Starting phenix.real_space_refine
on Thu Mar 13 22:18:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d66_46586/03_2025/9d66_46586.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d66_46586/03_2025/9d66_46586.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d66_46586/03_2025/9d66_46586.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d66_46586/03_2025/9d66_46586.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d66_46586/03_2025/9d66_46586.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d66_46586/03_2025/9d66_46586.cif"
  }
  resolution = 2.98
  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=   0.141
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Hg      3     10.96       5
     S      60      5.16       5
     Na      9      4.78       5
     C    6087      2.51       5
     N    1479      2.21       5
     O    1668      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9306
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 406, 3085
          Classifications: {'peptide': 406}
          Link IDs: {'PTRANS': 11, 'TRANS': 394}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' HG': 1, ' NA': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 13
          Unusual residues: {' HG': 1, ' NA': 3}
          Inner-chain residues flagged as termini: ['pdbres="ASP B 603 "']
          Classifications: {'peptide': 1, 'undetermined': 4}
          Modifications used: {'COO': 1}
          Link IDs: {None: 4}
    Chain: "C"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 13
          Unusual residues: {' HG': 1, ' NA': 3}
          Inner-chain residues flagged as termini: ['pdbres="ASP C 603 "']
          Classifications: {'peptide': 1, 'undetermined': 4}
          Modifications used: {'COO': 1}
          Link IDs: {None: 4}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1577  SG  CYS A 269      36.441  24.199  46.434  1.00 69.42           S
  ATOM   2858  SG  CYS A 441      35.971  26.061  44.199  1.00 71.84           S

  Restraints were copied for chains:
    B, C
  Time building chain proxies: 6.14, per 1000 atoms: 0.66
  Number of scatterers: 9306
  At special positions: 0
  Unit cell: (102.08, 107.88, 70.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Hg      3     79.96
     S      60     16.00
     Na      9     11.00
     O    1668      8.00
     N    1479      7.00
     C    6087      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: 2.56
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2256

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 3 sheets defined
      86.7% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 42
      removed outlier: 3.765A  pdb=" N   LEU A  22 " --> pdb=" O   ASN A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.556A  pdb=" N   PHE A  50 " --> pdb=" O   THR A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 81
      removed outlier: 3.644A  pdb=" N   LEU A  59 " --> pdb=" O   PRO A  55 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE A  66 " --> pdb=" O   MET A  62 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   LEU A  68 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
      Proline residue:  A  69  - end of helix
    Processing helix  chain 'A' and resid 84 through 117
      removed outlier: 4.385A  pdb=" N   ILE A  90 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 150
      removed outlier: 3.636A  pdb=" N   LEU A 145 " --> pdb=" O   ALA A 141 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ILE A 146 " --> pdb=" O   MET A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 158
    Processing helix  chain 'A' and resid 211 through 229
    Processing helix  chain 'A' and resid 230 through 232
      No H-bonds generated for 'chain 'A' and resid 230 through 232'
    Processing helix  chain 'A' and resid 233 through 272
      removed outlier: 4.064A  pdb=" N   TRP A 256 " --> pdb=" O   GLN A 252 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   TYR A 257 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      Proline residue:  A 259  - end of helix
      removed outlier: 3.672A  pdb=" N   CYS A 269 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 282
    Processing helix  chain 'A' and resid 282 through 299
    Processing helix  chain 'A' and resid 299 through 309
    Processing helix  chain 'A' and resid 312 through 320
      removed outlier: 3.685A  pdb=" N   PHE A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 331
    Processing helix  chain 'A' and resid 336 through 347
    Processing helix  chain 'A' and resid 351 through 366
      removed outlier: 4.612A  pdb=" N   PHE A 357 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU A 359 " --> pdb=" O   THR A 355 " (cutoff:3.500A)
      Proline residue:  A 360  - end of helix
      removed outlier: 4.455A  pdb=" N   THR A 364 " --> pdb=" O   PRO A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 385
    Processing helix  chain 'A' and resid 390 through 408
    Processing helix  chain 'A' and resid 414 through 426
      removed outlier: 3.564A  pdb=" N   THR A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL A 420 " --> pdb=" O   LEU A 416 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   ILE A 421 " --> pdb=" O   VAL A 417 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL A 422 " --> pdb=" O   THR A 418 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   VAL A 426 " --> pdb=" O   VAL A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 438
      removed outlier: 3.719A  pdb=" N   VAL A 433 " --> pdb=" O   ALA A 430 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   ILE A 437 " --> pdb=" O   THR A 434 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   ALA A 438 " --> pdb=" O   LEU A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 467
      removed outlier: 3.588A  pdb=" N   ARG A 445 " --> pdb=" O   CYS A 441 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE A 446 " --> pdb=" O   LEU A 442 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   MET A 449 " --> pdb=" O   ARG A 445 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ASP A 455 " --> pdb=" O   ASN A 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 42
      removed outlier: 3.765A  pdb=" N   LEU B  22 " --> pdb=" O   ASN B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 53
      removed outlier: 3.557A  pdb=" N   PHE B  50 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 81
      removed outlier: 3.644A  pdb=" N   LEU B  59 " --> pdb=" O   PRO B  55 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE B  66 " --> pdb=" O   MET B  62 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   LEU B  68 " --> pdb=" O   LYS B  64 " (cutoff:3.500A)
      Proline residue:  B  69  - end of helix
    Processing helix  chain 'B' and resid 84 through 117
      removed outlier: 4.385A  pdb=" N   ILE B  90 " --> pdb=" O   VAL B  86 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLY B  91 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 150
      removed outlier: 3.636A  pdb=" N   LEU B 145 " --> pdb=" O   ALA B 141 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ILE B 146 " --> pdb=" O   MET B 142 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   PHE B 150 " --> pdb=" O   ILE B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 158
    Processing helix  chain 'B' and resid 211 through 229
    Processing helix  chain 'B' and resid 230 through 232
      No H-bonds generated for 'chain 'B' and resid 230 through 232'
    Processing helix  chain 'B' and resid 233 through 272
      removed outlier: 4.064A  pdb=" N   TRP B 256 " --> pdb=" O   GLN B 252 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   TYR B 257 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
      Proline residue:  B 259  - end of helix
      removed outlier: 3.672A  pdb=" N   CYS B 269 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 282
    Processing helix  chain 'B' and resid 282 through 299
    Processing helix  chain 'B' and resid 299 through 309
    Processing helix  chain 'B' and resid 312 through 320
      removed outlier: 3.684A  pdb=" N   PHE B 316 " --> pdb=" O   ASN B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 331
    Processing helix  chain 'B' and resid 336 through 347
    Processing helix  chain 'B' and resid 351 through 366
      removed outlier: 4.612A  pdb=" N   PHE B 357 " --> pdb=" O   ARG B 353 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU B 359 " --> pdb=" O   THR B 355 " (cutoff:3.500A)
      Proline residue:  B 360  - end of helix
      removed outlier: 4.454A  pdb=" N   THR B 364 " --> pdb=" O   PRO B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 385
    Processing helix  chain 'B' and resid 390 through 408
    Processing helix  chain 'B' and resid 414 through 426
      removed outlier: 3.565A  pdb=" N   THR B 418 " --> pdb=" O   ALA B 414 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL B 420 " --> pdb=" O   LEU B 416 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   ILE B 421 " --> pdb=" O   VAL B 417 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL B 422 " --> pdb=" O   THR B 418 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   VAL B 426 " --> pdb=" O   VAL B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 438
      removed outlier: 3.719A  pdb=" N   VAL B 433 " --> pdb=" O   ALA B 430 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   ILE B 437 " --> pdb=" O   THR B 434 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   ALA B 438 " --> pdb=" O   LEU B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 467
      removed outlier: 3.589A  pdb=" N   ARG B 445 " --> pdb=" O   CYS B 441 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE B 446 " --> pdb=" O   LEU B 442 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   MET B 449 " --> pdb=" O   ARG B 445 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ASP B 455 " --> pdb=" O   ASN B 451 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 42
      removed outlier: 3.766A  pdb=" N   LEU C  22 " --> pdb=" O   ASN C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 53
      removed outlier: 3.557A  pdb=" N   PHE C  50 " --> pdb=" O   THR C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 81
      removed outlier: 3.644A  pdb=" N   LEU C  59 " --> pdb=" O   PRO C  55 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE C  66 " --> pdb=" O   MET C  62 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   LEU C  68 " --> pdb=" O   LYS C  64 " (cutoff:3.500A)
      Proline residue:  C  69  - end of helix
    Processing helix  chain 'C' and resid 84 through 117
      removed outlier: 4.385A  pdb=" N   ILE C  90 " --> pdb=" O   VAL C  86 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY C  91 " --> pdb=" O   SER C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 150
      removed outlier: 3.635A  pdb=" N   LEU C 145 " --> pdb=" O   ALA C 141 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ILE C 146 " --> pdb=" O   MET C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 158
    Processing helix  chain 'C' and resid 211 through 229
    Processing helix  chain 'C' and resid 230 through 232
      No H-bonds generated for 'chain 'C' and resid 230 through 232'
    Processing helix  chain 'C' and resid 233 through 272
      removed outlier: 4.064A  pdb=" N   TRP C 256 " --> pdb=" O   GLN C 252 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   TYR C 257 " --> pdb=" O   ILE C 253 " (cutoff:3.500A)
      Proline residue:  C 259  - end of helix
      removed outlier: 3.673A  pdb=" N   CYS C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 276 through 282
    Processing helix  chain 'C' and resid 282 through 299
    Processing helix  chain 'C' and resid 299 through 309
    Processing helix  chain 'C' and resid 312 through 320
      removed outlier: 3.684A  pdb=" N   PHE C 316 " --> pdb=" O   ASN C 312 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 320 through 331
    Processing helix  chain 'C' and resid 336 through 347
    Processing helix  chain 'C' and resid 351 through 366
      removed outlier: 4.613A  pdb=" N   PHE C 357 " --> pdb=" O   ARG C 353 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU C 359 " --> pdb=" O   THR C 355 " (cutoff:3.500A)
      Proline residue:  C 360  - end of helix
      removed outlier: 4.455A  pdb=" N   THR C 364 " --> pdb=" O   PRO C 360 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 367 through 385
    Processing helix  chain 'C' and resid 390 through 408
    Processing helix  chain 'C' and resid 414 through 426
      removed outlier: 3.564A  pdb=" N   THR C 418 " --> pdb=" O   ALA C 414 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL C 420 " --> pdb=" O   LEU C 416 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   ILE C 421 " --> pdb=" O   VAL C 417 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL C 422 " --> pdb=" O   THR C 418 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   VAL C 426 " --> pdb=" O   VAL C 422 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 438
      removed outlier: 3.720A  pdb=" N   VAL C 433 " --> pdb=" O   ALA C 430 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   ILE C 437 " --> pdb=" O   THR C 434 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   ALA C 438 " --> pdb=" O   LEU C 435 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 467
      removed outlier: 3.587A  pdb=" N   ARG C 445 " --> pdb=" O   CYS C 441 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE C 446 " --> pdb=" O   LEU C 442 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   MET C 449 " --> pdb=" O   ARG C 445 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ASP C 455 " --> pdb=" O   ASN C 451 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167
    Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 167
    Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 167

    725 hydrogen bonds defined for protein.
    2130 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.64

  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: 1831
        1.33 -     1.45: 1904
        1.45 -     1.57: 5571
        1.57 -     1.69: 0
        1.69 -     1.81: 111
  Bond restraints: 9417
  Sorted by residual:
  bond pdb=" N   VAL B 411 "
       pdb=" CA  VAL B 411 "
    ideal  model  delta    sigma   weight residual
    1.461  1.489 -0.029 8.70e-03 1.32e+04 1.09e+01
  bond pdb=" N   VAL C 411 "
       pdb=" CA  VAL C 411 "
    ideal  model  delta    sigma   weight residual
    1.461  1.488 -0.028 8.70e-03 1.32e+04 1.02e+01
  bond pdb=" N   VAL A 411 "
       pdb=" CA  VAL A 411 "
    ideal  model  delta    sigma   weight residual
    1.461  1.488 -0.028 8.70e-03 1.32e+04 1.00e+01
  bond pdb=" N   VAL A 417 "
       pdb=" CA  VAL A 417 "
    ideal  model  delta    sigma   weight residual
    1.461  1.497 -0.036 1.19e-02 7.06e+03 9.30e+00
  bond pdb=" N   VAL B 417 "
       pdb=" CA  VAL B 417 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.036 1.19e-02 7.06e+03 9.03e+00
  ... (remaining 9412 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 11953
        1.22 -     2.45: 680
        2.45 -     3.67: 108
        3.67 -     4.89: 33
        4.89 -     6.11: 9
  Bond angle restraints: 12783
  Sorted by residual:
  angle pdb=" N   ALA A 414 "
        pdb=" CA  ALA A 414 "
        pdb=" C   ALA A 414 "
      ideal   model   delta    sigma   weight residual
     113.50  107.79    5.71 1.23e+00 6.61e-01 2.16e+01
  angle pdb=" N   ALA C 414 "
        pdb=" CA  ALA C 414 "
        pdb=" C   ALA C 414 "
      ideal   model   delta    sigma   weight residual
     113.50  107.81    5.69 1.23e+00 6.61e-01 2.14e+01
  angle pdb=" N   ALA B 414 "
        pdb=" CA  ALA B 414 "
        pdb=" C   ALA B 414 "
      ideal   model   delta    sigma   weight residual
     113.50  107.83    5.67 1.23e+00 6.61e-01 2.13e+01
  angle pdb=" C   ALA A 414 "
        pdb=" N   GLY A 415 "
        pdb=" CA  GLY A 415 "
      ideal   model   delta    sigma   weight residual
     119.98  124.14   -4.16 1.11e+00 8.12e-01 1.40e+01
  angle pdb=" C   ALA C 414 "
        pdb=" N   GLY C 415 "
        pdb=" CA  GLY C 415 "
      ideal   model   delta    sigma   weight residual
     119.98  124.12   -4.14 1.11e+00 8.12e-01 1.39e+01
  ... (remaining 12778 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.18: 5183
       17.18 -    34.35: 313
       34.35 -    51.53: 85
       51.53 -    68.70: 29
       68.70 -    85.88: 12
  Dihedral angle restraints: 5622
    sinusoidal: 2127
      harmonic: 3495
  Sorted by residual:
  dihedral pdb=" CG  ARG C 280 "
           pdb=" CD  ARG C 280 "
           pdb=" NE  ARG C 280 "
           pdb=" CZ  ARG C 280 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.36   48.64     2      1.50e+01 4.44e-03 1.20e+01
  dihedral pdb=" CG  ARG B 280 "
           pdb=" CD  ARG B 280 "
           pdb=" NE  ARG B 280 "
           pdb=" CZ  ARG B 280 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.39   48.61     2      1.50e+01 4.44e-03 1.20e+01
  dihedral pdb=" CG  ARG A 280 "
           pdb=" CD  ARG A 280 "
           pdb=" NE  ARG A 280 "
           pdb=" CZ  ARG A 280 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.48   48.52     2      1.50e+01 4.44e-03 1.20e+01
  ... (remaining 5619 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1146
       0.039 -    0.077: 384
       0.077 -    0.116: 68
       0.116 -    0.154: 25
       0.154 -    0.193: 3
  Chirality restraints: 1626
  Sorted by residual:
  chirality pdb=" CA  VAL B 411 "
            pdb=" N   VAL B 411 "
            pdb=" C   VAL B 411 "
            pdb=" CB  VAL B 411 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.30e-01
  chirality pdb=" CA  VAL C 411 "
            pdb=" N   VAL C 411 "
            pdb=" C   VAL C 411 "
            pdb=" CB  VAL C 411 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.87e-01
  chirality pdb=" CA  VAL A 411 "
            pdb=" N   VAL A 411 "
            pdb=" C   VAL A 411 "
            pdb=" CB  VAL A 411 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.63e-01
  ... (remaining 1623 not shown)

  Planarity restraints: 1557
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  39 "    0.149 9.50e-02 1.11e+02   6.74e-02 3.34e+00
        pdb=" NE  ARG B  39 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  39 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  39 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  39 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  39 "   -0.150 9.50e-02 1.11e+02   6.75e-02 3.30e+00
        pdb=" NE  ARG C  39 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  39 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  39 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  39 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  39 "    0.148 9.50e-02 1.11e+02   6.69e-02 3.26e+00
        pdb=" NE  ARG A  39 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  39 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  39 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  39 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1554 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.62: 103
        2.62 -     3.19: 9119
        3.19 -     3.76: 14445
        3.76 -     4.33: 21323
        4.33 -     4.90: 34404
  Nonbonded interactions: 79394
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 368 "
            pdb="NA    NA B 601 "
     model   vdw
     2.055 2.470
  nonbonded pdb=" OD1 ASP C 368 "
            pdb="NA    NA C 601 "
     model   vdw
     2.056 2.470
  nonbonded pdb=" OD1 ASP A 368 "
            pdb="NA    NA A 603 "
     model   vdw
     2.056 2.470
  nonbonded pdb=" SG  CYS A 269 "
            pdb="HG    HG A 604 "
     model   vdw
     2.078 2.880
  nonbonded pdb=" SG  CYS C 269 "
            pdb="HG    HG C 605 "
     model   vdw
     2.078 2.880
  ... (remaining 79389 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: 0.03
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 17 through 470 or resid 601))
  selection = (chain 'B' and (resid 17 through 470 or resid 602))
  selection = (chain 'C' and (resid 17 through 470 or resid 602))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             0.990
  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:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     24.660
  Find NCS groups from input model:        0.530
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9417  Z= 0.232
  Angle     :  0.684   6.115  12783  Z= 0.428
  Chirality :  0.041   0.193   1626
  Planarity :  0.005   0.068   1557
  Dihedral  : 13.815  85.876   3366
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  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: -1.67 (0.22), residues: 1200
  helix: -1.15 (0.15), residues: 945
  sheet:  0.17 (0.68), residues: 54
  loop : -0.06 (0.47), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP C  19 
 HIS   0.003   0.001   HIS C 296 
 PHE   0.018   0.002   PHE C 279 
 TYR   0.018   0.004   TYR A  98 
 ARG   0.013   0.002   ARG B  39 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 1.430 
Fit side-chains
REVERT: A  149 MET cc_start: 0.8956 (mtm) cc_final: 0.8741 (mtp)
REVERT: A  205 MET cc_start: 0.8290 (ptm) cc_final: 0.7919 (ptt)
REVERT: A  229 MET cc_start: 0.8831 (mtm) cc_final: 0.8544 (mtm)
REVERT: A  256 TRP cc_start: 0.8195 (m100) cc_final: 0.7427 (m-10)
REVERT: A  272 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7157 (mt-10)
REVERT: A  278 ILE cc_start: 0.7780 (mt) cc_final: 0.7469 (mp)
REVERT: A  280 ARG cc_start: 0.7260 (ttp80) cc_final: 0.6754 (ttm170)
REVERT: A  281 LYS cc_start: 0.7194 (tttt) cc_final: 0.6412 (mmtp)
REVERT: A  286 MET cc_start: 0.8152 (mtp) cc_final: 0.7786 (mtm)
REVERT: A  318 MET cc_start: 0.7073 (tpt) cc_final: 0.6430 (ttp)
REVERT: A  352 LYS cc_start: 0.7480 (tmtt) cc_final: 0.6913 (mttt)
REVERT: A  445 ARG cc_start: 0.8356 (mtt90) cc_final: 0.8140 (mtt90)
REVERT: B  205 MET cc_start: 0.8425 (ptm) cc_final: 0.8108 (ptt)
REVERT: B  232 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7853 (ttpt)
REVERT: B  249 LYS cc_start: 0.8344 (mttt) cc_final: 0.7931 (mttm)
REVERT: B  258 MET cc_start: 0.8275 (ttt) cc_final: 0.8007 (ttt)
REVERT: B  260 LEU cc_start: 0.7648 (tm) cc_final: 0.7430 (tt)
REVERT: B  272 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7052 (mt-10)
REVERT: B  278 ILE cc_start: 0.7933 (mt) cc_final: 0.7635 (OUTLIER)
REVERT: B  280 ARG cc_start: 0.7193 (ttp80) cc_final: 0.6851 (ttm170)
REVERT: B  281 LYS cc_start: 0.7258 (tttt) cc_final: 0.6261 (mmtp)
REVERT: B  286 MET cc_start: 0.8260 (mtp) cc_final: 0.8046 (mtm)
REVERT: B  304 ILE cc_start: 0.7938 (pt) cc_final: 0.7563 (mt)
REVERT: B  315 ARG cc_start: 0.7620 (tpp-160) cc_final: 0.7094 (ttm110)
REVERT: B  318 MET cc_start: 0.7126 (tpt) cc_final: 0.6394 (ttp)
REVERT: B  352 LYS cc_start: 0.7692 (tmtt) cc_final: 0.7186 (mttt)
REVERT: B  356 ARG cc_start: 0.6689 (tpm170) cc_final: 0.6255 (ptp-170)
REVERT: B  357 PHE cc_start: 0.7910 (t80) cc_final: 0.7585 (t80)
REVERT: C   99 PHE cc_start: 0.7550 (t80) cc_final: 0.7295 (t80)
REVERT: C  232 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7301 (tptm)
REVERT: C  256 TRP cc_start: 0.8167 (m100) cc_final: 0.7421 (m-10)
REVERT: C  258 MET cc_start: 0.8390 (ttt) cc_final: 0.7945 (ttt)
REVERT: C  275 ASP cc_start: 0.6784 (m-30) cc_final: 0.6522 (t0)
REVERT: C  278 ILE cc_start: 0.7815 (mt) cc_final: 0.7553 (mp)
REVERT: C  280 ARG cc_start: 0.7450 (ttp80) cc_final: 0.7006 (ttm170)
REVERT: C  281 LYS cc_start: 0.7405 (tttt) cc_final: 0.6640 (mmtp)
REVERT: C  286 MET cc_start: 0.8136 (mtp) cc_final: 0.7737 (mtt)
REVERT: C  304 ILE cc_start: 0.7831 (pt) cc_final: 0.7382 (mt)
REVERT: C  318 MET cc_start: 0.7420 (tpt) cc_final: 0.6849 (ttp)
REVERT: C  322 GLN cc_start: 0.8159 (tt0) cc_final: 0.7752 (tt0)
REVERT: C  325 LEU cc_start: 0.7877 (mt) cc_final: 0.7649 (tp)
REVERT: C  352 LYS cc_start: 0.7483 (tmtt) cc_final: 0.7028 (mttt)
REVERT: C  356 ARG cc_start: 0.6348 (tpm170) cc_final: 0.6131 (ptp-170)
  outliers start: 0
  outliers final: 1
  residues processed: 207
  average time/residue: 1.5293
  time to fit residues: 336.6165
Evaluate side-chains
  167 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 1.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.6980
   chunk 90 optimal weight:    0.3980
   chunk 50 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0670
   chunk 48 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 57 optimal weight:    0.1980
   chunk 70 optimal weight:    0.9990
   chunk 108 optimal weight:    1.9990
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
A 211 ASN
A 252 GLN
A 312 ASN
A 348 ASN
A 385 ASN
B 211 ASN
B 252 GLN
C 211 ASN
C 252 GLN
C 312 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.188123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.151374 restraints weight = 2538.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 0.72
r_work: 0.3148 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9417  Z= 0.188
  Angle     :  0.536   7.215  12783  Z= 0.284
  Chirality :  0.040   0.153   1626
  Planarity :  0.004   0.039   1557
  Dihedral  :  3.977  13.419   1281
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 10.85 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.23), residues: 1200
  helix:  0.66 (0.16), residues: 954
  sheet:  0.42 (0.75), residues: 54
  loop :  0.01 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  19 
 HIS   0.001   0.000   HIS C 296 
 PHE   0.027   0.002   PHE B 222 
 TYR   0.010   0.002   TYR B 373 
 ARG   0.006   0.001   ARG C 280 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 178
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6763 (mt-10)
REVERT: A  117 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7917 (mttm)
REVERT: A  163 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7392 (pttp)
REVERT: A  229 MET cc_start: 0.8778 (mtm) cc_final: 0.8484 (mtm)
REVERT: A  256 TRP cc_start: 0.8509 (m100) cc_final: 0.7683 (m-10)
REVERT: A  272 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6834 (mt-10)
REVERT: A  280 ARG cc_start: 0.6999 (ttp80) cc_final: 0.6491 (ttm170)
REVERT: A  281 LYS cc_start: 0.6948 (tttt) cc_final: 0.6140 (mmtp)
REVERT: A  286 MET cc_start: 0.8318 (mtp) cc_final: 0.7946 (mtm)
REVERT: A  315 ARG cc_start: 0.7655 (tpp-160) cc_final: 0.7360 (ttm110)
REVERT: A  318 MET cc_start: 0.7289 (tpt) cc_final: 0.6781 (ttp)
REVERT: A  352 LYS cc_start: 0.7054 (tmtt) cc_final: 0.6717 (mttt)
REVERT: A  356 ARG cc_start: 0.6546 (tpm170) cc_final: 0.6071 (ptp-110)
REVERT: A  359 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8198 (mp)
REVERT: A  368 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7454 (m-30)
REVERT: A  444 ASP cc_start: 0.7708 (t0) cc_final: 0.7499 (t0)
REVERT: A  464 LYS cc_start: 0.7179 (tppp) cc_final: 0.6547 (tppt)
REVERT: B  205 MET cc_start: 0.8473 (ptm) cc_final: 0.8183 (ptt)
REVERT: B  232 LYS cc_start: 0.7903 (ttpt) cc_final: 0.7435 (mtpt)
REVERT: B  272 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6847 (mt-10)
REVERT: B  281 LYS cc_start: 0.6756 (tttt) cc_final: 0.5851 (mmtp)
REVERT: B  304 ILE cc_start: 0.7717 (pt) cc_final: 0.7323 (mt)
REVERT: B  318 MET cc_start: 0.7179 (tpt) cc_final: 0.6576 (ttp)
REVERT: B  352 LYS cc_start: 0.6993 (tmtt) cc_final: 0.6626 (mttt)
REVERT: B  356 ARG cc_start: 0.6668 (tpm170) cc_final: 0.6092 (ptp-110)
REVERT: C  232 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7679 (mtmp)
REVERT: C  256 TRP cc_start: 0.8493 (m100) cc_final: 0.7591 (m-10)
REVERT: C  258 MET cc_start: 0.8156 (ttt) cc_final: 0.7870 (ttt)
REVERT: C  280 ARG cc_start: 0.7355 (ttp80) cc_final: 0.6910 (ttm170)
REVERT: C  281 LYS cc_start: 0.7166 (tttt) cc_final: 0.6415 (mmtp)
REVERT: C  286 MET cc_start: 0.8244 (mtp) cc_final: 0.7910 (mtm)
REVERT: C  304 ILE cc_start: 0.7455 (pt) cc_final: 0.7122 (mt)
REVERT: C  315 ARG cc_start: 0.7625 (tpp-160) cc_final: 0.7297 (ttm110)
REVERT: C  318 MET cc_start: 0.7375 (tpt) cc_final: 0.6839 (ttp)
REVERT: C  329 MET cc_start: 0.8214 (mmt) cc_final: 0.8012 (mpp)
REVERT: C  348 ASN cc_start: 0.8168 (m-40) cc_final: 0.7915 (m-40)
REVERT: C  352 LYS cc_start: 0.7197 (tmtt) cc_final: 0.6791 (mttt)
  outliers start: 26
  outliers final: 8
  residues processed: 191
  average time/residue: 1.2907
  time to fit residues: 262.1695
Evaluate side-chains
  177 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 167
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  368 ASP
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  359 LEU
Chi-restraints excluded: chain C residue  368 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 104 optimal weight:    0.0070
   chunk 20 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0020
   chunk 45 optimal weight:    0.8980
   chunk 116 optimal weight:    0.9980
   chunk 93 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.4206

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

Flipped N/Q/H residues before XYZ refinement:
A 348 ASN
B 348 ASN
C 252 GLN
C 312 ASN
C 348 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.184708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.145100 restraints weight = 2656.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 0.82
r_work: 0.3538 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3404 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9417  Z= 0.171
  Angle     :  0.490   6.016  12783  Z= 0.257
  Chirality :  0.039   0.156   1626
  Planarity :  0.004   0.034   1557
  Dihedral  :  3.674  12.033   1281
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 11.83 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.24), residues: 1200
  helix:  1.19 (0.16), residues: 960
  sheet:  0.67 (0.76), residues: 54
  loop :  0.24 (0.46), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  19 
 HIS   0.001   0.001   HIS C 296 
 PHE   0.016   0.001   PHE A 222 
 TYR   0.010   0.001   TYR B 373 
 ARG   0.006   0.001   ARG C 353 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 170
  time to evaluate  : 1.092 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6810 (mt-10)
REVERT: A   48 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7431 (mt-10)
REVERT: A   60 MET cc_start: 0.8456 (mmm) cc_final: 0.8119 (mmm)
REVERT: A  229 MET cc_start: 0.8735 (mtm) cc_final: 0.8491 (mtm)
REVERT: A  256 TRP cc_start: 0.8425 (m100) cc_final: 0.7599 (m-10)
REVERT: A  272 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6700 (mt-10)
REVERT: A  280 ARG cc_start: 0.6920 (ttp80) cc_final: 0.6456 (ttm170)
REVERT: A  281 LYS cc_start: 0.7067 (tttt) cc_final: 0.6117 (mmtp)
REVERT: A  286 MET cc_start: 0.8184 (mtp) cc_final: 0.7932 (mtm)
REVERT: A  315 ARG cc_start: 0.7557 (tpp-160) cc_final: 0.7297 (tpt170)
REVERT: A  318 MET cc_start: 0.7112 (tpt) cc_final: 0.6633 (ttp)
REVERT: A  347 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.7954 (m110)
REVERT: A  352 LYS cc_start: 0.6967 (tmtt) cc_final: 0.6677 (mttt)
REVERT: A  356 ARG cc_start: 0.6568 (tpm170) cc_final: 0.5994 (ptp-110)
REVERT: A  357 PHE cc_start: 0.8066 (t80) cc_final: 0.7861 (t80)
REVERT: A  359 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8038 (mp)
REVERT: A  368 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7398 (m-30)
REVERT: B   40 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6925 (mt-10)
REVERT: B   99 PHE cc_start: 0.7895 (t80) cc_final: 0.7524 (t80)
REVERT: B  205 MET cc_start: 0.8528 (ptm) cc_final: 0.8207 (ptt)
REVERT: B  269 CYS cc_start: 0.7349 (t) cc_final: 0.6974 (t)
REVERT: B  272 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6665 (mt-10)
REVERT: B  281 LYS cc_start: 0.6854 (tttt) cc_final: 0.5898 (mmtp)
REVERT: B  318 MET cc_start: 0.7143 (tpt) cc_final: 0.6691 (ttp)
REVERT: B  352 LYS cc_start: 0.6948 (tmtt) cc_final: 0.6593 (mttt)
REVERT: B  356 ARG cc_start: 0.6683 (tpm170) cc_final: 0.6018 (ptp-110)
REVERT: B  444 ASP cc_start: 0.7636 (t0) cc_final: 0.7297 (t0)
REVERT: C  232 LYS cc_start: 0.7849 (ttpt) cc_final: 0.7596 (mtmt)
REVERT: C  256 TRP cc_start: 0.8449 (m100) cc_final: 0.7510 (m-10)
REVERT: C  258 MET cc_start: 0.8198 (ttt) cc_final: 0.7900 (ttt)
REVERT: C  280 ARG cc_start: 0.7342 (ttp80) cc_final: 0.6875 (ttm170)
REVERT: C  281 LYS cc_start: 0.7109 (tttt) cc_final: 0.6346 (mmtp)
REVERT: C  286 MET cc_start: 0.8116 (mtp) cc_final: 0.7842 (mtm)
REVERT: C  315 ARG cc_start: 0.7559 (tpp-160) cc_final: 0.7307 (ttm110)
REVERT: C  318 MET cc_start: 0.7316 (tpt) cc_final: 0.6751 (ttp)
REVERT: C  352 LYS cc_start: 0.7149 (tmtt) cc_final: 0.6734 (mttt)
  outliers start: 25
  outliers final: 12
  residues processed: 180
  average time/residue: 1.5381
  time to fit residues: 295.2348
Evaluate side-chains
  174 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 158
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   40 GLU
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  365 ILE
Chi-restraints excluded: chain B residue  368 ASP
Chi-restraints excluded: chain B residue  403 SER
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  368 ASP
Chi-restraints excluded: chain C residue  403 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9980
   chunk 106 optimal weight:    4.9990
   chunk 85 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 118 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 95 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   chunk 109 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN
A 348 ASN
C 252 GLN
C 312 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.190658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.154257 restraints weight = 2669.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 0.72
r_work: 0.3132 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9417  Z= 0.202
  Angle     :  0.489   5.529  12783  Z= 0.257
  Chirality :  0.040   0.167   1626
  Planarity :  0.004   0.033   1557
  Dihedral  :  3.614  12.082   1281
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 13.51 %
    Favored  : 83.33 %
  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:  1.56 (0.24), residues: 1200
  helix:  1.30 (0.17), residues: 960
  sheet:  0.60 (0.74), residues: 54
  loop :  0.17 (0.45), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 276 
 HIS   0.001   0.000   HIS C 296 
 PHE   0.013   0.002   PHE C 240 
 TYR   0.010   0.001   TYR B 373 
 ARG   0.005   0.001   ARG C 353 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 163
  time to evaluate  : 1.238 
Fit side-chains
REVERT: A  231 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7343 (tm-30)
REVERT: A  256 TRP cc_start: 0.8521 (m100) cc_final: 0.7703 (m-10)
REVERT: A  272 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6750 (mt-10)
REVERT: A  280 ARG cc_start: 0.7035 (ttp80) cc_final: 0.6556 (ttm170)
REVERT: A  281 LYS cc_start: 0.7109 (tttt) cc_final: 0.6120 (mmtp)
REVERT: A  286 MET cc_start: 0.8248 (mtp) cc_final: 0.8031 (mtm)
REVERT: A  318 MET cc_start: 0.7311 (tpt) cc_final: 0.6920 (ttp)
REVERT: A  348 ASN cc_start: 0.8039 (m-40) cc_final: 0.7831 (m-40)
REVERT: A  352 LYS cc_start: 0.7120 (tmtt) cc_final: 0.6836 (mttt)
REVERT: A  356 ARG cc_start: 0.6676 (tpm170) cc_final: 0.6209 (ptp-110)
REVERT: A  357 PHE cc_start: 0.8185 (t80) cc_final: 0.7921 (t80)
REVERT: A  368 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7541 (m-30)
REVERT: A  419 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.6859 (tmm)
REVERT: B   40 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7093 (mt-10)
REVERT: B   99 PHE cc_start: 0.8003 (t80) cc_final: 0.7627 (t80)
REVERT: B  142 MET cc_start: 0.8285 (mmm) cc_final: 0.7854 (tpp)
REVERT: B  205 MET cc_start: 0.8522 (ptm) cc_final: 0.8225 (ptt)
REVERT: B  231 GLU cc_start: 0.7919 (tt0) cc_final: 0.7592 (tm-30)
REVERT: B  269 CYS cc_start: 0.7334 (t) cc_final: 0.6948 (t)
REVERT: B  272 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6776 (mt-10)
REVERT: B  281 LYS cc_start: 0.6991 (tttt) cc_final: 0.5969 (mmtp)
REVERT: B  318 MET cc_start: 0.7264 (tpt) cc_final: 0.6909 (ttp)
REVERT: B  352 LYS cc_start: 0.6990 (tmtt) cc_final: 0.6648 (mttt)
REVERT: B  356 ARG cc_start: 0.6755 (tpm170) cc_final: 0.6189 (ptp-110)
REVERT: B  357 PHE cc_start: 0.8080 (t80) cc_final: 0.7802 (t80)
REVERT: B  444 ASP cc_start: 0.7774 (t0) cc_final: 0.7432 (t0)
REVERT: C   40 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6933 (mp0)
REVERT: C  142 MET cc_start: 0.8593 (mmm) cc_final: 0.8363 (tpp)
REVERT: C  232 LYS cc_start: 0.7814 (ttpt) cc_final: 0.7565 (mtmt)
REVERT: C  256 TRP cc_start: 0.8529 (m100) cc_final: 0.7643 (m-10)
REVERT: C  258 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7946 (ttt)
REVERT: C  280 ARG cc_start: 0.7364 (ttp80) cc_final: 0.6920 (ttm170)
REVERT: C  281 LYS cc_start: 0.7157 (tttt) cc_final: 0.6359 (mmmm)
REVERT: C  286 MET cc_start: 0.8177 (mtp) cc_final: 0.7926 (mtm)
REVERT: C  307 ILE cc_start: 0.7525 (mm) cc_final: 0.7283 (mt)
REVERT: C  315 ARG cc_start: 0.7578 (tpp-160) cc_final: 0.7337 (ttm110)
REVERT: C  318 MET cc_start: 0.7486 (tpt) cc_final: 0.6995 (ttp)
REVERT: C  352 LYS cc_start: 0.7161 (tmtt) cc_final: 0.6860 (mttt)
REVERT: C  353 ARG cc_start: 0.7792 (mpp80) cc_final: 0.7590 (mpp80)
REVERT: C  368 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7641 (m-30)
  outliers start: 32
  outliers final: 7
  residues processed: 176
  average time/residue: 1.3287
  time to fit residues: 250.5791
Evaluate side-chains
  172 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 159
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain B residue   40 GLU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  368 ASP
Chi-restraints excluded: chain B residue  403 SER
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  368 ASP
Chi-restraints excluded: chain C residue  403 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 110 optimal weight:    9.9990
   chunk 56 optimal weight:    0.6980
   chunk 94 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN
C 252 GLN
** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.187131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.150900 restraints weight = 2674.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 0.70
r_work: 0.3136 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9417  Z= 0.238
  Angle     :  0.509   5.433  12783  Z= 0.266
  Chirality :  0.041   0.198   1626
  Planarity :  0.004   0.035   1557
  Dihedral  :  3.622  12.022   1281
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 14.50 %
    Favored  : 82.15 %
  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:  1.45 (0.24), residues: 1200
  helix:  1.23 (0.17), residues: 960
  sheet:  0.63 (0.76), residues: 54
  loop :  0.01 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 276 
 HIS   0.002   0.001   HIS B 296 
 PHE   0.014   0.002   PHE C 240 
 TYR   0.008   0.001   TYR B 285 
 ARG   0.004   0.001   ARG C 353 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 156
  time to evaluate  : 1.003 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6952 (mt-10)
REVERT: A  228 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8066 (mptt)
REVERT: A  256 TRP cc_start: 0.8514 (m100) cc_final: 0.7712 (m-10)
REVERT: A  269 CYS cc_start: 0.7386 (t) cc_final: 0.7071 (t)
REVERT: A  272 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6813 (mt-10)
REVERT: A  280 ARG cc_start: 0.7077 (ttp80) cc_final: 0.6591 (ttm170)
REVERT: A  281 LYS cc_start: 0.7125 (tttt) cc_final: 0.6097 (mmtp)
REVERT: A  286 MET cc_start: 0.8365 (mtp) cc_final: 0.8143 (mtm)
REVERT: A  318 MET cc_start: 0.7284 (tpt) cc_final: 0.6906 (ttp)
REVERT: A  348 ASN cc_start: 0.8185 (m-40) cc_final: 0.7978 (m-40)
REVERT: A  352 LYS cc_start: 0.6905 (tmtt) cc_final: 0.6696 (mttt)
REVERT: A  356 ARG cc_start: 0.6748 (tpm170) cc_final: 0.6310 (ptp-110)
REVERT: A  359 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8166 (mp)
REVERT: A  367 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8448 (mtm)
REVERT: A  368 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7552 (m-30)
REVERT: A  419 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.6936 (tmm)
REVERT: B   99 PHE cc_start: 0.7981 (t80) cc_final: 0.7619 (t80)
REVERT: B  142 MET cc_start: 0.8309 (mmm) cc_final: 0.7865 (tpp)
REVERT: B  205 MET cc_start: 0.8545 (ptm) cc_final: 0.8254 (ptt)
REVERT: B  269 CYS cc_start: 0.7375 (t) cc_final: 0.6995 (t)
REVERT: B  281 LYS cc_start: 0.7093 (tttt) cc_final: 0.5959 (mmtp)
REVERT: B  318 MET cc_start: 0.7250 (tpt) cc_final: 0.6981 (ttp)
REVERT: B  352 LYS cc_start: 0.6945 (tmtt) cc_final: 0.6729 (mttt)
REVERT: B  356 ARG cc_start: 0.6793 (tpm170) cc_final: 0.6196 (ptp-110)
REVERT: B  357 PHE cc_start: 0.8177 (t80) cc_final: 0.7932 (t80)
REVERT: B  444 ASP cc_start: 0.7717 (t0) cc_final: 0.7461 (t0)
REVERT: C   40 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6985 (mp0)
REVERT: C  232 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7642 (mtmt)
REVERT: C  256 TRP cc_start: 0.8577 (m100) cc_final: 0.7709 (m-10)
REVERT: C  258 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7912 (ttt)
REVERT: C  280 ARG cc_start: 0.7354 (ttp80) cc_final: 0.6925 (ttm170)
REVERT: C  281 LYS cc_start: 0.7179 (tttt) cc_final: 0.6289 (mmmm)
REVERT: C  286 MET cc_start: 0.8188 (mtp) cc_final: 0.7931 (mtm)
REVERT: C  307 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7346 (mt)
REVERT: C  315 ARG cc_start: 0.7641 (tpp-160) cc_final: 0.7362 (ttm110)
REVERT: C  318 MET cc_start: 0.7529 (tpt) cc_final: 0.7077 (ttp)
REVERT: C  352 LYS cc_start: 0.7265 (tmtt) cc_final: 0.6837 (mttt)
REVERT: C  444 ASP cc_start: 0.7486 (t0) cc_final: 0.6903 (t70)
  outliers start: 34
  outliers final: 10
  residues processed: 172
  average time/residue: 1.2043
  time to fit residues: 221.9356
Evaluate side-chains
  173 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 155
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  365 ILE
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  403 SER
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  307 ILE
Chi-restraints excluded: chain C residue  368 ASP
Chi-restraints excluded: chain C residue  403 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 66 optimal weight:    0.0770
   chunk 7 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0020
   chunk 119 optimal weight:    2.9990
   chunk 117 optimal weight:    0.3980
   chunk 73 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.3546

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN
A 348 ASN
C 312 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.191265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.155791 restraints weight = 2708.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 0.69
r_work: 0.3176 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9417  Z= 0.153
  Angle     :  0.463   4.989  12783  Z= 0.242
  Chirality :  0.039   0.196   1626
  Planarity :  0.004   0.033   1557
  Dihedral  :  3.420  11.669   1281
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 14.60 %
    Favored  : 81.85 %
  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:  1.88 (0.24), residues: 1200
  helix:  1.52 (0.17), residues: 960
  sheet:  1.93 (0.74), residues: 48
  loop : -0.04 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  19 
 HIS   0.001   0.000   HIS C 296 
 PHE   0.010   0.001   PHE A 222 
 TYR   0.008   0.001   TYR A 162 
 ARG   0.003   0.000   ARG C 353 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 164
  time to evaluate  : 1.102 
Fit side-chains
REVERT: A  256 TRP cc_start: 0.8497 (m100) cc_final: 0.7680 (m-10)
REVERT: A  272 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6835 (mt-10)
REVERT: A  280 ARG cc_start: 0.7195 (ttp80) cc_final: 0.6801 (ttm170)
REVERT: A  281 LYS cc_start: 0.7166 (tttt) cc_final: 0.6076 (mmtp)
REVERT: A  286 MET cc_start: 0.8322 (mtp) cc_final: 0.8096 (mtm)
REVERT: A  318 MET cc_start: 0.7248 (tpt) cc_final: 0.6856 (ttp)
REVERT: A  347 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8087 (m110)
REVERT: A  356 ARG cc_start: 0.6579 (tpm170) cc_final: 0.6101 (ptp-110)
REVERT: A  357 PHE cc_start: 0.8113 (t80) cc_final: 0.7908 (t80)
REVERT: A  359 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8111 (mp)
REVERT: A  367 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8317 (mtm)
REVERT: A  368 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7476 (m-30)
REVERT: B   42 SER cc_start: 0.8457 (t) cc_final: 0.8231 (m)
REVERT: B   99 PHE cc_start: 0.7969 (t80) cc_final: 0.7584 (t80)
REVERT: B  142 MET cc_start: 0.8243 (mmm) cc_final: 0.7904 (tpp)
REVERT: B  205 MET cc_start: 0.8547 (ptm) cc_final: 0.8242 (ptt)
REVERT: B  229 MET cc_start: 0.8581 (mtp) cc_final: 0.8350 (mtm)
REVERT: B  231 GLU cc_start: 0.7987 (tt0) cc_final: 0.7634 (tm-30)
REVERT: B  269 CYS cc_start: 0.7385 (t) cc_final: 0.6981 (t)
REVERT: B  281 LYS cc_start: 0.7092 (tttt) cc_final: 0.5923 (mmtp)
REVERT: B  307 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.7205 (mt)
REVERT: B  318 MET cc_start: 0.7163 (tpt) cc_final: 0.6917 (ttp)
REVERT: B  346 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6919 (mm-30)
REVERT: B  352 LYS cc_start: 0.6944 (tmtt) cc_final: 0.6651 (mttt)
REVERT: B  356 ARG cc_start: 0.6771 (tpm170) cc_final: 0.6168 (ptp-110)
REVERT: B  357 PHE cc_start: 0.8032 (t80) cc_final: 0.7765 (t80)
REVERT: C   40 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6896 (mp0)
REVERT: C  232 LYS cc_start: 0.7750 (ttpt) cc_final: 0.7508 (mtmt)
REVERT: C  256 TRP cc_start: 0.8563 (m100) cc_final: 0.7671 (m-10)
REVERT: C  258 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7879 (ttt)
REVERT: C  280 ARG cc_start: 0.7410 (ttp80) cc_final: 0.7019 (ttm170)
REVERT: C  281 LYS cc_start: 0.7207 (tttt) cc_final: 0.6328 (mmmm)
REVERT: C  286 MET cc_start: 0.8162 (mtp) cc_final: 0.7911 (mtm)
REVERT: C  307 ILE cc_start: 0.7582 (mm) cc_final: 0.7339 (mt)
REVERT: C  311 LYS cc_start: 0.7886 (mtmt) cc_final: 0.7652 (mtmt)
REVERT: C  315 ARG cc_start: 0.7594 (tpp-160) cc_final: 0.7094 (ttm170)
REVERT: C  318 MET cc_start: 0.7480 (tpt) cc_final: 0.7035 (ptt)
REVERT: C  352 LYS cc_start: 0.7204 (tmtt) cc_final: 0.6773 (mttt)
REVERT: C  368 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7513 (m-30)
  outliers start: 36
  outliers final: 8
  residues processed: 182
  average time/residue: 1.1725
  time to fit residues: 228.6558
Evaluate side-chains
  173 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  346 GLU
Chi-restraints excluded: chain B residue  365 ILE
Chi-restraints excluded: chain B residue  368 ASP
Chi-restraints excluded: chain B residue  403 SER
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  368 ASP
Chi-restraints excluded: chain C residue  403 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 111 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 104 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 115 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 348 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.189866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.153728 restraints weight = 2664.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 0.70
r_work: 0.3125 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9417  Z= 0.236
  Angle     :  0.509   5.151  12783  Z= 0.266
  Chirality :  0.040   0.199   1626
  Planarity :  0.004   0.034   1557
  Dihedral  :  3.527  11.878   1281
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.17 %
    Favored  : 81.07 %
  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:  1.63 (0.24), residues: 1200
  helix:  1.39 (0.17), residues: 948
  sheet:  0.75 (0.78), residues: 54
  loop : -0.05 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 276 
 HIS   0.002   0.001   HIS B 296 
 PHE   0.015   0.002   PHE C 240 
 TYR   0.008   0.001   TYR A 285 
 ARG   0.006   0.001   ARG C 353 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 1.033 
Fit side-chains
REVERT: A  256 TRP cc_start: 0.8514 (m100) cc_final: 0.7708 (m-10)
REVERT: A  269 CYS cc_start: 0.7323 (t) cc_final: 0.6974 (t)
REVERT: A  272 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6875 (mt-10)
REVERT: A  280 ARG cc_start: 0.7221 (ttp80) cc_final: 0.6787 (ttm170)
REVERT: A  281 LYS cc_start: 0.7148 (tttt) cc_final: 0.6083 (mmtp)
REVERT: A  286 MET cc_start: 0.8369 (mtp) cc_final: 0.8134 (mtm)
REVERT: A  318 MET cc_start: 0.7182 (tpt) cc_final: 0.6784 (ttp)
REVERT: A  347 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8029 (m110)
REVERT: A  356 ARG cc_start: 0.6754 (tpm170) cc_final: 0.6308 (ptp-110)
REVERT: A  368 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7576 (m-30)
REVERT: B   42 SER cc_start: 0.8454 (t) cc_final: 0.8232 (m)
REVERT: B   99 PHE cc_start: 0.7984 (t80) cc_final: 0.7589 (t80)
REVERT: B  142 MET cc_start: 0.8302 (mmm) cc_final: 0.7931 (tpp)
REVERT: B  205 MET cc_start: 0.8567 (ptm) cc_final: 0.8271 (ptt)
REVERT: B  269 CYS cc_start: 0.7505 (t) cc_final: 0.7117 (t)
REVERT: B  281 LYS cc_start: 0.7161 (tttt) cc_final: 0.5946 (mmtp)
REVERT: B  307 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7278 (mt)
REVERT: B  318 MET cc_start: 0.7262 (tpt) cc_final: 0.6997 (ttp)
REVERT: B  346 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6682 (mt-10)
REVERT: B  352 LYS cc_start: 0.6982 (tmtt) cc_final: 0.6710 (mttt)
REVERT: B  356 ARG cc_start: 0.6839 (tpm170) cc_final: 0.6245 (ptp-110)
REVERT: B  357 PHE cc_start: 0.8111 (t80) cc_final: 0.7789 (t80)
REVERT: C   40 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6882 (mp0)
REVERT: C   92 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6849 (mm)
REVERT: C  232 LYS cc_start: 0.7784 (ttpt) cc_final: 0.7514 (mtmt)
REVERT: C  256 TRP cc_start: 0.8595 (m100) cc_final: 0.7731 (m-10)
REVERT: C  258 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7899 (ttt)
REVERT: C  280 ARG cc_start: 0.7428 (ttp80) cc_final: 0.7028 (ttm170)
REVERT: C  281 LYS cc_start: 0.7192 (tttt) cc_final: 0.6273 (mmmm)
REVERT: C  286 MET cc_start: 0.8222 (mtp) cc_final: 0.7948 (mtm)
REVERT: C  307 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7343 (mt)
REVERT: C  311 LYS cc_start: 0.7920 (mtmt) cc_final: 0.7629 (mtmt)
REVERT: C  315 ARG cc_start: 0.7614 (tpp-160) cc_final: 0.7104 (ttm170)
REVERT: C  318 MET cc_start: 0.7467 (tpt) cc_final: 0.7008 (ptt)
REVERT: C  352 LYS cc_start: 0.7182 (tmtt) cc_final: 0.6817 (mttt)
REVERT: C  444 ASP cc_start: 0.7545 (t0) cc_final: 0.6954 (t70)
  outliers start: 28
  outliers final: 15
  residues processed: 172
  average time/residue: 1.1589
  time to fit residues: 213.7917
Evaluate side-chains
  178 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 156
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  346 GLU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  365 ILE
Chi-restraints excluded: chain B residue  368 ASP
Chi-restraints excluded: chain B residue  403 SER
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  269 CYS
Chi-restraints excluded: chain C residue  307 ILE
Chi-restraints excluded: chain C residue  368 ASP
Chi-restraints excluded: chain C residue  403 SER
Chi-restraints excluded: chain C residue  419 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 19 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 105 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.176527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.136502 restraints weight = 2734.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 0.81
r_work: 0.3083 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9417  Z= 0.270
  Angle     :  0.537   5.587  12783  Z= 0.280
  Chirality :  0.041   0.172   1626
  Planarity :  0.004   0.036   1557
  Dihedral  :  3.617  11.968   1281
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.47 %
    Favored  : 80.67 %
  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:  1.36 (0.24), residues: 1200
  helix:  1.22 (0.17), residues: 951
  sheet:  1.48 (0.73), residues: 48
  loop : -0.44 (0.41), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 276 
 HIS   0.002   0.001   HIS B 296 
 PHE   0.016   0.002   PHE C 240 
 TYR   0.008   0.001   TYR A 285 
 ARG   0.006   0.001   ARG B 353 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 156
  time to evaluate  : 1.009 
Fit side-chains
REVERT: A  256 TRP cc_start: 0.8487 (m100) cc_final: 0.7632 (m-10)
REVERT: A  269 CYS cc_start: 0.7389 (t) cc_final: 0.7008 (t)
REVERT: A  272 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6859 (mt-10)
REVERT: A  280 ARG cc_start: 0.7217 (ttp80) cc_final: 0.6773 (ttm170)
REVERT: A  281 LYS cc_start: 0.7100 (tttt) cc_final: 0.6032 (mmtp)
REVERT: A  286 MET cc_start: 0.8327 (mtp) cc_final: 0.8083 (mtm)
REVERT: A  318 MET cc_start: 0.7102 (tpt) cc_final: 0.6677 (ttp)
REVERT: A  347 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7965 (m110)
REVERT: A  356 ARG cc_start: 0.6782 (tpm170) cc_final: 0.6191 (ptp-110)
REVERT: A  367 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8446 (mtm)
REVERT: A  368 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7445 (m-30)
REVERT: B   40 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7083 (mt-10)
REVERT: B   42 SER cc_start: 0.8410 (t) cc_final: 0.8210 (m)
REVERT: B  142 MET cc_start: 0.8301 (mmm) cc_final: 0.7850 (tpp)
REVERT: B  205 MET cc_start: 0.8592 (ptm) cc_final: 0.8291 (ptt)
REVERT: B  269 CYS cc_start: 0.7455 (t) cc_final: 0.7069 (t)
REVERT: B  272 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6830 (mm-30)
REVERT: B  281 LYS cc_start: 0.6947 (tttt) cc_final: 0.5792 (mmtp)
REVERT: B  307 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7184 (mt)
REVERT: B  318 MET cc_start: 0.7287 (tpt) cc_final: 0.6982 (ttp)
REVERT: B  346 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6615 (mt-10)
REVERT: B  352 LYS cc_start: 0.6874 (tmtt) cc_final: 0.6624 (mttt)
REVERT: B  356 ARG cc_start: 0.6828 (tpm170) cc_final: 0.6194 (ptp-110)
REVERT: B  357 PHE cc_start: 0.7981 (t80) cc_final: 0.7661 (t80)
REVERT: B  419 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7945 (tpp)
REVERT: B  444 ASP cc_start: 0.7659 (t0) cc_final: 0.7386 (t0)
REVERT: C   40 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6843 (mp0)
REVERT: C   92 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6740 (mm)
REVERT: C  232 LYS cc_start: 0.7838 (ttpt) cc_final: 0.7542 (mtmt)
REVERT: C  256 TRP cc_start: 0.8570 (m100) cc_final: 0.7664 (m-10)
REVERT: C  258 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7869 (ttt)
REVERT: C  280 ARG cc_start: 0.7404 (ttp80) cc_final: 0.6978 (ttm170)
REVERT: C  281 LYS cc_start: 0.7156 (tttt) cc_final: 0.6209 (mmmm)
REVERT: C  286 MET cc_start: 0.8166 (mtp) cc_final: 0.7879 (mtm)
REVERT: C  307 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7272 (mt)
REVERT: C  311 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7611 (mtmt)
REVERT: C  315 ARG cc_start: 0.7562 (tpp-160) cc_final: 0.7051 (ttm170)
REVERT: C  318 MET cc_start: 0.7352 (tpt) cc_final: 0.6848 (ptt)
REVERT: C  352 LYS cc_start: 0.7127 (tmtt) cc_final: 0.6740 (mttt)
REVERT: C  385 ASN cc_start: 0.8173 (m-40) cc_final: 0.7887 (m110)
REVERT: C  444 ASP cc_start: 0.7427 (t0) cc_final: 0.6914 (t70)
  outliers start: 29
  outliers final: 13
  residues processed: 168
  average time/residue: 1.1367
  time to fit residues: 205.3413
Evaluate side-chains
  177 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 154
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain B residue   40 GLU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  346 GLU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  368 ASP
Chi-restraints excluded: chain B residue  403 SER
Chi-restraints excluded: chain B residue  419 MET
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  269 CYS
Chi-restraints excluded: chain C residue  307 ILE
Chi-restraints excluded: chain C residue  368 ASP
Chi-restraints excluded: chain C residue  403 SER
Chi-restraints excluded: chain C residue  419 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 102 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 348 ASN
A 413 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.190150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.154917 restraints weight = 2575.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 0.67
r_work: 0.3118 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9417  Z= 0.206
  Angle     :  0.501   8.664  12783  Z= 0.261
  Chirality :  0.040   0.163   1626
  Planarity :  0.004   0.035   1557
  Dihedral  :  3.498  11.753   1281
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.57 %
    Favored  : 80.57 %
  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:  1.56 (0.24), residues: 1200
  helix:  1.36 (0.17), residues: 948
  sheet:  1.48 (0.73), residues: 48
  loop : -0.34 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 276 
 HIS   0.001   0.000   HIS B 296 
 PHE   0.012   0.001   PHE C 240 
 TYR   0.008   0.001   TYR A 285 
 ARG   0.007   0.000   ARG C 353 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 159
  time to evaluate  : 1.067 
Fit side-chains
REVERT: A  256 TRP cc_start: 0.8490 (m100) cc_final: 0.7687 (m-10)
REVERT: A  272 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6865 (mt-10)
REVERT: A  280 ARG cc_start: 0.7241 (ttp80) cc_final: 0.6822 (ttm170)
REVERT: A  281 LYS cc_start: 0.7195 (tttt) cc_final: 0.6161 (mmtp)
REVERT: A  286 MET cc_start: 0.8353 (mtp) cc_final: 0.8113 (mtm)
REVERT: A  318 MET cc_start: 0.7225 (tpt) cc_final: 0.6891 (ttp)
REVERT: A  347 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.8016 (m110)
REVERT: A  356 ARG cc_start: 0.6747 (tpm170) cc_final: 0.6164 (ptp-110)
REVERT: A  359 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8153 (mp)
REVERT: A  368 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7382 (m-30)
REVERT: B   40 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7089 (mt-10)
REVERT: B   99 PHE cc_start: 0.7973 (t80) cc_final: 0.7610 (t80)
REVERT: B  142 MET cc_start: 0.8303 (mmm) cc_final: 0.7921 (tpp)
REVERT: B  205 MET cc_start: 0.8558 (ptm) cc_final: 0.8259 (ptt)
REVERT: B  269 CYS cc_start: 0.7565 (t) cc_final: 0.7133 (t)
REVERT: B  272 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6820 (mm-30)
REVERT: B  281 LYS cc_start: 0.7011 (tttt) cc_final: 0.5857 (mmtp)
REVERT: B  307 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.7230 (mt)
REVERT: B  318 MET cc_start: 0.7259 (tpt) cc_final: 0.7025 (ttp)
REVERT: B  346 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6647 (mt-10)
REVERT: B  352 LYS cc_start: 0.6927 (tmtt) cc_final: 0.6670 (mttt)
REVERT: B  353 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7857 (mpp80)
REVERT: B  356 ARG cc_start: 0.6833 (tpm170) cc_final: 0.6240 (ptp-110)
REVERT: B  357 PHE cc_start: 0.8002 (t80) cc_final: 0.7652 (t80)
REVERT: C   40 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6894 (mp0)
REVERT: C   92 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6772 (mm)
REVERT: C  232 LYS cc_start: 0.7736 (ttpt) cc_final: 0.7463 (mtmt)
REVERT: C  256 TRP cc_start: 0.8573 (m100) cc_final: 0.7704 (m-10)
REVERT: C  258 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7865 (ttt)
REVERT: C  274 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6625 (tp30)
REVERT: C  280 ARG cc_start: 0.7453 (ttp80) cc_final: 0.7062 (ttm170)
REVERT: C  281 LYS cc_start: 0.7210 (tttt) cc_final: 0.6289 (mmmm)
REVERT: C  286 MET cc_start: 0.8198 (mtp) cc_final: 0.7926 (mtm)
REVERT: C  307 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7348 (mt)
REVERT: C  311 LYS cc_start: 0.8019 (mtmt) cc_final: 0.7701 (mtmt)
REVERT: C  315 ARG cc_start: 0.7583 (tpp-160) cc_final: 0.7088 (ttm110)
REVERT: C  318 MET cc_start: 0.7353 (tpt) cc_final: 0.6873 (ptt)
REVERT: C  346 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6414 (mt-10)
REVERT: C  352 LYS cc_start: 0.7206 (tmtt) cc_final: 0.6836 (mttt)
REVERT: C  368 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7678 (m-30)
REVERT: C  385 ASN cc_start: 0.8212 (m-40) cc_final: 0.7937 (m110)
REVERT: C  444 ASP cc_start: 0.7414 (t0) cc_final: 0.6820 (t70)
  outliers start: 29
  outliers final: 13
  residues processed: 172
  average time/residue: 1.2190
  time to fit residues: 224.6433
Evaluate side-chains
  178 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 154
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain B residue   40 GLU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  346 GLU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  365 ILE
Chi-restraints excluded: chain B residue  368 ASP
Chi-restraints excluded: chain B residue  403 SER
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  269 CYS
Chi-restraints excluded: chain C residue  307 ILE
Chi-restraints excluded: chain C residue  346 GLU
Chi-restraints excluded: chain C residue  368 ASP
Chi-restraints excluded: chain C residue  403 SER
Chi-restraints excluded: chain C residue  419 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 118 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 77 optimal weight:    3.9990
   chunk 104 optimal weight:    0.0270
   chunk 86 optimal weight:    0.7980
   chunk 80 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 116 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.8440

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

Flipped N/Q/H residues before XYZ refinement:
A 413 GLN
C 348 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.168947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.127098 restraints weight = 2777.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 0.85
r_work: 0.3079 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9417  Z= 0.234
  Angle     :  0.523   9.651  12783  Z= 0.273
  Chirality :  0.041   0.198   1626
  Planarity :  0.004   0.035   1557
  Dihedral  :  3.537  11.839   1281
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.06 %
    Favored  : 80.37 %
  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:  1.48 (0.24), residues: 1200
  helix:  1.31 (0.17), residues: 948
  sheet:  1.32 (0.74), residues: 48
  loop : -0.38 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 276 
 HIS   0.002   0.001   HIS B 296 
 PHE   0.014   0.002   PHE C 240 
 TYR   0.008   0.001   TYR A 285 
 ARG   0.007   0.001   ARG C 353 

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

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

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2400 Ramachandran restraints generated.
    1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 1.131 
Fit side-chains
REVERT: A   92 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6505 (mm)
REVERT: A  256 TRP cc_start: 0.8502 (m100) cc_final: 0.7643 (m-10)
REVERT: A  269 CYS cc_start: 0.7447 (t) cc_final: 0.7064 (t)
REVERT: A  272 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6811 (mt-10)
REVERT: A  280 ARG cc_start: 0.7220 (ttp80) cc_final: 0.6776 (ttm170)
REVERT: A  281 LYS cc_start: 0.7105 (tttt) cc_final: 0.6036 (mmtp)
REVERT: A  286 MET cc_start: 0.8337 (mtp) cc_final: 0.8089 (mtm)
REVERT: A  318 MET cc_start: 0.7233 (tpt) cc_final: 0.6866 (ttp)
REVERT: A  347 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7952 (m110)
REVERT: A  356 ARG cc_start: 0.6764 (tpm170) cc_final: 0.6168 (ptp-110)
REVERT: A  357 PHE cc_start: 0.8158 (t80) cc_final: 0.7952 (t80)
REVERT: A  359 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8146 (mp)
REVERT: A  367 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8441 (mtm)
REVERT: A  368 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7382 (m-30)
REVERT: B   40 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7056 (mt-10)
REVERT: B   99 PHE cc_start: 0.7954 (t80) cc_final: 0.7587 (t80)
REVERT: B  142 MET cc_start: 0.8314 (mmm) cc_final: 0.7876 (tpp)
REVERT: B  205 MET cc_start: 0.8610 (ptm) cc_final: 0.8309 (ptt)
REVERT: B  269 CYS cc_start: 0.7461 (t) cc_final: 0.7016 (t)
REVERT: B  272 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6823 (mm-30)
REVERT: B  281 LYS cc_start: 0.6950 (tttt) cc_final: 0.5779 (mmtp)
REVERT: B  307 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.7168 (mt)
REVERT: B  318 MET cc_start: 0.7271 (tpt) cc_final: 0.6984 (ttp)
REVERT: B  346 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6535 (mt-10)
REVERT: B  352 LYS cc_start: 0.6869 (tmtt) cc_final: 0.6566 (mttt)
REVERT: B  353 ARG cc_start: 0.8010 (mtm-85) cc_final: 0.7798 (mpp80)
REVERT: B  356 ARG cc_start: 0.6755 (tpm170) cc_final: 0.6097 (ptp-110)
REVERT: B  357 PHE cc_start: 0.7971 (t80) cc_final: 0.7615 (t80)
REVERT: B  444 ASP cc_start: 0.7665 (t0) cc_final: 0.7430 (t0)
REVERT: C   92 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6749 (mm)
REVERT: C  232 LYS cc_start: 0.7807 (ttpt) cc_final: 0.7515 (mtmt)
REVERT: C  256 TRP cc_start: 0.8568 (m100) cc_final: 0.7662 (m-10)
REVERT: C  258 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7877 (ttt)
REVERT: C  274 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6647 (tp30)
REVERT: C  280 ARG cc_start: 0.7517 (ttp80) cc_final: 0.7028 (ttm170)
REVERT: C  281 LYS cc_start: 0.7176 (tttt) cc_final: 0.6225 (mmmm)
REVERT: C  286 MET cc_start: 0.8193 (mtp) cc_final: 0.7910 (mtm)
REVERT: C  307 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7275 (mt)
REVERT: C  311 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7678 (mtmt)
REVERT: C  315 ARG cc_start: 0.7547 (tpp-160) cc_final: 0.7032 (ttm110)
REVERT: C  318 MET cc_start: 0.7342 (tpt) cc_final: 0.6786 (ptt)
REVERT: C  346 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6358 (mt-10)
REVERT: C  352 LYS cc_start: 0.7156 (tmtt) cc_final: 0.6762 (mttt)
REVERT: C  385 ASN cc_start: 0.8126 (m-40) cc_final: 0.7874 (m110)
REVERT: C  444 ASP cc_start: 0.7343 (t0) cc_final: 0.6810 (t70)
  outliers start: 26
  outliers final: 12
  residues processed: 168
  average time/residue: 1.4885
  time to fit residues: 269.1067
Evaluate side-chains
  174 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 1.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain B residue   40 GLU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  307 ILE
Chi-restraints excluded: chain B residue  346 GLU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  368 ASP
Chi-restraints excluded: chain B residue  403 SER
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  258 MET
Chi-restraints excluded: chain C residue  269 CYS
Chi-restraints excluded: chain C residue  307 ILE
Chi-restraints excluded: chain C residue  346 GLU
Chi-restraints excluded: chain C residue  368 ASP
Chi-restraints excluded: chain C residue  403 SER
Chi-restraints excluded: chain C residue  419 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0000
   chunk 22 optimal weight:    0.9990
   chunk 92 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9980
   chunk 93 optimal weight:    0.3980
   overall best weight:    0.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 413 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.191818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.156369 restraints weight = 2567.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 0.69
r_work: 0.3184 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.3050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9417  Z= 0.174
  Angle     :  0.488   9.588  12783  Z= 0.255
  Chirality :  0.039   0.163   1626
  Planarity :  0.004   0.034   1557
  Dihedral  :  3.387  11.528   1281
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.96 %
    Favored  : 80.57 %
  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:  1.76 (0.24), residues: 1200
  helix:  1.50 (0.17), residues: 948
  sheet:  1.37 (0.75), residues: 48
  loop : -0.24 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  19 
 HIS   0.001   0.000   HIS B 296 
 PHE   0.011   0.001   PHE C 240 
 TYR   0.008   0.001   TYR A 162 
 ARG   0.007   0.000   ARG C 353 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7251.36 seconds
wall clock time: 129 minutes 52.21 seconds (7792.21 seconds total)