Starting phenix.real_space_refine
on Tue Jul 29 07:43:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6out_20205/07_2025/6out_20205.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6out_20205/07_2025/6out_20205.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6out_20205/07_2025/6out_20205.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6out_20205/07_2025/6out_20205.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6out_20205/07_2025/6out_20205.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6out_20205/07_2025/6out_20205.cif"
  }
  resolution = 2.6
  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=   0.005 sd=   0.060
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: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    7203      2.51       5
     N    1904      2.21       5
     O    2344      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11505
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3721
          Classifications: {'peptide': 492}
          Link IDs: {'PTRANS': 51, 'TRANS': 440}
    Chain: "B"
      Number of atoms: 3843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 511, 3843
          Classifications: {'peptide': 511}
          Link IDs: {'PTRANS': 52, 'TRANS': 458}
    Chain: "C"
      Number of atoms: 3715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 491, 3715
          Classifications: {'peptide': 491}
          Link IDs: {'PTRANS': 51, 'TRANS': 439}
    Chain: "A"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 71
          Classifications: {'water': 71}
          Link IDs: {None: 70}
    Chain: "B"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 84
          Classifications: {'water': 84}
          Link IDs: {None: 83}
    Chain: "C"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 71
          Classifications: {'water': 71}
          Link IDs: {None: 70}
  Time building chain proxies: 7.02, per 1000 atoms: 0.61
  Number of scatterers: 11505
  At special positions: 0
  Unit cell: (97.37, 110.21, 104.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    2344      8.00
     N    1904      7.00
     C    7203      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: 2.43
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2700

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 19 sheets defined
      11.6% alpha, 26.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 86 through 89
    Processing helix  chain 'A' and resid 90 through 97
    Processing helix  chain 'A' and resid 98 through 100
      No H-bonds generated for 'chain 'A' and resid 98 through 100'
    Processing helix  chain 'A' and resid 138 through 143
    Processing helix  chain 'A' and resid 225 through 229
      removed outlier: 3.813A  pdb=" N   THR A 228 " --> pdb=" O   GLU A 225 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ARG A 229 " --> pdb=" O   GLN A 226 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 225 through 229'
    Processing helix  chain 'A' and resid 237 through 241
    Processing helix  chain 'A' and resid 283 through 287
      removed outlier: 3.564A  pdb=" N   HIS A 286 " --> pdb=" O   SER A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 448
    Processing helix  chain 'A' and resid 491 through 495
      removed outlier: 3.640A  pdb=" N   GLN A 494 " --> pdb=" O   GLY A 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 42
      removed outlier: 3.707A  pdb=" N   THR B  41 " --> pdb=" O   GLY B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 58
      removed outlier: 3.771A  pdb=" N   ILE B  57 " --> pdb=" O   ASP B  53 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ASN B  58 " --> pdb=" O   PRO B  54 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 53 through 58'
    Processing helix  chain 'B' and resid 86 through 89
      removed outlier: 3.518A  pdb=" N   LEU B  89 " --> pdb=" O   GLY B  86 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 86 through 89'
    Processing helix  chain 'B' and resid 90 through 97
    Processing helix  chain 'B' and resid 98 through 100
      No H-bonds generated for 'chain 'B' and resid 98 through 100'
    Processing helix  chain 'B' and resid 140 through 145
      removed outlier: 3.574A  pdb=" N   PHE B 145 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 229
      removed outlier: 3.783A  pdb=" N   THR B 228 " --> pdb=" O   GLU B 225 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ARG B 229 " --> pdb=" O   GLN B 226 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 225 through 229'
    Processing helix  chain 'B' and resid 237 through 241
    Processing helix  chain 'B' and resid 283 through 287
      removed outlier: 3.585A  pdb=" N   HIS B 286 " --> pdb=" O   SER B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 448
    Processing helix  chain 'B' and resid 491 through 495
      removed outlier: 3.654A  pdb=" N   GLN B 494 " --> pdb=" O   GLY B 491 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 38 through 43
      removed outlier: 3.844A  pdb=" N   THR C  41 " --> pdb=" O   GLY C  38 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL C  43 " --> pdb=" O   SER C  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 98 through 100
      No H-bonds generated for 'chain 'C' and resid 98 through 100'
    Processing helix  chain 'C' and resid 138 through 143
    Processing helix  chain 'C' and resid 225 through 229
      removed outlier: 3.561A  pdb=" N   THR C 228 " --> pdb=" O   GLU C 225 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ARG C 229 " --> pdb=" O   GLN C 226 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 225 through 229'
    Processing helix  chain 'C' and resid 237 through 241
    Processing helix  chain 'C' and resid 283 through 287
      removed outlier: 3.578A  pdb=" N   HIS C 286 " --> pdb=" O   SER C 283 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 438 through 448
    Processing helix  chain 'C' and resid 491 through 495
      removed outlier: 3.635A  pdb=" N   LEU C 495 " --> pdb=" O   PRO C 492 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 70
      removed outlier: 12.482A  pdb=" N   GLN A  62 " --> pdb=" O   PRO A 210 " (cutoff:3.500A)
      removed outlier: 10.634A  pdb=" N   THR A 208 " --> pdb=" O   PRO A  64 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   GLY A  66 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ALA A 203 " --> pdb=" O   ALA A 114 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 84
      removed outlier: 7.289A  pdb=" N   VAL A  79 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   LEU A 186 " --> pdb=" O   VAL A  79 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   PHE A  81 " --> pdb=" O   CYS A 184 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172
    Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 120
    Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 255
      removed outlier: 4.189A  pdb=" N   TYR A 431 " --> pdb=" O   MET A 425 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 255
      removed outlier: 4.808A  pdb=" N   LEU A 481 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   PHE A 480 " --> pdb=" O   TYR A 476 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   TYR A 461 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   GLU A 472 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   LEU A 459 " --> pdb=" O   GLU A 472 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   LYS A 474 " --> pdb=" O   ALA A 457 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   ALA A 457 " --> pdb=" O   LYS A 474 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ALA A 456 " --> pdb=" O   TRP A 506 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   TRP A 506 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   LEU A 458 " --> pdb=" O   VAL A 504 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 344
      removed outlier: 4.092A  pdb=" N   TRP A 375 " --> pdb=" O   HIS A 329 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   ASN A 331 " --> pdb=" O   LEU A 373 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   LEU A 373 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   THR A 333 " --> pdb=" O   GLY A 371 " (cutoff:3.500A)
      removed outlier: 5.230A  pdb=" N   GLY A 371 " --> pdb=" O   THR A 333 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 12
      removed outlier: 6.040A  pdb=" N   ALA C 120 " --> pdb=" O   PRO C 189 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   LYS C 122 " --> pdb=" O   TYR C 187 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   LEU C 182 " --> pdb=" O   ASP C  82 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ASP C  82 " --> pdb=" O   LEU C 182 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   CYS C 184 " --> pdb=" O   LEU C  80 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 61 through 70
      removed outlier: 12.625A  pdb=" N   GLN B  62 " --> pdb=" O   PRO B 210 " (cutoff:3.500A)
      removed outlier: 10.610A  pdb=" N   THR B 208 " --> pdb=" O   PRO B  64 " (cutoff:3.500A)
      removed outlier: 5.059A  pdb=" N   GLY B  66 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 79 through 84
      removed outlier: 6.750A  pdb=" N   CYS B 184 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   ASP B  82 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   LEU B 182 " --> pdb=" O   ASP B  82 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   LYS B 122 " --> pdb=" O   TYR B 187 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   ALA B 120 " --> pdb=" O   PRO B 189 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 103 through 104
    Processing sheet with id=AB3, first strand: chain 'B' and resid 252 through 254
      removed outlier: 4.305A  pdb=" N   TYR B 431 " --> pdb=" O   MET B 425 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254
      removed outlier: 4.846A  pdb=" N   LEU B 481 " --> pdb=" O   VAL B 419 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   PHE B 480 " --> pdb=" O   TYR B 476 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLY B 471 " --> pdb=" O   TYR B 461 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ALA B 456 " --> pdb=" O   TRP B 506 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   TRP B 506 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   LEU B 458 " --> pdb=" O   VAL B 504 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 341 through 344
      removed outlier: 7.616A  pdb=" N   HIS B 329 " --> pdb=" O   SER B 374 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   SER B 374 " --> pdb=" O   HIS B 329 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 61 through 70
      removed outlier: 12.667A  pdb=" N   GLN C  62 " --> pdb=" O   PRO C 210 " (cutoff:3.500A)
      removed outlier: 11.117A  pdb=" N   THR C 208 " --> pdb=" O   PRO C  64 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   GLY C  66 " --> pdb=" O   VAL C 206 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ALA C 203 " --> pdb=" O   ALA C 114 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 171 through 172
      removed outlier: 3.541A  pdb=" N   TRP C 103 " --> pdb=" O   HIS C 171 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 250 through 254
      removed outlier: 7.946A  pdb=" N   ILE C 250 " --> pdb=" O   LYS C 424 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   LYS C 424 " --> pdb=" O   ILE C 250 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   TYR C 431 " --> pdb=" O   MET C 425 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 250 through 254
      removed outlier: 7.946A  pdb=" N   ILE C 250 " --> pdb=" O   LYS C 424 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   LYS C 424 " --> pdb=" O   ILE C 250 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   LEU C 481 " --> pdb=" O   VAL C 419 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   PHE C 480 " --> pdb=" O   TYR C 476 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   TYR C 461 " --> pdb=" O   LEU C 470 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   GLU C 472 " --> pdb=" O   LEU C 459 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   LEU C 459 " --> pdb=" O   GLU C 472 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   LYS C 474 " --> pdb=" O   ALA C 457 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ALA C 457 " --> pdb=" O   LYS C 474 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA C 456 " --> pdb=" O   VAL C 507 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   SER C 505 " --> pdb=" O   LEU C 458 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   HIS C 460 " --> pdb=" O   PHE C 503 " (cutoff:3.500A)
      removed outlier: 5.667A  pdb=" N   PHE C 503 " --> pdb=" O   HIS C 460 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   VAL C 462 " --> pdb=" O   PHE C 501 " (cutoff:3.500A)
      removed outlier: 5.666A  pdb=" N   PHE C 501 " --> pdb=" O   VAL C 462 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 341 through 343
      removed outlier: 7.508A  pdb=" N   HIS C 329 " --> pdb=" O   SER C 374 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   SER C 374 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)

    287 hydrogen bonds defined for protein.
    705 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: 3.50

  Time building geometry restraints manager: 2.99 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3470
        1.33 -     1.45: 1808
        1.45 -     1.57: 6257
        1.57 -     1.69: 0
        1.69 -     1.81: 87
  Bond restraints: 11622
  Sorted by residual:
  bond pdb=" C   ALA B 475 "
       pdb=" N   TYR B 476 "
    ideal  model  delta    sigma   weight residual
    1.327  1.282  0.045 1.39e-02 5.18e+03 1.03e+01
  bond pdb=" C   HIS A 381 "
       pdb=" N   PRO A 382 "
    ideal  model  delta    sigma   weight residual
    1.335  1.370 -0.034 1.30e-02 5.92e+03 7.00e+00
  bond pdb=" C   HIS B 381 "
       pdb=" N   PRO B 382 "
    ideal  model  delta    sigma   weight residual
    1.334  1.395 -0.061 2.34e-02 1.83e+03 6.81e+00
  bond pdb=" C   HIS C 381 "
       pdb=" N   PRO C 382 "
    ideal  model  delta    sigma   weight residual
    1.334  1.393 -0.059 2.34e-02 1.83e+03 6.46e+00
  bond pdb=" CA  ILE A 392 "
       pdb=" C   ILE A 392 "
    ideal  model  delta    sigma   weight residual
    1.524  1.499  0.026 1.05e-02 9.07e+03 5.98e+00
  ... (remaining 11617 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 15472
        2.37 -     4.74: 415
        4.74 -     7.11: 44
        7.11 -     9.47: 12
        9.47 -    11.84: 1
  Bond angle restraints: 15944
  Sorted by residual:
  angle pdb=" C   ILE A 392 "
        pdb=" N   PRO A 393 "
        pdb=" CA  PRO A 393 "
      ideal   model   delta    sigma   weight residual
     119.78  128.40   -8.62 1.03e+00 9.43e-01 7.01e+01
  angle pdb=" N   PRO A 382 "
        pdb=" CA  PRO A 382 "
        pdb=" C   PRO A 382 "
      ideal   model   delta    sigma   weight residual
     113.47  122.55   -9.08 1.43e+00 4.89e-01 4.04e+01
  angle pdb=" N   THR B 348 "
        pdb=" CA  THR B 348 "
        pdb=" C   THR B 348 "
      ideal   model   delta    sigma   weight residual
     113.16  120.82   -7.66 1.42e+00 4.96e-01 2.91e+01
  angle pdb=" N   GLY A 396 "
        pdb=" CA  GLY A 396 "
        pdb=" C   GLY A 396 "
      ideal   model   delta    sigma   weight residual
     111.36  117.28   -5.92 1.17e+00 7.31e-01 2.56e+01
  angle pdb=" N   GLY B  19 "
        pdb=" CA  GLY B  19 "
        pdb=" C   GLY B  19 "
      ideal   model   delta    sigma   weight residual
     115.30  121.63   -6.33 1.39e+00 5.18e-01 2.08e+01
  ... (remaining 15939 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 6317
       17.85 -    35.70: 448
       35.70 -    53.55: 70
       53.55 -    71.40: 8
       71.40 -    89.25: 6
  Dihedral angle restraints: 6849
    sinusoidal: 2625
      harmonic: 4224
  Sorted by residual:
  dihedral pdb=" CA  THR B 223 "
           pdb=" C   THR B 223 "
           pdb=" N   VAL B 224 "
           pdb=" CA  VAL B 224 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.82  -25.18     0      5.00e+00 4.00e-02 2.54e+01
  dihedral pdb=" CA  ASP B 198 "
           pdb=" C   ASP B 198 "
           pdb=" N   SER B 199 "
           pdb=" CA  SER B 199 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.71   24.29     0      5.00e+00 4.00e-02 2.36e+01
  dihedral pdb=" CA  HIS A 329 "
           pdb=" C   HIS A 329 "
           pdb=" N   ILE A 330 "
           pdb=" CA  ILE A 330 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.66  -23.34     0      5.00e+00 4.00e-02 2.18e+01
  ... (remaining 6846 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1517
       0.082 -    0.165: 249
       0.165 -    0.247: 18
       0.247 -    0.329: 2
       0.329 -    0.412: 1
  Chirality restraints: 1787
  Sorted by residual:
  chirality pdb=" CB  VAL A 220 "
            pdb=" CA  VAL A 220 "
            pdb=" CG1 VAL A 220 "
            pdb=" CG2 VAL A 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.22   -0.41 2.00e-01 2.50e+01 4.23e+00
  chirality pdb=" CA  GLN B  20 "
            pdb=" N   GLN B  20 "
            pdb=" C   GLN B  20 "
            pdb=" CB  GLN B  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" CA  PRO A 382 "
            pdb=" N   PRO A 382 "
            pdb=" C   PRO A 382 "
            pdb=" CB  PRO A 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.26 2.00e-01 2.50e+01 1.73e+00
  ... (remaining 1784 not shown)

  Planarity restraints: 2123
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  63 "    0.043 5.00e-02 4.00e+02   6.52e-02 6.79e+00
        pdb=" N   PRO A  64 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A  64 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A  64 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 377 "   -0.042 5.00e-02 4.00e+02   6.32e-02 6.39e+00
        pdb=" N   PRO A 378 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 378 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 378 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 211 "    0.041 5.00e-02 4.00e+02   6.22e-02 6.19e+00
        pdb=" N   PRO C 212 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO C 212 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C 212 "    0.034 5.00e-02 4.00e+02
  ... (remaining 2120 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 215
        2.66 -     3.22: 9398
        3.22 -     3.78: 17367
        3.78 -     4.34: 25308
        4.34 -     4.90: 41012
  Nonbonded interactions: 93300
  Sorted by model distance:
  nonbonded pdb=" O   GLN C 264 "
            pdb=" CG2 ILE C 392 "
     model   vdw
     2.099 3.460
  nonbonded pdb=" O   PRO A 249 "
            pdb=" O   HOH A 601 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   ASP A 478 "
            pdb=" O   HOH A 602 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OE1 GLN A 264 "
            pdb=" O   HOH A 603 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   THR B 179 "
            pdb=" O   HOH B 601 "
     model   vdw
     2.240 3.040
  ... (remaining 93295 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 29 through 519)
  selection = (chain 'B' and resid 29 through 519)
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     28.090
  Find NCS groups from input model:        0.530
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
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      :  0.007   0.070  11622  Z= 0.286
  Angle     :  0.926  11.843  15944  Z= 0.532
  Chirality :  0.061   0.412   1787
  Planarity :  0.010   0.065   2123
  Dihedral  : 12.598  89.251   4149
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.18), residues: 1488
  helix: -2.80 (0.42), residues: 76
  sheet:  0.09 (0.24), residues: 382
  loop : -2.02 (0.15), residues: 1030

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.004   TRP A 328 
 HIS   0.009   0.001   HIS A 329 
 PHE   0.027   0.003   PHE A 200 
 TYR   0.014   0.002   TYR A 369 
 ARG   0.008   0.001   ARG B 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16932 (  275)
  hydrogen bonds       : angle       7.51345 (  705)
  covalent geometry    : bond        0.00656 (11622)
  covalent geometry    : angle       0.92555 (15944)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 MET cc_start: 0.8320 (mtt) cc_final: 0.7910 (mtp)
REVERT: A  416 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8172 (mt-10)
REVERT: A  440 GLU cc_start: 0.8612 (mp0) cc_final: 0.8339 (mp0)
REVERT: C  227 LYS cc_start: 0.8891 (mttt) cc_final: 0.8491 (mmtt)
REVERT: C  282 VAL cc_start: 0.8914 (m) cc_final: 0.8654 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 1.1969
  time to fit residues: 286.4452
Evaluate side-chains
  164 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 125 optimal weight:    7.9990
   chunk 112 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 76 optimal weight:    3.9990
   chunk 60 optimal weight:    8.9990
   chunk 116 optimal weight:    8.9990
   chunk 45 optimal weight:    9.9990
   chunk 71 optimal weight:    9.9990
   chunk 86 optimal weight:    1.9990
   chunk 135 optimal weight:    0.0970
   overall best weight:    4.0186

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

Flipped N/Q/H residues before XYZ refinement:
A  50 ASN
A  74 ASN
A 106 ASN
A 259 ASN
A 266 GLN
B  58 ASN
B  74 ASN
B  95 HIS
B 171 HIS
B 355 HIS
B 460 HIS
B 469 ASN
B 512 GLN
C 171 HIS
C 177 GLN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.141046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.110604 restraints weight = 13433.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 1.96
r_work: 0.3124 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.1270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11622  Z= 0.140
  Angle     :  0.617   7.796  15944  Z= 0.317
  Chirality :  0.048   0.147   1787
  Planarity :  0.007   0.051   2123
  Dihedral  :  5.566  21.984   1569
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.16 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  :  9.48 %
    Favored  : 88.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.19), residues: 1488
  helix: -1.47 (0.54), residues: 82
  sheet:  0.42 (0.25), residues: 385
  loop : -1.40 (0.17), residues: 1021

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 328 
 HIS   0.006   0.001   HIS C 355 
 PHE   0.021   0.001   PHE A 200 
 TYR   0.011   0.002   TYR A 476 
 ARG   0.003   0.000   ARG B 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04083 (  275)
  hydrogen bonds       : angle       6.04343 (  705)
  covalent geometry    : bond        0.00344 (11622)
  covalent geometry    : angle       0.61682 (15944)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 188
  time to evaluate  : 1.250 
Fit side-chains
REVERT: A  185 MET cc_start: 0.9168 (mtt) cc_final: 0.8861 (mtp)
REVERT: A  327 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7724 (m-30)
REVERT: A  386 GLN cc_start: 0.7839 (mp10) cc_final: 0.7566 (mm110)
REVERT: A  416 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8229 (mt-10)
REVERT: B  468 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8154 (ttp-170)
REVERT: C  227 LYS cc_start: 0.9207 (mttt) cc_final: 0.8502 (mmtt)
REVERT: C  273 ASP cc_start: 0.8172 (m-30) cc_final: 0.7785 (m-30)
REVERT: C  282 VAL cc_start: 0.9120 (m) cc_final: 0.8878 (t)
REVERT: C  302 THR cc_start: 0.7832 (p) cc_final: 0.7284 (t)
REVERT: C  449 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7496 (mm110)
  outliers start: 30
  outliers final: 11
  residues processed: 199
  average time/residue: 1.2367
  time to fit residues: 266.9319
Evaluate side-chains
  183 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 169
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 ASP
Chi-restraints excluded: chain A residue  463 ASP
Chi-restraints excluded: chain B residue   58 ASN
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  468 ARG
Chi-restraints excluded: chain C residue   45 THR
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  277 VAL
Chi-restraints excluded: chain C residue  392 ILE
Chi-restraints excluded: chain C residue  449 GLN
Chi-restraints excluded: chain C residue  497 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 27 optimal weight:    7.9990
   chunk 12 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 89 optimal weight:   20.0000
   chunk 34 optimal weight:   20.0000
   chunk 115 optimal weight:    7.9990
   chunk 114 optimal weight:    0.9980
   chunk 138 optimal weight:   40.0000
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:   30.0000
   overall best weight:    6.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
B 116 ASN
C  50 ASN
C 173 ASN
C 177 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.138712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.108084 restraints weight = 13682.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.09
r_work: 0.3078 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  11622  Z= 0.187
  Angle     :  0.662   9.141  15944  Z= 0.338
  Chirality :  0.050   0.168   1787
  Planarity :  0.007   0.052   2123
  Dihedral  :  5.550  23.471   1569
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 10.27 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.20), residues: 1488
  helix: -1.01 (0.56), residues: 82
  sheet:  0.50 (0.25), residues: 385
  loop : -1.17 (0.18), residues: 1021

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 328 
 HIS   0.006   0.001   HIS C 355 
 PHE   0.026   0.002   PHE A 200 
 TYR   0.014   0.002   TYR C 431 
 ARG   0.003   0.000   ARG C 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04261 (  275)
  hydrogen bonds       : angle       5.93565 (  705)
  covalent geometry    : bond        0.00471 (11622)
  covalent geometry    : angle       0.66216 (15944)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 164
  time to evaluate  : 1.342 
Fit side-chains
REVERT: A  185 MET cc_start: 0.9225 (mtt) cc_final: 0.8914 (mtp)
REVERT: A  416 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8367 (mt-10)
REVERT: B   31 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8314 (tp)
REVERT: B  295 ASN cc_start: 0.7941 (t0) cc_final: 0.7334 (p0)
REVERT: B  468 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8166 (ttp-170)
REVERT: C   33 MET cc_start: 0.9108 (mtp) cc_final: 0.8878 (mtp)
REVERT: C  181 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8041 (ptm-80)
REVERT: C  227 LYS cc_start: 0.9231 (mttt) cc_final: 0.8528 (mmtt)
REVERT: C  273 ASP cc_start: 0.8168 (m-30) cc_final: 0.7729 (m-30)
REVERT: C  282 VAL cc_start: 0.9172 (m) cc_final: 0.8935 (t)
REVERT: C  302 THR cc_start: 0.7843 (p) cc_final: 0.7324 (t)
REVERT: C  449 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7600 (mm110)
  outliers start: 43
  outliers final: 21
  residues processed: 188
  average time/residue: 1.4055
  time to fit residues: 287.2645
Evaluate side-chains
  195 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 170
  time to evaluate  : 1.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  329 HIS
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue   58 ASN
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  116 ASN
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  468 ARG
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   45 THR
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain C residue  181 ARG
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  275 ARG
Chi-restraints excluded: chain C residue  277 VAL
Chi-restraints excluded: chain C residue  392 ILE
Chi-restraints excluded: chain C residue  409 VAL
Chi-restraints excluded: chain C residue  449 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 90 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0040
   chunk 130 optimal weight:   20.0000
   chunk 54 optimal weight:   10.0000
   chunk 141 optimal weight:   20.0000
   chunk 123 optimal weight:    0.0040
   chunk 106 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 107 optimal weight:    2.9990
   chunk 133 optimal weight:    9.9990
   overall best weight:    3.0010

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 116 ASN
C 177 GLN
C 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.141069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.110148 restraints weight = 13535.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 1.76
r_work: 0.3132 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3026 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11622  Z= 0.115
  Angle     :  0.573   7.037  15944  Z= 0.291
  Chirality :  0.047   0.149   1787
  Planarity :  0.006   0.048   2123
  Dihedral  :  5.186  22.879   1569
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.23 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 11.61 %
    Favored  : 86.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.20), residues: 1488
  helix: -0.65 (0.58), residues: 82
  sheet:  0.68 (0.25), residues: 376
  loop : -0.94 (0.18), residues: 1030

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 328 
 HIS   0.005   0.001   HIS C 355 
 PHE   0.017   0.001   PHE A 200 
 TYR   0.010   0.001   TYR C 431 
 ARG   0.003   0.000   ARG A 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03427 (  275)
  hydrogen bonds       : angle       5.65345 (  705)
  covalent geometry    : bond        0.00284 (11622)
  covalent geometry    : angle       0.57292 (15944)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 173
  time to evaluate  : 1.831 
Fit side-chains
REVERT: A  416 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8223 (mt-10)
REVERT: B  229 ARG cc_start: 0.8741 (ttm-80) cc_final: 0.8536 (ttm-80)
REVERT: B  295 ASN cc_start: 0.7847 (t0) cc_final: 0.7426 (p0)
REVERT: B  468 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8127 (ttp-170)
REVERT: C   33 MET cc_start: 0.9071 (mtp) cc_final: 0.8795 (mtp)
REVERT: C  181 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7832 (ptm-80)
REVERT: C  227 LYS cc_start: 0.9202 (mttt) cc_final: 0.8533 (mmtt)
REVERT: C  273 ASP cc_start: 0.8109 (m-30) cc_final: 0.7669 (m-30)
REVERT: C  302 THR cc_start: 0.7765 (p) cc_final: 0.7437 (t)
  outliers start: 30
  outliers final: 16
  residues processed: 193
  average time/residue: 1.3854
  time to fit residues: 289.3330
Evaluate side-chains
  193 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 176
  time to evaluate  : 1.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  329 HIS
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   45 THR
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain C residue  181 ARG
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  277 VAL
Chi-restraints excluded: chain C residue  409 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0770
   chunk 66 optimal weight:   20.0000
   chunk 24 optimal weight:    7.9990
   chunk 86 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 60 optimal weight:   20.0000
   chunk 5 optimal weight:   20.0000
   chunk 137 optimal weight:    2.9990
   overall best weight:    2.9544

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 259 ASN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  58 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.141579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.110606 restraints weight = 13545.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 1.77
r_work: 0.3139 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3033 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11622  Z= 0.113
  Angle     :  0.562   6.174  15944  Z= 0.284
  Chirality :  0.046   0.147   1787
  Planarity :  0.006   0.047   2123
  Dihedral  :  4.994  22.299   1569
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 11.85 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.21), residues: 1488
  helix: -0.42 (0.58), residues: 82
  sheet:  0.73 (0.25), residues: 373
  loop : -0.75 (0.18), residues: 1033

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 328 
 HIS   0.004   0.001   HIS C 355 
 PHE   0.015   0.001   PHE A 200 
 TYR   0.011   0.001   TYR C 431 
 ARG   0.003   0.000   ARG A 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03304 (  275)
  hydrogen bonds       : angle       5.51506 (  705)
  covalent geometry    : bond        0.00284 (11622)
  covalent geometry    : angle       0.56218 (15944)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 179
  time to evaluate  : 1.286 
Fit side-chains
REVERT: A  416 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8133 (mt-10)
REVERT: B   31 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8348 (tp)
REVERT: B  295 ASN cc_start: 0.7783 (t0) cc_final: 0.7491 (p0)
REVERT: B  329 HIS cc_start: 0.6668 (OUTLIER) cc_final: 0.5723 (p-80)
REVERT: C   33 MET cc_start: 0.9063 (mtp) cc_final: 0.8846 (mtp)
REVERT: C  181 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7753 (ptm-80)
REVERT: C  227 LYS cc_start: 0.9206 (mttt) cc_final: 0.8552 (mmtt)
REVERT: C  273 ASP cc_start: 0.8119 (m-30) cc_final: 0.7665 (m-30)
REVERT: C  275 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8075 (mtm-85)
REVERT: C  302 THR cc_start: 0.7743 (p) cc_final: 0.7477 (t)
REVERT: C  468 ARG cc_start: 0.8041 (ttm170) cc_final: 0.7801 (ttt-90)
  outliers start: 41
  outliers final: 19
  residues processed: 203
  average time/residue: 1.2106
  time to fit residues: 265.9655
Evaluate side-chains
  180 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  329 HIS
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  375 TRP
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  329 HIS
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   45 THR
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain C residue  181 ARG
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  275 ARG
Chi-restraints excluded: chain C residue  277 VAL
Chi-restraints excluded: chain C residue  392 ILE
Chi-restraints excluded: chain C residue  409 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 9 optimal weight:   20.0000
   chunk 62 optimal weight:    7.9990
   chunk 57 optimal weight:   10.0000
   chunk 75 optimal weight:    4.9990
   chunk 99 optimal weight:    9.9990
   chunk 71 optimal weight:    8.9990
   chunk 118 optimal weight:    9.9990
   chunk 102 optimal weight:    0.0370
   chunk 11 optimal weight:    5.9990
   chunk 51 optimal weight:   20.0000
   overall best weight:    5.2066

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 259 ASN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  58 ASN
B 116 ASN
C 135 HIS
C 178 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.139693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.108486 restraints weight = 13546.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 1.77
r_work: 0.3105 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2998 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11622  Z= 0.157
  Angle     :  0.613   7.909  15944  Z= 0.311
  Chirality :  0.048   0.150   1787
  Planarity :  0.006   0.049   2123
  Dihedral  :  5.188  23.992   1569
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 12.56 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.20), residues: 1488
  helix: -0.52 (0.57), residues: 82
  sheet:  0.75 (0.25), residues: 372
  loop : -0.74 (0.18), residues: 1034

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 328 
 HIS   0.004   0.001   HIS C 355 
 PHE   0.025   0.002   PHE B 312 
 TYR   0.012   0.002   TYR B 343 
 ARG   0.003   0.000   ARG A 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03824 (  275)
  hydrogen bonds       : angle       5.64582 (  705)
  covalent geometry    : bond        0.00391 (11622)
  covalent geometry    : angle       0.61280 (15944)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 163
  time to evaluate  : 1.382 
Fit side-chains
REVERT: A  261 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7701 (mp10)
REVERT: B   31 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8390 (tp)
REVERT: B  295 ASN cc_start: 0.7816 (t0) cc_final: 0.7464 (p0)
REVERT: B  329 HIS cc_start: 0.6935 (OUTLIER) cc_final: 0.6019 (p-80)
REVERT: B  468 ARG cc_start: 0.8563 (mtm180) cc_final: 0.8249 (ttp-170)
REVERT: C   33 MET cc_start: 0.9062 (mtp) cc_final: 0.8809 (mtp)
REVERT: C  227 LYS cc_start: 0.9214 (mttt) cc_final: 0.8552 (mmtt)
REVERT: C  273 ASP cc_start: 0.8116 (m-30) cc_final: 0.7659 (m-30)
REVERT: C  275 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.8053 (mtm-85)
REVERT: C  302 THR cc_start: 0.7724 (p) cc_final: 0.7457 (t)
REVERT: C  329 HIS cc_start: 0.6112 (OUTLIER) cc_final: 0.5771 (p-80)
REVERT: C  455 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7787 (tt0)
REVERT: C  468 ARG cc_start: 0.7981 (ttm170) cc_final: 0.7746 (ttt-90)
  outliers start: 37
  outliers final: 20
  residues processed: 189
  average time/residue: 1.1761
  time to fit residues: 241.7811
Evaluate side-chains
  198 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 172
  time to evaluate  : 1.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  261 GLN
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  329 HIS
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  375 TRP
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  329 HIS
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   45 THR
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain C residue  181 ARG
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  275 ARG
Chi-restraints excluded: chain C residue  277 VAL
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  329 HIS
Chi-restraints excluded: chain C residue  409 VAL
Chi-restraints excluded: chain C residue  455 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 137 optimal weight:    1.9990
   chunk 109 optimal weight:    6.9990
   chunk 122 optimal weight:   20.0000
   chunk 64 optimal weight:   10.0000
   chunk 114 optimal weight:    7.9990
   chunk 6 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   chunk 48 optimal weight:    7.9990
   chunk 129 optimal weight:    0.0570
   overall best weight:    4.4106

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 259 ASN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  58 ASN
B 116 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.139988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.109656 restraints weight = 13666.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 1.94
r_work: 0.3112 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11622  Z= 0.141
  Angle     :  0.596   7.030  15944  Z= 0.303
  Chirality :  0.048   0.157   1787
  Planarity :  0.006   0.054   2123
  Dihedral  :  5.126  24.017   1569
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.35 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.21), residues: 1488
  helix: -0.44 (0.58), residues: 82
  sheet:  0.79 (0.25), residues: 372
  loop : -0.68 (0.18), residues: 1034

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 328 
 HIS   0.004   0.001   HIS C 355 
 PHE   0.028   0.001   PHE B 312 
 TYR   0.012   0.002   TYR C 431 
 ARG   0.003   0.000   ARG A 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03589 (  275)
  hydrogen bonds       : angle       5.57575 (  705)
  covalent geometry    : bond        0.00351 (11622)
  covalent geometry    : angle       0.59641 (15944)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 170
  time to evaluate  : 1.233 
Fit side-chains
REVERT: A  261 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7713 (mp10)
REVERT: A  416 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8217 (mt-10)
REVERT: B  295 ASN cc_start: 0.7786 (t0) cc_final: 0.7447 (p0)
REVERT: B  329 HIS cc_start: 0.6984 (OUTLIER) cc_final: 0.6126 (p-80)
REVERT: B  468 ARG cc_start: 0.8567 (mtm180) cc_final: 0.8348 (mtp180)
REVERT: B  509 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7954 (ttm-80)
REVERT: C   33 MET cc_start: 0.9085 (mtp) cc_final: 0.8835 (mtp)
REVERT: C  227 LYS cc_start: 0.9214 (mttt) cc_final: 0.8521 (mmtt)
REVERT: C  273 ASP cc_start: 0.8123 (m-30) cc_final: 0.7639 (m-30)
REVERT: C  275 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8018 (mtm-85)
REVERT: C  302 THR cc_start: 0.7510 (p) cc_final: 0.7290 (t)
REVERT: C  455 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7735 (tt0)
  outliers start: 34
  outliers final: 21
  residues processed: 193
  average time/residue: 1.2630
  time to fit residues: 263.5653
Evaluate side-chains
  188 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 162
  time to evaluate  : 1.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  261 GLN
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  329 HIS
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  375 TRP
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  329 HIS
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  509 ARG
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   45 THR
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain C residue  181 ARG
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  275 ARG
Chi-restraints excluded: chain C residue  277 VAL
Chi-restraints excluded: chain C residue  327 ASP
Chi-restraints excluded: chain C residue  409 VAL
Chi-restraints excluded: chain C residue  455 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 5 optimal weight:    7.9990
   chunk 135 optimal weight:    4.9990
   chunk 83 optimal weight:    5.9990
   chunk 106 optimal weight:    0.6980
   chunk 141 optimal weight:   20.0000
   chunk 49 optimal weight:    4.9990
   chunk 86 optimal weight:   20.0000
   chunk 28 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    4.5388

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 259 ASN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 116 ASN
C 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.139907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.109605 restraints weight = 13597.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.99
r_work: 0.3107 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11622  Z= 0.143
  Angle     :  0.598   7.418  15944  Z= 0.304
  Chirality :  0.048   0.158   1787
  Planarity :  0.006   0.058   2123
  Dihedral  :  5.119  24.092   1569
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.43 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.21), residues: 1488
  helix: -0.45 (0.57), residues: 82
  sheet:  0.74 (0.25), residues: 376
  loop : -0.64 (0.18), residues: 1030

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 328 
 HIS   0.004   0.001   HIS C 355 
 PHE   0.031   0.001   PHE B 312 
 TYR   0.015   0.002   TYR B 343 
 ARG   0.003   0.000   ARG A 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03630 (  275)
  hydrogen bonds       : angle       5.57537 (  705)
  covalent geometry    : bond        0.00359 (11622)
  covalent geometry    : angle       0.59800 (15944)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 167
  time to evaluate  : 1.232 
Fit side-chains
REVERT: A  261 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7715 (mp10)
REVERT: A  416 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8203 (mt-10)
REVERT: B  295 ASN cc_start: 0.7789 (t0) cc_final: 0.7454 (p0)
REVERT: B  313 GLU cc_start: 0.7795 (pm20) cc_final: 0.7501 (pm20)
REVERT: B  329 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6113 (p-80)
REVERT: B  468 ARG cc_start: 0.8551 (mtm180) cc_final: 0.8339 (mtp180)
REVERT: B  509 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7964 (ttm-80)
REVERT: C   33 MET cc_start: 0.9094 (mtp) cc_final: 0.8814 (mtp)
REVERT: C  163 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8294 (mp0)
REVERT: C  181 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7851 (ptm-80)
REVERT: C  227 LYS cc_start: 0.9196 (mttt) cc_final: 0.8505 (mmtt)
REVERT: C  273 ASP cc_start: 0.8136 (m-30) cc_final: 0.7643 (m-30)
REVERT: C  302 THR cc_start: 0.7496 (p) cc_final: 0.7281 (t)
REVERT: C  455 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7794 (tt0)
REVERT: C  468 ARG cc_start: 0.7951 (ttm170) cc_final: 0.7710 (ttt-90)
  outliers start: 33
  outliers final: 20
  residues processed: 189
  average time/residue: 1.2765
  time to fit residues: 261.3288
Evaluate side-chains
  187 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 162
  time to evaluate  : 1.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  261 GLN
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  329 HIS
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  375 TRP
Chi-restraints excluded: chain B residue   58 ASN
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  329 HIS
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  509 ARG
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   45 THR
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain C residue  181 ARG
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  277 VAL
Chi-restraints excluded: chain C residue  409 VAL
Chi-restraints excluded: chain C residue  455 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 113 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 125 optimal weight:    8.9990
   chunk 75 optimal weight:   20.0000
   chunk 11 optimal weight:    0.0670
   chunk 64 optimal weight:   10.0000
   chunk 68 optimal weight:   20.0000
   chunk 20 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 134 optimal weight:    0.8980
   overall best weight:    1.3522

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 259 ASN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 116 ASN
C 178 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.143828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.113089 restraints weight = 13640.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 1.79
r_work: 0.3169 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  11622  Z= 0.093
  Angle     :  0.522   6.109  15944  Z= 0.264
  Chirality :  0.046   0.169   1787
  Planarity :  0.005   0.062   2123
  Dihedral  :  4.660  21.340   1569
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.14 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.21), residues: 1488
  helix: -0.01 (0.62), residues: 77
  sheet:  0.80 (0.25), residues: 376
  loop : -0.40 (0.19), residues: 1035

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 375 
 HIS   0.003   0.001   HIS C 355 
 PHE   0.026   0.001   PHE B 312 
 TYR   0.008   0.001   TYR C 431 
 ARG   0.002   0.000   ARG B 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02793 (  275)
  hydrogen bonds       : angle       5.27377 (  705)
  covalent geometry    : bond        0.00232 (11622)
  covalent geometry    : angle       0.52208 (15944)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 171
  time to evaluate  : 1.514 
Fit side-chains
REVERT: A  416 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8047 (mt-10)
REVERT: B  313 GLU cc_start: 0.7754 (pm20) cc_final: 0.7502 (pm20)
REVERT: B  329 HIS cc_start: 0.6800 (OUTLIER) cc_final: 0.5944 (p-80)
REVERT: B  468 ARG cc_start: 0.8535 (mtm180) cc_final: 0.8323 (mtp180)
REVERT: C   33 MET cc_start: 0.9083 (mtp) cc_final: 0.8832 (mtp)
REVERT: C  163 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8107 (mp0)
REVERT: C  227 LYS cc_start: 0.9094 (mttt) cc_final: 0.8444 (mmtt)
REVERT: C  273 ASP cc_start: 0.8133 (m-30) cc_final: 0.7660 (m-30)
REVERT: C  275 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7986 (mtm-85)
REVERT: C  313 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.5799 (mm-30)
  outliers start: 26
  outliers final: 16
  residues processed: 189
  average time/residue: 1.5691
  time to fit residues: 320.9365
Evaluate side-chains
  181 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 162
  time to evaluate  : 2.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  329 HIS
Chi-restraints excluded: chain A residue  375 TRP
Chi-restraints excluded: chain A residue  510 PHE
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  262 SER
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  329 HIS
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain C residue   45 THR
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  275 ARG
Chi-restraints excluded: chain C residue  277 VAL
Chi-restraints excluded: chain C residue  313 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 90 optimal weight:    7.9990
   chunk 100 optimal weight:    0.0980
   chunk 52 optimal weight:    0.0470
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:    0.6980
   chunk 91 optimal weight:   10.0000
   chunk 83 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 99 optimal weight:    0.4980
   chunk 141 optimal weight:   20.0000
   chunk 8 optimal weight:   10.0000
   overall best weight:    1.4680

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 259 ASN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 355 HIS
B 116 ASN
C 178 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.143997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.113481 restraints weight = 13533.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.77
r_work: 0.3177 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  11622  Z= 0.093
  Angle     :  0.530   7.527  15944  Z= 0.266
  Chirality :  0.046   0.157   1787
  Planarity :  0.005   0.074   2123
  Dihedral  :  4.535  20.532   1569
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.09 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.21), residues: 1488
  helix:  0.12 (0.62), residues: 77
  sheet:  0.81 (0.25), residues: 376
  loop : -0.30 (0.19), residues: 1035

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 375 
 HIS   0.003   0.001   HIS B  95 
 PHE   0.012   0.001   PHE B 312 
 TYR   0.012   0.001   TYR C 431 
 ARG   0.003   0.000   ARG B 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02814 (  275)
  hydrogen bonds       : angle       5.21770 (  705)
  covalent geometry    : bond        0.00232 (11622)
  covalent geometry    : angle       0.52959 (15944)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 1.270 
Fit side-chains
REVERT: B  329 HIS cc_start: 0.6827 (OUTLIER) cc_final: 0.6013 (p-80)
REVERT: B  468 ARG cc_start: 0.8529 (mtm180) cc_final: 0.8317 (mtp180)
REVERT: C   33 MET cc_start: 0.9074 (mtp) cc_final: 0.8830 (mtp)
REVERT: C  227 LYS cc_start: 0.9070 (mttt) cc_final: 0.8429 (mmtt)
REVERT: C  273 ASP cc_start: 0.8119 (m-30) cc_final: 0.7650 (m-30)
REVERT: C  313 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5788 (mm-30)
REVERT: C  437 LEU cc_start: 0.8203 (mt) cc_final: 0.7998 (mt)
  outliers start: 19
  outliers final: 15
  residues processed: 178
  average time/residue: 1.4856
  time to fit residues: 285.0574
Evaluate side-chains
  179 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 162
  time to evaluate  : 1.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  329 HIS
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  375 TRP
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  329 HIS
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain C residue   45 THR
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain C residue  199 SER
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  277 VAL
Chi-restraints excluded: chain C residue  313 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 16 optimal weight:    0.2980
   chunk 20 optimal weight:    2.9990
   chunk 81 optimal weight:   20.0000
   chunk 126 optimal weight:   30.0000
   chunk 109 optimal weight:    7.9990
   chunk 141 optimal weight:   20.0000
   chunk 28 optimal weight:    0.9990
   chunk 26 optimal weight:    7.9990
   chunk 9 optimal weight:    9.9990
   chunk 57 optimal weight:    9.9990
   overall best weight:    4.0588

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 259 ASN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 116 ASN
B 460 HIS
C 178 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.141239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.110643 restraints weight = 13694.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 1.78
r_work: 0.3132 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11622  Z= 0.135
  Angle     :  0.586   7.357  15944  Z= 0.297
  Chirality :  0.048   0.175   1787
  Planarity :  0.006   0.083   2123
  Dihedral  :  4.780  22.252   1569
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 15.17 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.21), residues: 1488
  helix:  0.11 (0.62), residues: 76
  sheet:  0.78 (0.25), residues: 376
  loop : -0.37 (0.19), residues: 1036

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 328 
 HIS   0.003   0.001   HIS C 355 
 PHE   0.016   0.001   PHE A 200 
 TYR   0.017   0.002   TYR B 343 
 ARG   0.006   0.000   ARG A 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03383 (  275)
  hydrogen bonds       : angle       5.40256 (  705)
  covalent geometry    : bond        0.00340 (11622)
  covalent geometry    : angle       0.58642 (15944)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9690.46 seconds
wall clock time: 173 minutes 47.75 seconds (10427.75 seconds total)