.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.074072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.064710 restraints weight = 32678.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.066737 restraints weight = 16979.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.068126 restraints weight = 10465.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.3844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9192  Z= 0.202
  Angle     :  0.641   9.750  12400  Z= 0.323
  Chirality :  0.042   0.143   1388
  Planarity :  0.004   0.033   1596
  Dihedral  :  7.939  60.306   1346
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 13.59 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.25), residues: 1174
  helix:  2.04 (0.20), residues: 690
  sheet: -0.31 (0.62), residues: 72
  loop :  0.20 (0.34), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 250 
 HIS   0.010   0.002   HIS B 182 
 PHE   0.015   0.002   PHE B 422 
 TYR   0.015   0.002   TYR B 392 
 ARG   0.002   0.000   ARG B 614 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04698 (  569)
  hydrogen bonds       : angle       4.10075 ( 1647)
  covalent geometry    : bond        0.00446 ( 9192)
  covalent geometry    : angle       0.64146 (12400)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  218 THR cc_start: 0.9002 (m) cc_final: 0.8230 (p)
REVERT: B  301 MET cc_start: 0.8464 (mmm) cc_final: 0.8141 (mmm)
REVERT: B  382 GLU cc_start: 0.8810 (pt0) cc_final: 0.8114 (pp20)
REVERT: B  503 MET cc_start: 0.5434 (mmt) cc_final: 0.4075 (tmm)
REVERT: A  218 THR cc_start: 0.8976 (m) cc_final: 0.8233 (p)
REVERT: A  382 GLU cc_start: 0.8758 (pp20) cc_final: 0.8537 (pp20)
REVERT: A  438 MET cc_start: 0.9036 (mmm) cc_final: 0.8401 (mmm)
REVERT: A  450 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8264 (pt0)
  outliers start: 21
  outliers final: 19
  residues processed: 88
  average time/residue: 0.1660
  time to fit residues: 22.7918
Evaluate side-chains
  91 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 1.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  345 MET
Chi-restraints excluded: chain B residue  353 MET
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  475 LEU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain B residue  648 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  648 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 101 optimal weight:    0.0170
   chunk 9 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.7420

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.077237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.067906 restraints weight = 32153.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.069956 restraints weight = 16588.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.071436 restraints weight = 10200.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.4228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9192  Z= 0.110
  Angle     :  0.560   9.913  12400  Z= 0.279
  Chirality :  0.039   0.135   1388
  Planarity :  0.003   0.035   1596
  Dihedral  :  7.772  58.975   1346
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 14.44 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.26), residues: 1174
  helix:  2.17 (0.19), residues: 704
  sheet: -0.15 (0.63), residues: 72
  loop :  0.35 (0.35), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 607 
 HIS   0.005   0.001   HIS A 182 
 PHE   0.013   0.001   PHE B 422 
 TYR   0.008   0.001   TYR B 392 
 ARG   0.002   0.000   ARG A 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04087 (  569)
  hydrogen bonds       : angle       3.81999 ( 1647)
  covalent geometry    : bond        0.00234 ( 9192)
  covalent geometry    : angle       0.55990 (12400)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  218 THR cc_start: 0.8784 (m) cc_final: 0.8082 (p)
REVERT: B  382 GLU cc_start: 0.8756 (pt0) cc_final: 0.8017 (pp20)
REVERT: B  441 MET cc_start: 0.8597 (ttm) cc_final: 0.8368 (ttm)
REVERT: B  503 MET cc_start: 0.5298 (mmt) cc_final: 0.4617 (tmm)
REVERT: A  218 THR cc_start: 0.8847 (m) cc_final: 0.8142 (p)
REVERT: A  382 GLU cc_start: 0.8763 (pp20) cc_final: 0.8501 (pp20)
REVERT: A  438 MET cc_start: 0.8953 (mmm) cc_final: 0.8343 (mmm)
  outliers start: 13
  outliers final: 12
  residues processed: 94
  average time/residue: 0.1677
  time to fit residues: 24.4448
Evaluate side-chains
  90 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  345 MET
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain B residue  648 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  488 LEU
Chi-restraints excluded: chain A residue  648 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0020
   chunk 63 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0050
   chunk 8 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 58 optimal weight:   20.0000
   overall best weight:    0.6004

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

Flipped N/Q/H residues before XYZ refinement:
** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 118 ASN ** 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 = 0.3321 r_free = 0.3321 target = 0.078567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.069049 restraints weight = 32153.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.071186 restraints weight = 16549.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.072610 restraints weight = 10070.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.4471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9192  Z= 0.106
  Angle     :  0.562   9.530  12400  Z= 0.279
  Chirality :  0.039   0.133   1388
  Planarity :  0.003   0.037   1596
  Dihedral  :  7.649  57.137   1346
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 14.97 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.26), residues: 1174
  helix:  2.22 (0.19), residues: 706
  sheet: -0.10 (0.63), residues: 72
  loop :  0.46 (0.36), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 607 
 HIS   0.005   0.001   HIS B 182 
 PHE   0.013   0.001   PHE B 422 
 TYR   0.008   0.001   TYR B 392 
 ARG   0.002   0.000   ARG B 532 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03991 (  569)
  hydrogen bonds       : angle       3.76876 ( 1647)
  covalent geometry    : bond        0.00223 ( 9192)
  covalent geometry    : angle       0.56248 (12400)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2447.09 seconds
wall clock time: 44 minutes 4.09 seconds (2644.09 seconds total)