Starting phenix.real_space_refine
on Wed Mar 12 02:01:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qbn_18316/03_2025/8qbn_18316.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qbn_18316/03_2025/8qbn_18316.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qbn_18316/03_2025/8qbn_18316.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qbn_18316/03_2025/8qbn_18316.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qbn_18316/03_2025/8qbn_18316.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qbn_18316/03_2025/8qbn_18316.cif"
  }
  resolution = 3.2
  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=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      3      6.06       5
     S      43      5.16       5
     C    4399      2.51       5
     N    1267      2.21       5
     O    1309      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7021
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "7"
      Number of atoms: 3025
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 387, 3002
          Classifications: {'peptide': 387}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 14, 'TRANS': 372}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 109
          Unresolved non-hydrogen dihedrals: 70
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 58
      Conformer: "B"
        Number of residues, atoms: 387, 3002
          Classifications: {'peptide': 387}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 14, 'TRANS': 372}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 109
          Unresolved non-hydrogen dihedrals: 70
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 58
          bond proxies already assigned to first conformer: 3043
    Chain: "W"
      Number of atoms: 3058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 391, 3058
          Classifications: {'peptide': 391}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 15, 'TRANS': 375}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 32
    Chain: "Y"
      Number of atoms: 935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 935
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 1, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "7"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "W"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "Y"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    473  SG  CYS 7 300      38.682  73.606  62.497  1.00 51.16           S
  ATOM    605  SG  CYS 7 322      37.760  74.057  66.052  1.00 55.21           S
  ATOM   3498  SG  CYS W 300      26.251  64.816  41.836  1.00 44.85           S
  ATOM   3665  SG  CYS W 322      26.214  64.719  38.134  1.00 49.11           S
  ATOM   6208  SG  CYS Y  17      52.061  18.219  43.038  1.00 37.81           S
  ATOM   6227  SG  CYS Y  20      50.220  20.004  40.221  1.00 39.91           S
  ATOM   6639  SG  CYS Y  73      49.856  21.149  43.820  1.00 32.24           S
  ATOM   6662  SG  CYS Y  76      48.366  17.906  42.809  1.00 36.22           S

  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AARG 7 299 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG 7 299 " occ=0.50
    residue:
      pdb=" N  ATYR 7 330 " occ=0.50
      ... (22 atoms not shown)
      pdb=" OH BTYR 7 330 " occ=0.50
  Time building chain proxies: 7.55, per 1000 atoms: 1.08
  Number of scatterers: 7021
  At special positions: 0
  Unit cell: (78.12, 115.785, 110.205, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      3     29.99
     S      43     16.00
     O    1309      8.00
     N    1267      7.00
     C    4399      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.73
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN 7 701 "
        pdb="ZN    ZN 7 701 " - pdb=" ND1 HIS 7 303 "
        pdb="ZN    ZN 7 701 " - pdb=" NE2 HIS 7 320 "
        pdb="ZN    ZN 7 701 " - pdb=" SG  CYS 7 322 "
        pdb="ZN    ZN 7 701 " - pdb=" SG  CYS 7 300 "
      pdb="  ZN W 701 "
        pdb="ZN    ZN W 701 " - pdb=" ND1 HIS W 303 "
        pdb="ZN    ZN W 701 " - pdb=" NE2 HIS W 320 "
        pdb="ZN    ZN W 701 " - pdb=" SG  CYS W 300 "
        pdb="ZN    ZN W 701 " - pdb=" SG  CYS W 322 "
      pdb="  ZN Y 501 "
        pdb="ZN    ZN Y 501 " - pdb=" SG  CYS Y  17 "
        pdb="ZN    ZN Y 501 " - pdb=" SG  CYS Y  20 "
        pdb="ZN    ZN Y 501 " - pdb=" SG  CYS Y  73 "
        pdb="ZN    ZN Y 501 " - pdb=" SG  CYS Y  76 "
      Number of angles added : 10


  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1668

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 16 sheets defined
      11.8% alpha, 30.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain '7' and resid 121 through 139
      removed outlier: 3.804A  pdb=" N   GLY 7 139 " --> pdb=" O   LEU 7 135 " (cutoff:3.500A)
    Processing helix  chain '7' and resid 142 through 152
    Processing helix  chain '7' and resid 283 through 299
      removed outlier: 3.628A  pdb=" N   THR 7 287 " --> pdb=" O   ARG 7 283 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N  AARG 7 299 " --> pdb=" O   LEU 7 295 " (cutoff:3.500A)
    Processing helix  chain '7' and resid 323 through 327
    Processing helix  chain 'W' and resid 122 through 137
      removed outlier: 3.723A  pdb=" N   GLY W 137 " --> pdb=" O   GLN W 133 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 141 through 151
    Processing helix  chain 'W' and resid 283 through 299
      removed outlier: 3.735A  pdb=" N   THR W 287 " --> pdb=" O   ARG W 283 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 323 through 326
      removed outlier: 4.028A  pdb=" N   GLN W 326 " --> pdb=" O   SER W 323 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'W' and resid 323 through 326'
    Processing helix  chain 'Y' and resid 89 through 94
      removed outlier: 4.503A  pdb=" N   TYR Y  94 " --> pdb=" O   SER Y  91 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain '7' and resid 330 through 335
      removed outlier: 6.543A  pdb=" N   ILE 7 624 " --> pdb=" O   GLN 7 332 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   ILE 7 334 " --> pdb=" O   VAL 7 622 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   VAL 7 622 " --> pdb=" O   ILE 7 334 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain '7' and resid 342 through 347
      removed outlier: 3.638A  pdb=" N   PHE 7 344 " --> pdb=" O   GLY 7 357 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   VAL 7 363 " --> pdb=" O   THR 7 380 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   THR 7 380 " --> pdb=" O   VAL 7 363 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ILE 7 365 " --> pdb=" O   LEU 7 378 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain '7' and resid 390 through 393
      removed outlier: 4.034A  pdb=" N   TYR 7 390 " --> pdb=" O   CYS 7 403 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain '7' and resid 435 through 438
      removed outlier: 3.530A  pdb=" N   SER 7 435 " --> pdb=" O   GLY 7 448 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLY 7 448 " --> pdb=" O   SER 7 435 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   ASP 7 458 " --> pdb=" O   LEU 7 463 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   LEU 7 463 " --> pdb=" O   ASP 7 458 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain '7' and resid 474 through 477
      removed outlier: 3.696A  pdb=" N   CYS 7 474 " --> pdb=" O   SER 7 487 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ILE 7 493 " --> pdb=" O   ILE 7 506 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain '7' and resid 513 through 518
      removed outlier: 3.970A  pdb=" N   SER 7 515 " --> pdb=" O   ASN 7 528 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   VAL 7 534 " --> pdb=" O   LYS 7 547 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   LYS 7 547 " --> pdb=" O   VAL 7 534 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   LEU 7 536 " --> pdb=" O   VAL 7 545 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain '7' and resid 560 through 563
      removed outlier: 3.649A  pdb=" N   ALA 7 591 " --> pdb=" O   ILE 7 581 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'W' and resid 328 through 335
      removed outlier: 5.021A  pdb=" N   THR W 331 " --> pdb=" O   GLY W 626 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   GLY W 626 " --> pdb=" O   THR W 331 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLN W 333 " --> pdb=" O   ILE W 624 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   CYS W 602 " --> pdb=" O   ALA W 616 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'W' and resid 342 through 347
      removed outlier: 3.566A  pdb=" N   SER W 358 " --> pdb=" O   THR W 362 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   THR W 362 " --> pdb=" O   SER W 358 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LYS W 379 " --> pdb=" O   ILE W 365 " (cutoff:3.500A)
      removed outlier: 5.461A  pdb=" N   GLN W 367 " --> pdb=" O   LEU W 377 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   LEU W 377 " --> pdb=" O   GLN W 367 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'W' and resid 391 through 393
      removed outlier: 3.597A  pdb=" N   THR W 423 " --> pdb=" O   LEU W 413 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   ASN W 415 " --> pdb=" O   LEU W 421 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   LEU W 421 " --> pdb=" O   ASN W 415 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'W' and resid 435 through 438
      removed outlier: 4.130A  pdb=" N   PHE W 454 " --> pdb=" O   TRP W 467 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   ASP W 458 " --> pdb=" O   LEU W 463 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   LEU W 463 " --> pdb=" O   ASP W 458 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'W' and resid 472 through 477
      removed outlier: 3.623A  pdb=" N   CYS W 474 " --> pdb=" O   SER W 487 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'W' and resid 513 through 518
      removed outlier: 3.799A  pdb=" N   SER W 515 " --> pdb=" O   ASN W 528 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ARG W 546 " --> pdb=" O   LEU W 536 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ASP W 538 " --> pdb=" O   LEU W 544 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   LEU W 544 " --> pdb=" O   ASP W 538 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'W' and resid 560 through 563
    Processing sheet with id=AB6, first strand: chain 'Y' and resid 23 through 26
      removed outlier: 6.684A  pdb=" N   ILE Y  23 " --> pdb=" O   CYS Y  17 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   CYS Y  17 " --> pdb=" O   ILE Y  23 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   THR Y  25 " --> pdb=" O   PHE Y  15 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'Y' and resid 30 through 36
      removed outlier: 7.048A  pdb=" N   LEU Y  44 " --> pdb=" O   ILE Y  31 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   THR Y  33 " --> pdb=" O   ALA Y  42 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   ALA Y  42 " --> pdb=" O   THR Y  33 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL Y  99 " --> pdb=" O   PHE Y  45 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   LEU Y  80 " --> pdb=" O   GLU Y 102 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   LYS Y  79 " --> pdb=" O   CYS Y  73 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   CYS Y  73 " --> pdb=" O   LYS Y  79 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLY Y  81 " --> pdb=" O   VAL Y  71 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   MET Y  67 " --> pdb=" O   GLU Y  85 " (cutoff:3.500A)
      removed outlier: 5.098A  pdb=" N   ALA Y  87 " --> pdb=" O   ARG Y  65 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   ARG Y  65 " --> pdb=" O   ALA Y  87 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ASP Y  70 " --> pdb=" O   GLU Y  55 " (cutoff:3.500A)
      removed outlier: 5.365A  pdb=" N   GLU Y  55 " --> pdb=" O   ASP Y  70 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   SER Y  72 " --> pdb=" O   TYR Y  53 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   TYR Y  53 " --> pdb=" O   SER Y  72 " (cutoff:3.500A)

    227 hydrogen bonds defined for protein.
    615 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: 2.02

  Time building geometry restraints manager: 1.91 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2373
        1.34 -     1.46: 1626
        1.46 -     1.58: 3119
        1.58 -     1.71: 0
        1.71 -     1.83: 56
  Bond restraints: 7174
  Sorted by residual:
  bond pdb=" N   VAL Y 116 "
       pdb=" CA  VAL Y 116 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.035 7.50e-03 1.78e+04 2.14e+01
  bond pdb=" N   VAL 7 507 "
       pdb=" CA  VAL 7 507 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.19e-02 7.06e+03 9.26e+00
  bond pdb=" N   VAL W 603 "
       pdb=" CA  VAL W 603 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.036 1.19e-02 7.06e+03 8.95e+00
  bond pdb=" N   TRP W 476 "
       pdb=" CA  TRP W 476 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.18e-02 7.18e+03 7.67e+00
  bond pdb=" N   ILE 7 506 "
       pdb=" CA  ILE 7 506 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.25e-02 6.40e+03 7.31e+00
  ... (remaining 7169 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 9499
        1.53 -     3.06: 219
        3.06 -     4.59: 25
        4.59 -     6.12: 8
        6.12 -     7.66: 4
  Bond angle restraints: 9755
  Sorted by residual:
  angle pdb=" N   ARG W 324 "
        pdb=" CA  ARG W 324 "
        pdb=" C   ARG W 324 "
      ideal   model   delta    sigma   weight residual
     113.15  108.54    4.61 1.19e+00 7.06e-01 1.50e+01
  angle pdb=" CA  ARG 7 504 "
        pdb=" C   ARG 7 504 "
        pdb=" O   ARG 7 504 "
      ideal   model   delta    sigma   weight residual
     121.51  117.41    4.10 1.12e+00 7.97e-01 1.34e+01
  angle pdb=" CA  ILE W 518 "
        pdb=" C   ILE W 518 "
        pdb=" O   ILE W 518 "
      ideal   model   delta    sigma   weight residual
     121.93  118.02    3.91 1.12e+00 7.97e-01 1.22e+01
  angle pdb=" C   SER 7 121 "
        pdb=" CA  SER 7 121 "
        pdb=" CB  SER 7 121 "
      ideal   model   delta    sigma   weight residual
     111.78  104.12    7.66 2.20e+00 2.07e-01 1.21e+01
  angle pdb=" CA  HIS Y 115 "
        pdb=" CB  HIS Y 115 "
        pdb=" CG  HIS Y 115 "
      ideal   model   delta    sigma   weight residual
     113.80  117.18   -3.38 1.00e+00 1.00e+00 1.14e+01
  ... (remaining 9750 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.74: 3743
       16.74 -    33.49: 373
       33.49 -    50.23: 91
       50.23 -    66.97: 16
       66.97 -    83.72: 5
  Dihedral angle restraints: 4228
    sinusoidal: 1642
      harmonic: 2586
  Sorted by residual:
  dihedral pdb=" CA  TYR W 302 "
           pdb=" C   TYR W 302 "
           pdb=" N   HIS W 303 "
           pdb=" CA  HIS W 303 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.93  -18.07     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" C   SER 7 121 "
           pdb=" N   SER 7 121 "
           pdb=" CA  SER 7 121 "
           pdb=" CB  SER 7 121 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.78   -8.82     0      2.50e+00 1.60e-01 1.25e+01
  dihedral pdb=" CA  CYS W 561 "
           pdb=" C   CYS W 561 "
           pdb=" N   PHE W 562 "
           pdb=" CA  PHE W 562 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.93   17.07     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 4225 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 808
       0.049 -    0.097: 206
       0.097 -    0.146: 69
       0.146 -    0.194: 2
       0.194 -    0.243: 4
  Chirality restraints: 1089
  Sorted by residual:
  chirality pdb=" CA  SER 7 121 "
            pdb=" N   SER 7 121 "
            pdb=" C   SER 7 121 "
            pdb=" CB  SER 7 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  VAL W 603 "
            pdb=" N   VAL W 603 "
            pdb=" C   VAL W 603 "
            pdb=" CB  VAL W 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  ILE 7 506 "
            pdb=" N   ILE 7 506 "
            pdb=" C   ILE 7 506 "
            pdb=" CB  ILE 7 506 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 1086 not shown)

  Planarity restraints: 1263
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP W 605 "    0.014 2.00e-02 2.50e+03   1.47e-02 5.38e+00
        pdb=" CG  TRP W 605 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TRP W 605 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP W 605 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP W 605 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP W 605 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP W 605 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP W 605 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP W 605 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP W 605 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN W 439 "    0.036 5.00e-02 4.00e+02   5.46e-02 4.77e+00
        pdb=" N   PRO W 440 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO W 440 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO W 440 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG 7 504 "    0.148 9.50e-02 1.11e+02   6.63e-02 2.80e+00
        pdb=" NE  ARG 7 504 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG 7 504 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG 7 504 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG 7 504 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1260 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 593
        2.74 -     3.28: 6068
        3.28 -     3.82: 10575
        3.82 -     4.36: 13006
        4.36 -     4.90: 23811
  Nonbonded interactions: 54053
  Sorted by model distance:
  nonbonded pdb=" OG  SER W 574 "
            pdb=" OD1 ASP W 576 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   GLU W 341 "
            pdb=" OG  SER W 358 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OG  SER 7 574 "
            pdb=" OD1 ASP 7 576 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   ASN 7 304 "
            pdb=" OD1 ASN 7 304 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OG  SER W 428 "
            pdb=" OD1 ASP W 431 "
     model   vdw
     2.307 3.040
  ... (remaining 54048 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain '7' and ((resid 121 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 122 through 123 or (resid 124 through 125 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 126 through 141 or (resid 142 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 143 through 298 or resi \ 
d 300 through 312 or (resid 313 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 314 through 320 or (resid 321 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 322 through 329 or resid 331 through 375 or (r \ 
esid 376 and (name N or name CA or name C or name O or name CB )) or resid 377 t \ 
hrough 419 or (resid 420 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 421 through 481 or (resid 482 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 483 through 498 or (resid 499 and (name N or name CA  \ 
or name C or name O or name CB )) or resid 500 through 629 or resid 701))
  selection = (chain 'W' and (resid 121 through 124 or (resid 125 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 126 through 140 or (resid 141 through 142  \ 
and (name N or name CA or name C or name O or name CB )) or resid 143 through 14 \ 
4 or (resid 145 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 146 through 154 or (resid 155 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 276 through 278 or (resid 279 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 280 through 293 or (resid 294 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 295 through 298 or resid 300 t \ 
hrough 304 or (resid 305 through 308 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 313 through 322 or (resid 323 and (name N or name CA or n \ 
ame C or name O or name CB )) or resid 324 through 329 or resid 331 through 405  \ 
or (resid 406 through 407 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 408 through 457 or (resid 458 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 459 or (resid 460 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 461 through 554 or (resid 555 through 556 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 557 through 629 or r \ 
esid 701))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             2.350
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     23.960
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
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   0.038   7174  Z= 0.244
  Angle     :  0.589   7.655   9755  Z= 0.344
  Chirality :  0.048   0.243   1089
  Planarity :  0.004   0.066   1263
  Dihedral  : 14.296  83.717   2560
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.53 %
    Favored  : 99.20 %
  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: -0.65 (0.28), residues: 891
  helix:  2.75 (0.59), residues: 87
  sheet: -0.12 (0.31), residues: 274
  loop : -1.18 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP W 605 
 HIS   0.008   0.001   HIS W 565 
 PHE   0.020   0.002   PHE 7 454 
 TYR   0.009   0.001   TYR W 330 
 ARG   0.006   0.000   ARG 7 504 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.743 
Fit side-chains
REVERT: 7  318 ILE cc_start: 0.8770 (mt) cc_final: 0.8241 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 51
  average time/residue: 0.2059
  time to fit residues: 14.5822
Evaluate side-chains
  37 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0770
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   chunk 26 optimal weight:    0.3980
   chunk 41 optimal weight:    0.0470
   chunk 51 optimal weight:    0.9980
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.3636

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

Flipped N/Q/H residues before XYZ refinement:
7 384 HIS
W 417 GLN
Y  50 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.093121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.077562 restraints weight = 35331.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 2.97
r_work: 0.2746 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2761
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2761 r_free = 0.2761    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2761 r_free = 0.2761    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2761
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.0632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7174  Z= 0.156
  Angle     :  0.502   7.849   9755  Z= 0.268
  Chirality :  0.045   0.244   1089
  Planarity :  0.003   0.046   1263
  Dihedral  :  4.226  16.473    974
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  3.59 %
    Favored  : 95.88 %
  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: -0.35 (0.28), residues: 891
  helix:  3.08 (0.57), residues: 90
  sheet:  0.12 (0.31), residues: 277
  loop : -1.06 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP W 605 
 HIS   0.004   0.001   HIS W 303 
 PHE   0.017   0.001   PHE 7 454 
 TYR   0.009   0.001   TYR 7 302 
 ARG   0.003   0.000   ARG W 324 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.806 
Fit side-chains
REVERT: 7  148 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7480 (mmm)
REVERT: 7  318 ILE cc_start: 0.8612 (mt) cc_final: 0.8018 (tp)
  outliers start: 3
  outliers final: 1
  residues processed: 46
  average time/residue: 0.1578
  time to fit residues: 10.9850
Evaluate side-chains
  45 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 7 residue  148 MET
Chi-restraints excluded: chain Y residue  100 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 82 optimal weight:    0.2980
   chunk 36 optimal weight:    0.0970
   chunk 65 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
W 417 GLN
W 473 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.091437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.076303 restraints weight = 31169.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 2.77
r_work: 0.2727 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.0761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   7174  Z= 0.229
  Angle     :  0.524   5.882   9755  Z= 0.279
  Chirality :  0.045   0.180   1089
  Planarity :  0.003   0.039   1263
  Dihedral  :  4.326  16.542    974
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  7.18 %
    Favored  : 92.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.28), residues: 891
  helix:  2.65 (0.57), residues: 96
  sheet:  0.16 (0.32), residues: 271
  loop : -1.09 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP 7 605 
 HIS   0.005   0.001   HIS W 577 
 PHE   0.024   0.002   PHE 7 454 
 TYR   0.010   0.001   TYR 7 302 
 ARG   0.003   0.000   ARG Y  27 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.771 
Fit side-chains
REVERT: 7  148 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7580 (mmm)
  outliers start: 2
  outliers final: 1
  residues processed: 44
  average time/residue: 0.1672
  time to fit residues: 11.0626
Evaluate side-chains
  44 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 7 residue  148 MET
Chi-restraints excluded: chain W residue  590 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 58 optimal weight:    0.1980
   chunk 28 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 82 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
W 417 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.090799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.075320 restraints weight = 36338.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 2.97
r_work: 0.2710 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.0889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   7174  Z= 0.239
  Angle     :  0.524   6.155   9755  Z= 0.279
  Chirality :  0.045   0.155   1089
  Planarity :  0.003   0.039   1263
  Dihedral  :  4.387  16.926    974
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  8.91 %
    Favored  : 90.03 %
  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: -0.41 (0.28), residues: 891
  helix:  2.63 (0.57), residues: 97
  sheet:  0.19 (0.31), residues: 277
  loop : -1.15 (0.26), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP 7 605 
 HIS   0.007   0.001   HIS W 577 
 PHE   0.025   0.002   PHE 7 454 
 TYR   0.011   0.001   TYR W 390 
 ARG   0.003   0.000   ARG Y  27 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.824 
Fit side-chains
REVERT: 7  148 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7565 (mmm)
REVERT: Y   14 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8528 (mt)
  outliers start: 7
  outliers final: 5
  residues processed: 44
  average time/residue: 0.1621
  time to fit residues: 10.9270
Evaluate side-chains
  46 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 7 residue  148 MET
Chi-restraints excluded: chain W residue  127 VAL
Chi-restraints excluded: chain W residue  318 ILE
Chi-restraints excluded: chain W residue  565 HIS
Chi-restraints excluded: chain W residue  590 ILE
Chi-restraints excluded: chain Y residue   14 LEU
Chi-restraints excluded: chain Y residue   23 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 3 optimal weight:    0.3980
   chunk 69 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 6 optimal weight:    0.3980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
W 417 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.090283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.074132 restraints weight = 46323.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 3.35
r_work: 0.2673 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2683
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.0946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   7174  Z= 0.233
  Angle     :  0.518   6.658   9755  Z= 0.277
  Chirality :  0.045   0.160   1089
  Planarity :  0.003   0.039   1263
  Dihedral  :  4.382  16.586    974
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 10.11 %
    Favored  : 88.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.28), residues: 891
  helix:  2.64 (0.57), residues: 97
  sheet:  0.22 (0.31), residues: 277
  loop : -1.14 (0.26), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP 7 605 
 HIS   0.006   0.001   HIS W 577 
 PHE   0.023   0.002   PHE 7 454 
 TYR   0.010   0.001   TYR W 390 
 ARG   0.003   0.000   ARG Y  27 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.749 
Fit side-chains
REVERT: 7  148 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7591 (mmm)
REVERT: Y   14 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8568 (mt)
  outliers start: 7
  outliers final: 5
  residues processed: 44
  average time/residue: 0.1536
  time to fit residues: 10.3304
Evaluate side-chains
  45 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 7 residue  148 MET
Chi-restraints excluded: chain W residue  127 VAL
Chi-restraints excluded: chain W residue  318 ILE
Chi-restraints excluded: chain W residue  565 HIS
Chi-restraints excluded: chain W residue  590 ILE
Chi-restraints excluded: chain Y residue   12 THR
Chi-restraints excluded: chain Y residue   14 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
W 417 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.090279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.075728 restraints weight = 25219.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 2.47
r_work: 0.2739 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2613 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2613
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.0989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7174  Z= 0.227
  Angle     :  0.513   7.213   9755  Z= 0.274
  Chirality :  0.045   0.155   1089
  Planarity :  0.003   0.039   1263
  Dihedral  :  4.377  16.352    974
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 10.90 %
    Favored  : 87.90 %
  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: -0.37 (0.28), residues: 891
  helix:  2.60 (0.57), residues: 98
  sheet:  0.25 (0.31), residues: 277
  loop : -1.15 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP 7 582 
 HIS   0.006   0.001   HIS W 577 
 PHE   0.022   0.002   PHE 7 454 
 TYR   0.010   0.001   TYR W 390 
 ARG   0.003   0.000   ARG Y  27 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.756 
Fit side-chains
REVERT: 7  148 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7623 (mmm)
REVERT: Y   14 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8592 (mt)
  outliers start: 8
  outliers final: 6
  residues processed: 43
  average time/residue: 0.1597
  time to fit residues: 10.5380
Evaluate side-chains
  46 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 7 residue  148 MET
Chi-restraints excluded: chain W residue  127 VAL
Chi-restraints excluded: chain W residue  318 ILE
Chi-restraints excluded: chain W residue  565 HIS
Chi-restraints excluded: chain W residue  590 ILE
Chi-restraints excluded: chain Y residue   12 THR
Chi-restraints excluded: chain Y residue   14 LEU
Chi-restraints excluded: chain Y residue   23 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 42 optimal weight:    0.4980
   chunk 68 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
W 417 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.089947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.074953 restraints weight = 29144.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 2.67
r_work: 0.2702 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2712
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2712 r_free = 0.2712    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2712 r_free = 0.2712    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2712
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.1042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7174  Z= 0.265
  Angle     :  0.537   8.002   9755  Z= 0.286
  Chirality :  0.045   0.166   1089
  Planarity :  0.003   0.040   1263
  Dihedral  :  4.466  16.952    974
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.90 %
    Favored  : 87.37 %
  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: -0.37 (0.28), residues: 891
  helix:  2.56 (0.57), residues: 98
  sheet:  0.34 (0.32), residues: 271
  loop : -1.17 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP 7 605 
 HIS   0.007   0.001   HIS W 577 
 PHE   0.025   0.002   PHE 7 454 
 TYR   0.011   0.001   TYR W 390 
 ARG   0.003   0.000   ARG Y  27 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 39
  time to evaluate  : 0.769 
Fit side-chains
REVERT: 7  148 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7643 (mmm)
REVERT: Y   14 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8564 (mt)
  outliers start: 12
  outliers final: 10
  residues processed: 48
  average time/residue: 0.1516
  time to fit residues: 11.1530
Evaluate side-chains
  50 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 38
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 7 residue  148 MET
Chi-restraints excluded: chain 7 residue  600 VAL
Chi-restraints excluded: chain W residue  127 VAL
Chi-restraints excluded: chain W residue  318 ILE
Chi-restraints excluded: chain W residue  502 THR
Chi-restraints excluded: chain W residue  517 THR
Chi-restraints excluded: chain W residue  552 THR
Chi-restraints excluded: chain W residue  565 HIS
Chi-restraints excluded: chain W residue  590 ILE
Chi-restraints excluded: chain Y residue   12 THR
Chi-restraints excluded: chain Y residue   14 LEU
Chi-restraints excluded: chain Y residue   23 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 66 optimal weight:    0.3980
   chunk 67 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
W 417 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.089917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.074602 restraints weight = 33709.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.2819 rms_B_bonded: 2.84
r_work: 0.2695 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.1071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   7174  Z= 0.265
  Angle     :  0.537   8.255   9755  Z= 0.287
  Chirality :  0.045   0.165   1089
  Planarity :  0.003   0.040   1263
  Dihedral  :  4.501  16.982    974
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.44 %
    Favored  : 86.70 %
  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: -0.36 (0.28), residues: 891
  helix:  2.51 (0.57), residues: 98
  sheet:  0.36 (0.32), residues: 271
  loop : -1.16 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP 7 582 
 HIS   0.006   0.001   HIS W 577 
 PHE   0.024   0.002   PHE 7 454 
 TYR   0.011   0.001   TYR W 390 
 ARG   0.005   0.000   ARG 7 523 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.770 
Fit side-chains
REVERT: 7  148 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7664 (mmm)
REVERT: Y   14 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8569 (mt)
  outliers start: 13
  outliers final: 11
  residues processed: 48
  average time/residue: 0.1517
  time to fit residues: 11.1663
Evaluate side-chains
  51 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 7 residue  148 MET
Chi-restraints excluded: chain 7 residue  600 VAL
Chi-restraints excluded: chain W residue  127 VAL
Chi-restraints excluded: chain W residue  318 ILE
Chi-restraints excluded: chain W residue  502 THR
Chi-restraints excluded: chain W residue  517 THR
Chi-restraints excluded: chain W residue  552 THR
Chi-restraints excluded: chain W residue  565 HIS
Chi-restraints excluded: chain W residue  590 ILE
Chi-restraints excluded: chain Y residue   12 THR
Chi-restraints excluded: chain Y residue   14 LEU
Chi-restraints excluded: chain Y residue   23 ILE
Chi-restraints excluded: chain Y residue  100 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
W 417 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.088429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.073097 restraints weight = 34985.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.2801 rms_B_bonded: 2.88
r_work: 0.2675 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2683
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   7174  Z= 0.369
  Angle     :  0.602   8.231   9755  Z= 0.320
  Chirality :  0.048   0.180   1089
  Planarity :  0.004   0.043   1263
  Dihedral  :  4.745  18.407    974
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 11.57 %
    Favored  : 86.30 %
  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: -0.52 (0.28), residues: 891
  helix:  2.51 (0.57), residues: 96
  sheet:  0.19 (0.32), residues: 269
  loop : -1.24 (0.26), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP 7 605 
 HIS   0.008   0.001   HIS W 577 
 PHE   0.031   0.003   PHE 7 454 
 TYR   0.013   0.002   TYR W 390 
 ARG   0.004   0.000   ARG Y  27 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 37
  time to evaluate  : 0.774 
Fit side-chains
REVERT: Y   14 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8574 (mt)
  outliers start: 15
  outliers final: 12
  residues processed: 48
  average time/residue: 0.1563
  time to fit residues: 11.6083
Evaluate side-chains
  49 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 7 residue  148 MET
Chi-restraints excluded: chain 7 residue  600 VAL
Chi-restraints excluded: chain W residue  127 VAL
Chi-restraints excluded: chain W residue  318 ILE
Chi-restraints excluded: chain W residue  502 THR
Chi-restraints excluded: chain W residue  517 THR
Chi-restraints excluded: chain W residue  552 THR
Chi-restraints excluded: chain W residue  565 HIS
Chi-restraints excluded: chain W residue  590 ILE
Chi-restraints excluded: chain Y residue   12 THR
Chi-restraints excluded: chain Y residue   14 LEU
Chi-restraints excluded: chain Y residue   23 ILE
Chi-restraints excluded: chain Y residue  100 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 84 optimal weight:    0.0770
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
W 417 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.089553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.073787 restraints weight = 39775.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.2819 rms_B_bonded: 3.11
r_work: 0.2686 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2694
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2694
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   7174  Z= 0.235
  Angle     :  0.528   8.353   9755  Z= 0.282
  Chirality :  0.045   0.162   1089
  Planarity :  0.003   0.041   1263
  Dihedral  :  4.556  17.088    974
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.97 %
    Favored  : 86.17 %
  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: -0.45 (0.28), residues: 891
  helix:  2.56 (0.57), residues: 96
  sheet:  0.37 (0.32), residues: 266
  loop : -1.26 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP 7 582 
 HIS   0.005   0.001   HIS W 577 
 PHE   0.022   0.002   PHE 7 454 
 TYR   0.011   0.001   TYR W 390 
 ARG   0.002   0.000   ARG Y  27 

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.837 
Fit side-chains
REVERT: 7  148 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7577 (mmm)
REVERT: Y   14 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8577 (mt)
  outliers start: 13
  outliers final: 10
  residues processed: 48
  average time/residue: 0.1731
  time to fit residues: 12.3768
Evaluate side-chains
  49 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 37
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain 7 residue  148 MET
Chi-restraints excluded: chain 7 residue  600 VAL
Chi-restraints excluded: chain W residue  127 VAL
Chi-restraints excluded: chain W residue  318 ILE
Chi-restraints excluded: chain W residue  502 THR
Chi-restraints excluded: chain W residue  517 THR
Chi-restraints excluded: chain W residue  552 THR
Chi-restraints excluded: chain W residue  565 HIS
Chi-restraints excluded: chain W residue  590 ILE
Chi-restraints excluded: chain Y residue   12 THR
Chi-restraints excluded: chain Y residue   14 LEU
Chi-restraints excluded: chain Y residue   23 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0970
   chunk 78 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0670
   chunk 74 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0070
   chunk 39 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.3134

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

Flipped N/Q/H residues before XYZ refinement:
W 417 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.091829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.077473 restraints weight = 23869.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 2.41
r_work: 0.2760 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2636 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2645 r_free = 0.2645    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2645 r_free = 0.2645    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8695
moved from start:          0.1122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7174  Z= 0.139
  Angle     :  0.473   8.295   9755  Z= 0.253
  Chirality :  0.044   0.138   1089
  Planarity :  0.003   0.040   1263
  Dihedral  :  4.213  15.243    974
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 12.23 %
    Favored  : 86.30 %
  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: -0.28 (0.28), residues: 891
  helix:  2.63 (0.57), residues: 98
  sheet:  0.37 (0.31), residues: 274
  loop : -1.10 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP 7 582 
 HIS   0.003   0.001   HIS W 577 
 PHE   0.014   0.001   PHE 7 454 
 TYR   0.007   0.001   TYR 7 302 
 ARG   0.006   0.000   ARG W 324 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3363.02 seconds
wall clock time: 58 minutes 22.96 seconds (3502.96 seconds total)