Starting phenix.real_space_refine
on Wed Feb  4 03:30:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u6g_63905/02_2026/9u6g_63905.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u6g_63905/02_2026/9u6g_63905.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u6g_63905/02_2026/9u6g_63905.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u6g_63905/02_2026/9u6g_63905.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u6g_63905/02_2026/9u6g_63905.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u6g_63905/02_2026/9u6g_63905.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      19      5.16       5
     C    5667      2.51       5
     N    1449      2.21       5
     O    1492      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8627
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "N"
      Number of atoms: 2479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2479
          Classifications: {'peptide': 314}
          Link IDs: {'PTRANS': 15, 'TRANS': 298}
    Chain: "O"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 509
          Classifications: {'peptide': 73}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "P"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 509
          Classifications: {'peptide': 73}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "Q"
      Number of atoms: 515
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 515
          Classifications: {'peptide': 74}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
    Chain: "R"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 509
          Classifications: {'peptide': 73}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "S"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 509
          Classifications: {'peptide': 73}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "T"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 509
          Classifications: {'peptide': 73}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "U"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 509
          Classifications: {'peptide': 73}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "V"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 509
          Classifications: {'peptide': 73}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "W"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 509
          Classifications: {'peptide': 73}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "X"
      Number of atoms: 505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 505
          Classifications: {'peptide': 72}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 70}
    Chain: "Y"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 509
          Classifications: {'peptide': 73}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "Z"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 509
          Classifications: {'peptide': 73}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "N"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 33
          Classifications: {'water': 33}
          Link IDs: {None: 32}
    Chain: "X"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "Y"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.33, per 1000 atoms: 0.27
  Number of scatterers: 8627
  At special positions: 0
  Unit cell: (92.316, 95.142, 78.186, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      19     16.00
     O    1492      8.00
     N    1449      7.00
     C    5667      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 342.9 milliseconds
  

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1970

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 2 sheets defined
      90.3% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'N' and resid 327 through 336
      removed outlier: 3.727A  pdb=" N   LEU N 332 " --> pdb=" O   LYS N 328 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   LEU N 333 " --> pdb=" O   PRO N 329 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   PHE N 336 " --> pdb=" O   LEU N 332 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 349 through 364
      removed outlier: 4.014A  pdb=" N   VAL N 353 " --> pdb=" O   PRO N 349 " (cutoff:3.500A)
      Proline residue:  N 356  - end of helix
    Processing helix  chain 'N' and resid 365 through 385
    Processing helix  chain 'N' and resid 400 through 425
    Processing helix  chain 'N' and resid 455 through 489
      removed outlier: 5.638A  pdb=" N   ASN N 461 " --> pdb=" O   ALA N 457 " (cutoff:3.500A)
      removed outlier: 5.360A  pdb=" N   LEU N 462 " --> pdb=" O   LYS N 458 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LEU N 466 " --> pdb=" O   LEU N 462 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 491 through 518
      removed outlier: 3.596A  pdb=" N   GLU N 497 " --> pdb=" O   ALA N 493 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ASN N 518 " --> pdb=" O   SER N 514 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 520 through 543
      removed outlier: 3.681A  pdb=" N   LEU N 524 " --> pdb=" O   GLN N 520 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLN N 525 " --> pdb=" O   ALA N 521 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   GLY N 526 " --> pdb=" O   GLY N 522 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ARG N 543 " --> pdb=" O   VAL N 539 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 546 through 560
      removed outlier: 4.755A  pdb=" N   PHE N 552 " --> pdb=" O   ILE N 548 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   THR N 553 " --> pdb=" O   PRO N 549 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 562 through 590
    Processing helix  chain 'N' and resid 592 through 626
      removed outlier: 4.167A  pdb=" N   LEU N 596 " --> pdb=" O   LEU N 592 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   LEU N 614 " --> pdb=" O   LEU N 610 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   GLY N 615 " --> pdb=" O   LEU N 611 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   HIS N 616 " --> pdb=" O   THR N 612 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   MET N 617 " --> pdb=" O   THR N 613 " (cutoff:3.500A)
      Proline residue:  N 620  - end of helix
      removed outlier: 3.607A  pdb=" N   LEU N 624 " --> pdb=" O   PRO N 620 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 628 through 633
      removed outlier: 3.533A  pdb=" N   PHE N 632 " --> pdb=" O   PHE N 629 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY N 633 " --> pdb=" O   THR N 630 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 9 through 48
      removed outlier: 3.978A  pdb=" N   ARG O  36 " --> pdb=" O   VAL O  32 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 51 through 61
    Processing helix  chain 'O' and resid 63 through 80
    Processing helix  chain 'P' and resid 9 through 48
      removed outlier: 3.842A  pdb=" N   GLY P  13 " --> pdb=" O   GLY P   9 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ARG P  36 " --> pdb=" O   VAL P  32 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 51 through 61
    Processing helix  chain 'P' and resid 62 through 78
      removed outlier: 4.416A  pdb=" N   VAL P  66 " --> pdb=" O   PRO P  62 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 9 through 49
      removed outlier: 4.028A  pdb=" N   ARG Q  36 " --> pdb=" O   VAL Q  32 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 51 through 61
    Processing helix  chain 'Q' and resid 62 through 78
      removed outlier: 4.331A  pdb=" N   VAL Q  66 " --> pdb=" O   PRO Q  62 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 9 through 48
      removed outlier: 4.473A  pdb=" N   GLY R  13 " --> pdb=" O   GLY R   9 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ARG R  36 " --> pdb=" O   VAL R  32 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 51 through 61
    Processing helix  chain 'R' and resid 62 through 80
      removed outlier: 4.437A  pdb=" N   VAL R  66 " --> pdb=" O   PRO R  62 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 10 through 48
      removed outlier: 3.996A  pdb=" N   ARG S  36 " --> pdb=" O   VAL S  32 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 51 through 61
    Processing helix  chain 'S' and resid 62 through 80
      removed outlier: 4.334A  pdb=" N   VAL S  66 " --> pdb=" O   PRO S  62 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 9 through 48
      removed outlier: 4.092A  pdb=" N   ARG T  36 " --> pdb=" O   VAL T  32 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 51 through 61
    Processing helix  chain 'T' and resid 62 through 80
      removed outlier: 4.434A  pdb=" N   VAL T  66 " --> pdb=" O   PRO T  62 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU T  80 " --> pdb=" O   LEU T  76 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 9 through 48
      removed outlier: 4.001A  pdb=" N   ARG U  36 " --> pdb=" O   VAL U  32 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 51 through 61
    Processing helix  chain 'U' and resid 62 through 80
      removed outlier: 4.316A  pdb=" N   VAL U  66 " --> pdb=" O   PRO U  62 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 9 through 48
      removed outlier: 3.955A  pdb=" N   GLY V  13 " --> pdb=" O   GLY V   9 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   ARG V  36 " --> pdb=" O   VAL V  32 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 51 through 61
    Processing helix  chain 'V' and resid 62 through 80
      removed outlier: 4.443A  pdb=" N   VAL V  66 " --> pdb=" O   PRO V  62 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 9 through 48
      removed outlier: 4.137A  pdb=" N   GLY W  13 " --> pdb=" O   GLY W   9 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ARG W  36 " --> pdb=" O   VAL W  32 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 51 through 61
    Processing helix  chain 'W' and resid 62 through 80
      removed outlier: 4.449A  pdb=" N   VAL W  66 " --> pdb=" O   PRO W  62 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 10 through 49
      removed outlier: 4.227A  pdb=" N   LEU X  14 " --> pdb=" O   LEU X  10 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ARG X  36 " --> pdb=" O   VAL X  32 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 51 through 61
    Processing helix  chain 'X' and resid 63 through 79
    Processing helix  chain 'Y' and resid 10 through 48
      removed outlier: 3.979A  pdb=" N   ARG Y  36 " --> pdb=" O   VAL Y  32 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 51 through 61
    Processing helix  chain 'Y' and resid 63 through 79
      removed outlier: 3.649A  pdb=" N   ARG Y  79 " --> pdb=" O   ILE Y  75 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 9 through 48
      removed outlier: 4.057A  pdb=" N   ARG Z  36 " --> pdb=" O   VAL Z  32 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 51 through 61
    Processing helix  chain 'Z' and resid 63 through 80
    Processing sheet with id=AA1, first strand: chain 'N' and resid 389 through 391
      removed outlier: 3.840A  pdb=" N   LEU N 389 " --> pdb=" O   LEU N 398 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU N 398 " --> pdb=" O   LEU N 389 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'N' and resid 438 through 439

    834 hydrogen bonds defined for protein.
    2496 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: 1.76

  Time building geometry restraints manager: 0.98 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: 2724
        1.34 -     1.46: 1054
        1.46 -     1.57: 4903
        1.57 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 8719
  Sorted by residual:
  bond pdb=" C   LEU Z  61 "
       pdb=" N   PRO Z  62 "
    ideal  model  delta    sigma   weight residual
    1.334  1.364 -0.031 8.40e-03 1.42e+04 1.33e+01
  bond pdb=" C   LEU X  61 "
       pdb=" N   PRO X  62 "
    ideal  model  delta    sigma   weight residual
    1.334  1.362 -0.028 8.40e-03 1.42e+04 1.13e+01
  bond pdb=" C   LYS N 399 "
       pdb=" N   PRO N 400 "
    ideal  model  delta    sigma   weight residual
    1.334  1.379 -0.045 2.34e-02 1.83e+03 3.66e+00
  bond pdb=" C   LEU Y  61 "
       pdb=" N   PRO Y  62 "
    ideal  model  delta    sigma   weight residual
    1.334  1.364 -0.030 2.34e-02 1.83e+03 1.64e+00
  bond pdb=" CB  THR Y  30 "
       pdb=" CG2 THR Y  30 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.60e+00
  ... (remaining 8714 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 11673
        2.42 -     4.84: 110
        4.84 -     7.26: 36
        7.26 -     9.67: 4
        9.67 -    12.09: 3
  Bond angle restraints: 11826
  Sorted by residual:
  angle pdb=" C   LEU N 398 "
        pdb=" N   LYS N 399 "
        pdb=" CA  LYS N 399 "
      ideal   model   delta    sigma   weight residual
     121.80  113.09    8.71 2.44e+00 1.68e-01 1.27e+01
  angle pdb=" CA  LEU N 398 "
        pdb=" CB  LEU N 398 "
        pdb=" CG  LEU N 398 "
      ideal   model   delta    sigma   weight residual
     116.30  128.39  -12.09 3.50e+00 8.16e-02 1.19e+01
  angle pdb=" C   ASP U  48 "
        pdb=" N   ARG U  49 "
        pdb=" CA  ARG U  49 "
      ideal   model   delta    sigma   weight residual
     121.54  127.63   -6.09 1.91e+00 2.74e-01 1.02e+01
  angle pdb=" CA  ARG R  49 "
        pdb=" CB  ARG R  49 "
        pdb=" CG  ARG R  49 "
      ideal   model   delta    sigma   weight residual
     114.10  120.24   -6.14 2.00e+00 2.50e-01 9.41e+00
  angle pdb=" C   ASP S  48 "
        pdb=" N   ARG S  49 "
        pdb=" CA  ARG S  49 "
      ideal   model   delta    sigma   weight residual
     121.54  127.37   -5.83 1.91e+00 2.74e-01 9.32e+00
  ... (remaining 11821 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.52: 4195
       15.52 -    31.05: 504
       31.05 -    46.57: 188
       46.57 -    62.09: 43
       62.09 -    77.62: 6
  Dihedral angle restraints: 4936
    sinusoidal: 1778
      harmonic: 3158
  Sorted by residual:
  dihedral pdb=" CA  PRO N 400 "
           pdb=" C   PRO N 400 "
           pdb=" N   GLN N 401 "
           pdb=" CA  GLN N 401 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.65  -25.35     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  SER O  50 "
           pdb=" C   SER O  50 "
           pdb=" N   ASN O  51 "
           pdb=" CA  ASN O  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.77   18.23     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  GLU Q  47 "
           pdb=" C   GLU Q  47 "
           pdb=" N   ASP Q  48 "
           pdb=" CA  ASP Q  48 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.98  -16.02     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 4933 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1041
       0.044 -    0.089: 336
       0.089 -    0.133: 70
       0.133 -    0.177: 8
       0.177 -    0.222: 2
  Chirality restraints: 1457
  Sorted by residual:
  chirality pdb=" CG  LEU N 540 "
            pdb=" CB  LEU N 540 "
            pdb=" CD1 LEU N 540 "
            pdb=" CD2 LEU N 540 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CG  LEU N 606 "
            pdb=" CB  LEU N 606 "
            pdb=" CD1 LEU N 606 "
            pdb=" CD2 LEU N 606 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" CA  LYS N 399 "
            pdb=" N   LYS N 399 "
            pdb=" C   LYS N 399 "
            pdb=" CB  LYS N 399 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.27e-01
  ... (remaining 1454 not shown)

  Planarity restraints: 1489
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG R  49 "    0.013 2.00e-02 2.50e+03   2.61e-02 6.84e+00
        pdb=" C   ARG R  49 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ARG R  49 "    0.017 2.00e-02 2.50e+03
        pdb=" N   SER R  50 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG U  49 "   -0.010 2.00e-02 2.50e+03   1.94e-02 3.78e+00
        pdb=" C   ARG U  49 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ARG U  49 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER U  50 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG Z  49 "   -0.010 2.00e-02 2.50e+03   1.92e-02 3.70e+00
        pdb=" C   ARG Z  49 "    0.033 2.00e-02 2.50e+03
        pdb=" O   ARG Z  49 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   SER Z  50 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1486 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 2683
        2.83 -     3.35: 8917
        3.35 -     3.87: 14896
        3.87 -     4.38: 17011
        4.38 -     4.90: 29713
  Nonbonded interactions: 73220
  Sorted by model distance:
  nonbonded pdb=" O   LEU N 611 "
            pdb=" O   HOH N 701 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   GLU N 636 "
            pdb=" O   HOH N 702 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   HOH N 722 "
            pdb=" O   HOH Y 101 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" O   HOH N 720 "
            pdb=" O   HOH N 724 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" NH2 ARG O  49 "
            pdb=" OD1 ASN Z  51 "
     model   vdw
     2.359 3.120
  ... (remaining 73215 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 'O' and resid 9 through 80)
  selection = (chain 'P' and resid 9 through 80)
  selection = (chain 'Q' and resid 9 through 80)
  selection = (chain 'R' and resid 9 through 80)
  selection = (chain 'S' and resid 9 through 80)
  selection = (chain 'T' and resid 9 through 80)
  selection = (chain 'U' and resid 9 through 80)
  selection = (chain 'V' and resid 9 through 80)
  selection = (chain 'W' and resid 9 through 80)
  selection = chain 'X'
  selection = (chain 'Y' and resid 9 through 80)
  selection = (chain 'Z' and resid 9 through 80)
}

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:             3.480
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.130
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:8.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
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   0.054   8719  Z= 0.191
  Angle     :  0.714  12.092  11826  Z= 0.367
  Chirality :  0.044   0.222   1457
  Planarity :  0.005   0.044   1489
  Dihedral  : 15.789  77.617   2966
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.26 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  8.30 %
    Allowed  : 20.27 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.24), residues: 1164
  helix:  1.27 (0.16), residues: 1026
  sheet: -1.71 (2.04), residues: 10
  loop : -1.49 (0.54), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG X  12 
 TYR   0.006   0.001   TYR N 565 
 PHE   0.019   0.001   PHE Z  68 
 TRP   0.009   0.001   TRP N 378 
 HIS   0.005   0.001   HIS N 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 8719)
  covalent geometry    : angle       0.71383 (11826)
  hydrogen bonds       : bond        0.08089 (  834)
  hydrogen bonds       : angle       4.28873 ( 2496)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 223
  time to evaluate  : 0.325 
Fit side-chains
REVERT: N  339 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8252 (t)
REVERT: N  426 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7218 (mt-10)
REVERT: N  431 PHE cc_start: 0.7295 (t80) cc_final: 0.6865 (t80)
REVERT: N  438 PHE cc_start: 0.7982 (m-80) cc_final: 0.7764 (m-10)
REVERT: N  453 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7903 (tmm-80)
REVERT: N  461 ASN cc_start: 0.7140 (p0) cc_final: 0.6400 (t0)
REVERT: N  462 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8678 (tm)
REVERT: N  550 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7543 (mm-30)
REVERT: P   75 ILE cc_start: 0.9368 (mm) cc_final: 0.9147 (mp)
REVERT: Q   50 SER cc_start: 0.8568 (p) cc_final: 0.8172 (p)
REVERT: R   49 ARG cc_start: 0.7720 (tpp-160) cc_final: 0.7511 (tpp-160)
REVERT: U   56 LEU cc_start: 0.9014 (tp) cc_final: 0.8798 (tm)
REVERT: V   47 GLU cc_start: 0.5899 (mm-30) cc_final: 0.5651 (mp0)
REVERT: V   63 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.7714 (mp0)
REVERT: V   74 PHE cc_start: 0.9172 (m-80) cc_final: 0.8904 (m-80)
REVERT: W   11 ASP cc_start: 0.8512 (p0) cc_final: 0.8063 (p0)
REVERT: W   50 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8693 (p)
REVERT: W   51 ASN cc_start: 0.9086 (m-40) cc_final: 0.8786 (m110)
REVERT: X   12 ARG cc_start: 0.8198 (ptp90) cc_final: 0.7806 (ptp90)
REVERT: Y   48 ASP cc_start: 0.8241 (t0) cc_final: 0.8004 (t0)
REVERT: Y   49 ARG cc_start: 0.8585 (tpp80) cc_final: 0.8177 (tpp-160)
  outliers start: 68
  outliers final: 28
  residues processed: 284
  average time/residue: 0.4284
  time to fit residues: 132.0932
Evaluate side-chains
  228 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 195
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  335 SER
Chi-restraints excluded: chain N residue  339 THR
Chi-restraints excluded: chain N residue  390 VAL
Chi-restraints excluded: chain N residue  453 ARG
Chi-restraints excluded: chain N residue  456 THR
Chi-restraints excluded: chain N residue  462 LEU
Chi-restraints excluded: chain N residue  487 LEU
Chi-restraints excluded: chain N residue  537 LEU
Chi-restraints excluded: chain N residue  546 LEU
Chi-restraints excluded: chain N residue  560 SER
Chi-restraints excluded: chain N residue  607 LEU
Chi-restraints excluded: chain O residue   56 LEU
Chi-restraints excluded: chain O residue   61 LEU
Chi-restraints excluded: chain P residue   54 THR
Chi-restraints excluded: chain P residue   56 LEU
Chi-restraints excluded: chain Q residue   54 THR
Chi-restraints excluded: chain Q residue   61 LEU
Chi-restraints excluded: chain R residue   54 THR
Chi-restraints excluded: chain S residue   50 SER
Chi-restraints excluded: chain T residue   50 SER
Chi-restraints excluded: chain T residue   51 ASN
Chi-restraints excluded: chain U residue   51 ASN
Chi-restraints excluded: chain V residue   51 ASN
Chi-restraints excluded: chain V residue   63 GLU
Chi-restraints excluded: chain W residue   50 SER
Chi-restraints excluded: chain W residue   54 THR
Chi-restraints excluded: chain W residue   57 ILE
Chi-restraints excluded: chain W residue   61 LEU
Chi-restraints excluded: chain X residue   54 THR
Chi-restraints excluded: chain Y residue   11 ASP
Chi-restraints excluded: chain Y residue   72 ILE
Chi-restraints excluded: chain Z residue   54 THR
Chi-restraints excluded: chain Z residue   80 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
N 605 HIS
O  77 ASN
W  51 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.106198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.078305 restraints weight = 14937.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 2.17
r_work: 0.2952 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.0969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8719  Z= 0.143
  Angle     :  0.589   8.418  11826  Z= 0.297
  Chirality :  0.040   0.228   1457
  Planarity :  0.004   0.040   1489
  Dihedral  :  7.111  57.307   1312
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.44 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  6.96 %
    Allowed  : 23.08 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.25 (0.25), residues: 1164
  helix:  1.85 (0.16), residues: 1034
  sheet: -1.17 (2.03), residues: 10
  loop : -1.40 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N 588 
 TYR   0.006   0.001   TYR N 565 
 PHE   0.011   0.001   PHE N 345 
 TRP   0.008   0.001   TRP N 378 
 HIS   0.005   0.001   HIS N 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8719)
  covalent geometry    : angle       0.58877 (11826)
  hydrogen bonds       : bond        0.04811 (  834)
  hydrogen bonds       : angle       3.72161 ( 2496)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 208
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: N  426 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7453 (mt-10)
REVERT: N  461 ASN cc_start: 0.7318 (p0) cc_final: 0.6451 (t0)
REVERT: N  550 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7624 (mm-30)
REVERT: P   49 ARG cc_start: 0.8123 (tpt170) cc_final: 0.7877 (tpp-160)
REVERT: P   75 ILE cc_start: 0.9363 (mm) cc_final: 0.9144 (mp)
REVERT: Q   71 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8928 (tp)
REVERT: R   49 ARG cc_start: 0.7800 (tpp-160) cc_final: 0.7565 (tpp-160)
REVERT: T   49 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7285 (tpp-160)
REVERT: U   56 LEU cc_start: 0.8948 (tp) cc_final: 0.8726 (tm)
REVERT: V   47 GLU cc_start: 0.5996 (mm-30) cc_final: 0.5547 (mp0)
REVERT: W   11 ASP cc_start: 0.8352 (p0) cc_final: 0.7886 (p0)
REVERT: X   49 ARG cc_start: 0.8363 (tpt170) cc_final: 0.8087 (tpp-160)
REVERT: Z   47 GLU cc_start: 0.3836 (OUTLIER) cc_final: 0.2921 (tp30)
REVERT: Z   49 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7379 (ttm170)
  outliers start: 57
  outliers final: 22
  residues processed: 241
  average time/residue: 0.4879
  time to fit residues: 126.5551
Evaluate side-chains
  219 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 193
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  332 LEU
Chi-restraints excluded: chain N residue  390 VAL
Chi-restraints excluded: chain N residue  456 THR
Chi-restraints excluded: chain N residue  487 LEU
Chi-restraints excluded: chain N residue  494 HIS
Chi-restraints excluded: chain N residue  558 ILE
Chi-restraints excluded: chain N residue  607 LEU
Chi-restraints excluded: chain O residue   61 LEU
Chi-restraints excluded: chain P residue   54 THR
Chi-restraints excluded: chain Q residue   19 MET
Chi-restraints excluded: chain Q residue   54 THR
Chi-restraints excluded: chain Q residue   61 LEU
Chi-restraints excluded: chain Q residue   71 LEU
Chi-restraints excluded: chain R residue   54 THR
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain T residue   49 ARG
Chi-restraints excluded: chain T residue   54 THR
Chi-restraints excluded: chain U residue   51 ASN
Chi-restraints excluded: chain V residue   51 ASN
Chi-restraints excluded: chain V residue   66 VAL
Chi-restraints excluded: chain W residue   61 LEU
Chi-restraints excluded: chain X residue   47 GLU
Chi-restraints excluded: chain Y residue   11 ASP
Chi-restraints excluded: chain Z residue   47 GLU
Chi-restraints excluded: chain Z residue   49 ARG
Chi-restraints excluded: chain Z residue   80 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 4 optimal weight:    6.9990
   chunk 26 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 80 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 91 optimal weight:    0.0470
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.7678

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

Flipped N/Q/H residues before XYZ refinement:
N 494 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.105652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.077657 restraints weight = 14892.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 2.18
r_work: 0.2944 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.1246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8719  Z= 0.147
  Angle     :  0.587   8.296  11826  Z= 0.294
  Chirality :  0.040   0.226   1457
  Planarity :  0.004   0.039   1489
  Dihedral  :  5.853  59.019   1280
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.52 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  7.08 %
    Allowed  : 24.66 %
    Favored  : 68.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.51 (0.25), residues: 1164
  helix:  2.02 (0.16), residues: 1034
  sheet: -1.22 (2.03), residues: 10
  loop : -1.24 (0.61), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N 482 
 TYR   0.006   0.001   TYR N 565 
 PHE   0.010   0.001   PHE N 345 
 TRP   0.010   0.001   TRP N 378 
 HIS   0.008   0.001   HIS N 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8719)
  covalent geometry    : angle       0.58716 (11826)
  hydrogen bonds       : bond        0.04760 (  834)
  hydrogen bonds       : angle       3.64534 ( 2496)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 203
  time to evaluate  : 0.328 
Fit side-chains
REVERT: N  426 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7399 (mt-10)
REVERT: N  453 ARG cc_start: 0.8052 (tmm-80) cc_final: 0.7706 (tmm-80)
REVERT: N  461 ASN cc_start: 0.7233 (p0) cc_final: 0.6400 (t0)
REVERT: N  494 HIS cc_start: 0.7094 (OUTLIER) cc_final: 0.6835 (t70)
REVERT: N  550 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7680 (mm-30)
REVERT: N  587 GLU cc_start: 0.7196 (tp30) cc_final: 0.6897 (mm-30)
REVERT: P   49 ARG cc_start: 0.7948 (tpt170) cc_final: 0.7733 (tpp-160)
REVERT: P   75 ILE cc_start: 0.9362 (mm) cc_final: 0.9147 (mp)
REVERT: P   79 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8130 (mmt90)
REVERT: T   49 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7375 (tpp-160)
REVERT: U   56 LEU cc_start: 0.8983 (tp) cc_final: 0.8739 (tm)
REVERT: V   47 GLU cc_start: 0.6013 (mm-30) cc_final: 0.5549 (mp0)
REVERT: V   74 PHE cc_start: 0.9119 (m-80) cc_final: 0.8895 (m-80)
REVERT: W   11 ASP cc_start: 0.8300 (p0) cc_final: 0.7861 (p0)
REVERT: X   12 ARG cc_start: 0.8067 (pmm-80) cc_final: 0.7767 (pmm-80)
REVERT: Y   49 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8274 (tpp80)
REVERT: Z   47 GLU cc_start: 0.3806 (OUTLIER) cc_final: 0.1797 (tp30)
REVERT: Z   49 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7266 (ttm170)
  outliers start: 58
  outliers final: 23
  residues processed: 237
  average time/residue: 0.5108
  time to fit residues: 129.8770
Evaluate side-chains
  217 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 188
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  332 LEU
Chi-restraints excluded: chain N residue  383 VAL
Chi-restraints excluded: chain N residue  390 VAL
Chi-restraints excluded: chain N residue  422 VAL
Chi-restraints excluded: chain N residue  487 LEU
Chi-restraints excluded: chain N residue  494 HIS
Chi-restraints excluded: chain N residue  558 ILE
Chi-restraints excluded: chain O residue   10 LEU
Chi-restraints excluded: chain O residue   61 LEU
Chi-restraints excluded: chain P residue   11 ASP
Chi-restraints excluded: chain P residue   79 ARG
Chi-restraints excluded: chain Q residue   19 MET
Chi-restraints excluded: chain Q residue   61 LEU
Chi-restraints excluded: chain R residue   54 THR
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain S residue   50 SER
Chi-restraints excluded: chain S residue   66 VAL
Chi-restraints excluded: chain T residue   49 ARG
Chi-restraints excluded: chain T residue   54 THR
Chi-restraints excluded: chain V residue   54 THR
Chi-restraints excluded: chain V residue   66 VAL
Chi-restraints excluded: chain W residue   61 LEU
Chi-restraints excluded: chain X residue   47 GLU
Chi-restraints excluded: chain Y residue   10 LEU
Chi-restraints excluded: chain Y residue   11 ASP
Chi-restraints excluded: chain Y residue   49 ARG
Chi-restraints excluded: chain Z residue   47 GLU
Chi-restraints excluded: chain Z residue   49 ARG
Chi-restraints excluded: chain Z residue   80 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0270
   chunk 35 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0670
   chunk 21 optimal weight:    0.9990
   chunk 109 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
N 494 HIS
Q  51 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.106319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.078327 restraints weight = 15066.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 2.22
r_work: 0.2958 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8719  Z= 0.139
  Angle     :  0.587   8.398  11826  Z= 0.293
  Chirality :  0.041   0.233   1457
  Planarity :  0.004   0.040   1489
  Dihedral  :  5.332  59.907   1271
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.35 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 26.50 %
    Favored  : 68.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.64 (0.25), residues: 1164
  helix:  2.12 (0.16), residues: 1034
  sheet: -1.33 (2.02), residues: 10
  loop : -1.24 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Z  12 
 TYR   0.006   0.001   TYR N 565 
 PHE   0.013   0.001   PHE N 438 
 TRP   0.011   0.001   TRP N 378 
 HIS   0.003   0.000   HIS N 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8719)
  covalent geometry    : angle       0.58653 (11826)
  hydrogen bonds       : bond        0.04626 (  834)
  hydrogen bonds       : angle       3.59708 ( 2496)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 199
  time to evaluate  : 0.329 
Fit side-chains
REVERT: N  426 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7373 (mt-10)
REVERT: N  453 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7642 (tmm-80)
REVERT: N  461 ASN cc_start: 0.7140 (p0) cc_final: 0.6417 (t0)
REVERT: N  550 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7596 (mm-30)
REVERT: N  587 GLU cc_start: 0.7199 (tp30) cc_final: 0.6931 (mm-30)
REVERT: P   49 ARG cc_start: 0.7912 (tpt170) cc_final: 0.7687 (tpp-160)
REVERT: P   79 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8153 (mmt90)
REVERT: Q   12 ARG cc_start: 0.6504 (tpt170) cc_final: 0.5975 (mmt180)
REVERT: T   49 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7235 (tpp-160)
REVERT: U   56 LEU cc_start: 0.8981 (tp) cc_final: 0.8742 (tm)
REVERT: V   47 GLU cc_start: 0.5958 (mm-30) cc_final: 0.5479 (mp0)
REVERT: V   74 PHE cc_start: 0.9112 (m-80) cc_final: 0.8854 (m-80)
REVERT: W   11 ASP cc_start: 0.8248 (p0) cc_final: 0.7776 (p0)
REVERT: X   12 ARG cc_start: 0.8114 (pmm-80) cc_final: 0.7440 (mtm-85)
REVERT: Y   49 ARG cc_start: 0.8569 (tpp80) cc_final: 0.8353 (tpp80)
REVERT: Z   47 GLU cc_start: 0.3905 (OUTLIER) cc_final: 0.1686 (tp30)
  outliers start: 45
  outliers final: 27
  residues processed: 221
  average time/residue: 0.5049
  time to fit residues: 119.2492
Evaluate side-chains
  219 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 188
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  328 LYS
Chi-restraints excluded: chain N residue  332 LEU
Chi-restraints excluded: chain N residue  383 VAL
Chi-restraints excluded: chain N residue  390 VAL
Chi-restraints excluded: chain N residue  453 ARG
Chi-restraints excluded: chain N residue  487 LEU
Chi-restraints excluded: chain N residue  558 ILE
Chi-restraints excluded: chain O residue   10 LEU
Chi-restraints excluded: chain O residue   61 LEU
Chi-restraints excluded: chain P residue   72 ILE
Chi-restraints excluded: chain P residue   79 ARG
Chi-restraints excluded: chain Q residue   19 MET
Chi-restraints excluded: chain Q residue   61 LEU
Chi-restraints excluded: chain R residue   51 ASN
Chi-restraints excluded: chain R residue   54 THR
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain S residue   66 VAL
Chi-restraints excluded: chain T residue   49 ARG
Chi-restraints excluded: chain T residue   54 THR
Chi-restraints excluded: chain U residue   66 VAL
Chi-restraints excluded: chain V residue   66 VAL
Chi-restraints excluded: chain W residue   50 SER
Chi-restraints excluded: chain W residue   57 ILE
Chi-restraints excluded: chain W residue   61 LEU
Chi-restraints excluded: chain X residue   47 GLU
Chi-restraints excluded: chain X residue   61 LEU
Chi-restraints excluded: chain Y residue   10 LEU
Chi-restraints excluded: chain Y residue   11 ASP
Chi-restraints excluded: chain Y residue   75 ILE
Chi-restraints excluded: chain Z residue   47 GLU
Chi-restraints excluded: chain Z residue   80 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 59 optimal weight:    0.4980
   chunk 5 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 104 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0050
   chunk 53 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 110 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.5994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.106250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.078423 restraints weight = 14887.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 2.18
r_work: 0.2924 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2809 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8719  Z= 0.142
  Angle     :  0.591   7.963  11826  Z= 0.296
  Chirality :  0.041   0.241   1457
  Planarity :  0.004   0.036   1489
  Dihedral  :  5.234  58.747   1271
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.26 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  : 25.76 %
    Favored  : 67.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.70 (0.25), residues: 1164
  helix:  2.16 (0.16), residues: 1033
  sheet: -1.63 (1.99), residues: 10
  loop : -1.27 (0.61), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG O  49 
 TYR   0.007   0.001   TYR N 565 
 PHE   0.018   0.001   PHE Z  68 
 TRP   0.012   0.001   TRP N 378 
 HIS   0.008   0.001   HIS N 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8719)
  covalent geometry    : angle       0.59103 (11826)
  hydrogen bonds       : bond        0.04578 (  834)
  hydrogen bonds       : angle       3.57094 ( 2496)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 200
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: N  426 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7333 (mt-10)
REVERT: N  453 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7596 (tmm-80)
REVERT: N  461 ASN cc_start: 0.7125 (p0) cc_final: 0.6419 (t0)
REVERT: N  550 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7581 (mm-30)
REVERT: N  587 GLU cc_start: 0.7251 (tp30) cc_final: 0.7011 (mm-30)
REVERT: P   49 ARG cc_start: 0.7916 (tpt170) cc_final: 0.7707 (tpp-160)
REVERT: P   79 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8155 (mmt90)
REVERT: T   49 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7165 (tpp-160)
REVERT: U   56 LEU cc_start: 0.8969 (tp) cc_final: 0.8723 (tm)
REVERT: V   11 ASP cc_start: 0.8654 (p0) cc_final: 0.8430 (p0)
REVERT: V   47 GLU cc_start: 0.5984 (mm-30) cc_final: 0.5534 (mp0)
REVERT: V   74 PHE cc_start: 0.9106 (m-80) cc_final: 0.8831 (m-80)
REVERT: W   11 ASP cc_start: 0.8199 (p0) cc_final: 0.7691 (p0)
REVERT: W   12 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7247 (mtm-85)
REVERT: X   12 ARG cc_start: 0.8107 (pmm-80) cc_final: 0.7507 (mtm-85)
REVERT: X   49 ARG cc_start: 0.8440 (tpt170) cc_final: 0.8154 (tpp-160)
REVERT: Y   49 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8346 (tpp80)
REVERT: Z   47 GLU cc_start: 0.3880 (OUTLIER) cc_final: 0.1433 (tp30)
  outliers start: 53
  outliers final: 26
  residues processed: 228
  average time/residue: 0.4243
  time to fit residues: 103.6473
Evaluate side-chains
  221 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 189
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  328 LYS
Chi-restraints excluded: chain N residue  332 LEU
Chi-restraints excluded: chain N residue  338 ASN
Chi-restraints excluded: chain N residue  383 VAL
Chi-restraints excluded: chain N residue  422 VAL
Chi-restraints excluded: chain N residue  453 ARG
Chi-restraints excluded: chain N residue  487 LEU
Chi-restraints excluded: chain N residue  558 ILE
Chi-restraints excluded: chain N residue  607 LEU
Chi-restraints excluded: chain O residue   10 LEU
Chi-restraints excluded: chain P residue   11 ASP
Chi-restraints excluded: chain P residue   72 ILE
Chi-restraints excluded: chain P residue   79 ARG
Chi-restraints excluded: chain Q residue   19 MET
Chi-restraints excluded: chain Q residue   61 LEU
Chi-restraints excluded: chain R residue   51 ASN
Chi-restraints excluded: chain R residue   54 THR
Chi-restraints excluded: chain S residue   66 VAL
Chi-restraints excluded: chain T residue   49 ARG
Chi-restraints excluded: chain T residue   54 THR
Chi-restraints excluded: chain U residue   66 VAL
Chi-restraints excluded: chain V residue   61 LEU
Chi-restraints excluded: chain V residue   66 VAL
Chi-restraints excluded: chain W residue   12 ARG
Chi-restraints excluded: chain W residue   57 ILE
Chi-restraints excluded: chain W residue   61 LEU
Chi-restraints excluded: chain X residue   47 GLU
Chi-restraints excluded: chain Y residue   11 ASP
Chi-restraints excluded: chain Y residue   49 ARG
Chi-restraints excluded: chain Y residue   66 VAL
Chi-restraints excluded: chain Z residue   47 GLU
Chi-restraints excluded: chain Z residue   80 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 52 optimal weight:    7.9990
   chunk 94 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
W  77 ASN
Z  51 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.100921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.073015 restraints weight = 15092.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 2.14
r_work: 0.2833 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064   8719  Z= 0.233
  Angle     :  0.673   9.543  11826  Z= 0.339
  Chirality :  0.045   0.284   1457
  Planarity :  0.004   0.038   1489
  Dihedral  :  5.162  56.563   1268
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.44 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  6.59 %
    Allowed  : 26.98 %
    Favored  : 66.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.56 (0.25), residues: 1164
  helix:  2.05 (0.16), residues: 1035
  sheet: -2.33 (1.78), residues: 10
  loop : -1.11 (0.63), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG X  12 
 TYR   0.007   0.001   TYR N 565 
 PHE   0.022   0.001   PHE Z  68 
 TRP   0.011   0.001   TRP N 378 
 HIS   0.009   0.001   HIS N 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 ( 8719)
  covalent geometry    : angle       0.67340 (11826)
  hydrogen bonds       : bond        0.05498 (  834)
  hydrogen bonds       : angle       3.79839 ( 2496)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 197
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: N  426 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7123 (mt-10)
REVERT: N  453 ARG cc_start: 0.8231 (tmm-80) cc_final: 0.7696 (tmm-80)
REVERT: N  461 ASN cc_start: 0.7243 (p0) cc_final: 0.6487 (t0)
REVERT: N  550 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7557 (mm-30)
REVERT: N  587 GLU cc_start: 0.7322 (tp30) cc_final: 0.7119 (mm-30)
REVERT: N  627 GLU cc_start: 0.8945 (mp0) cc_final: 0.8734 (mp0)
REVERT: P   79 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8098 (mmt90)
REVERT: T   47 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7880 (mp0)
REVERT: T   49 ARG cc_start: 0.8236 (tpp-160) cc_final: 0.7810 (tpp80)
REVERT: U   56 LEU cc_start: 0.9002 (tp) cc_final: 0.8740 (tm)
REVERT: V   47 GLU cc_start: 0.6113 (mm-30) cc_final: 0.5662 (mp0)
REVERT: W   11 ASP cc_start: 0.8257 (p0) cc_final: 0.7786 (p0)
REVERT: W   12 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7357 (mtm-85)
REVERT: X   12 ARG cc_start: 0.8130 (pmm-80) cc_final: 0.7604 (mtm-85)
REVERT: X   49 ARG cc_start: 0.8434 (tpt170) cc_final: 0.8154 (tpp-160)
REVERT: Y   49 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8411 (tpp80)
REVERT: Z   47 GLU cc_start: 0.4706 (OUTLIER) cc_final: 0.3572 (mm-30)
  outliers start: 54
  outliers final: 28
  residues processed: 227
  average time/residue: 0.4632
  time to fit residues: 112.4584
Evaluate side-chains
  219 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 186
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  328 LYS
Chi-restraints excluded: chain N residue  332 LEU
Chi-restraints excluded: chain N residue  338 ASN
Chi-restraints excluded: chain N residue  422 VAL
Chi-restraints excluded: chain N residue  487 LEU
Chi-restraints excluded: chain N residue  558 ILE
Chi-restraints excluded: chain N residue  607 LEU
Chi-restraints excluded: chain N residue  617 MET
Chi-restraints excluded: chain O residue   10 LEU
Chi-restraints excluded: chain P residue   79 ARG
Chi-restraints excluded: chain Q residue   19 MET
Chi-restraints excluded: chain Q residue   61 LEU
Chi-restraints excluded: chain R residue   54 THR
Chi-restraints excluded: chain S residue   50 SER
Chi-restraints excluded: chain S residue   51 ASN
Chi-restraints excluded: chain S residue   66 VAL
Chi-restraints excluded: chain T residue   47 GLU
Chi-restraints excluded: chain T residue   54 THR
Chi-restraints excluded: chain U residue   66 VAL
Chi-restraints excluded: chain V residue   54 THR
Chi-restraints excluded: chain V residue   66 VAL
Chi-restraints excluded: chain W residue   12 ARG
Chi-restraints excluded: chain W residue   50 SER
Chi-restraints excluded: chain W residue   51 ASN
Chi-restraints excluded: chain W residue   57 ILE
Chi-restraints excluded: chain W residue   61 LEU
Chi-restraints excluded: chain X residue   61 LEU
Chi-restraints excluded: chain X residue   67 ILE
Chi-restraints excluded: chain Y residue   11 ASP
Chi-restraints excluded: chain Y residue   49 ARG
Chi-restraints excluded: chain Z residue   47 GLU
Chi-restraints excluded: chain Z residue   50 SER
Chi-restraints excluded: chain Z residue   80 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9980
   chunk 105 optimal weight:    0.8980
   chunk 103 optimal weight:    0.6980
   chunk 70 optimal weight:    0.8980
   chunk 6 optimal weight:    8.9990
   chunk 13 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 83 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0000
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
W  34 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.104581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.076653 restraints weight = 15038.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 2.17
r_work: 0.2896 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8719  Z= 0.147
  Angle     :  0.624   9.374  11826  Z= 0.311
  Chirality :  0.042   0.311   1457
  Planarity :  0.004   0.037   1489
  Dihedral  :  5.055  53.479   1268
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.44 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 29.43 %
    Favored  : 65.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.78 (0.25), residues: 1164
  helix:  2.22 (0.16), residues: 1033
  sheet: -2.31 (1.84), residues: 10
  loop : -1.22 (0.61), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O  49 
 TYR   0.007   0.001   TYR N 565 
 PHE   0.021   0.001   PHE Z  68 
 TRP   0.017   0.001   TRP N 378 
 HIS   0.006   0.001   HIS N 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8719)
  covalent geometry    : angle       0.62395 (11826)
  hydrogen bonds       : bond        0.04795 (  834)
  hydrogen bonds       : angle       3.62119 ( 2496)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 201
  time to evaluate  : 0.245 
Fit side-chains
REVERT: N  426 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7198 (mt-10)
REVERT: N  453 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7500 (tmm-80)
REVERT: N  461 ASN cc_start: 0.7213 (p0) cc_final: 0.6431 (t0)
REVERT: N  550 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7548 (mm-30)
REVERT: P   79 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8090 (mmt90)
REVERT: Q   12 ARG cc_start: 0.6347 (tpt170) cc_final: 0.5892 (mmt180)
REVERT: T   49 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7657 (tpp80)
REVERT: U   56 LEU cc_start: 0.8983 (tp) cc_final: 0.8751 (tm)
REVERT: V   63 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.7932 (mp0)
REVERT: W   11 ASP cc_start: 0.8159 (p0) cc_final: 0.7653 (p0)
REVERT: W   12 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7260 (mtm-85)
REVERT: X   12 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7527 (mtm-85)
REVERT: Y   49 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8322 (tpp80)
REVERT: Z   47 GLU cc_start: 0.4234 (OUTLIER) cc_final: 0.3041 (mm-30)
  outliers start: 39
  outliers final: 22
  residues processed: 218
  average time/residue: 0.4906
  time to fit residues: 114.3133
Evaluate side-chains
  226 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 196
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  328 LYS
Chi-restraints excluded: chain N residue  332 LEU
Chi-restraints excluded: chain N residue  383 VAL
Chi-restraints excluded: chain N residue  453 ARG
Chi-restraints excluded: chain N residue  558 ILE
Chi-restraints excluded: chain N residue  607 LEU
Chi-restraints excluded: chain O residue   10 LEU
Chi-restraints excluded: chain P residue   79 ARG
Chi-restraints excluded: chain Q residue   19 MET
Chi-restraints excluded: chain Q residue   61 LEU
Chi-restraints excluded: chain R residue   54 THR
Chi-restraints excluded: chain S residue   51 ASN
Chi-restraints excluded: chain S residue   66 VAL
Chi-restraints excluded: chain T residue   49 ARG
Chi-restraints excluded: chain U residue   19 MET
Chi-restraints excluded: chain U residue   66 VAL
Chi-restraints excluded: chain V residue   63 GLU
Chi-restraints excluded: chain V residue   66 VAL
Chi-restraints excluded: chain W residue   12 ARG
Chi-restraints excluded: chain W residue   51 ASN
Chi-restraints excluded: chain W residue   61 LEU
Chi-restraints excluded: chain X residue   12 ARG
Chi-restraints excluded: chain X residue   47 GLU
Chi-restraints excluded: chain X residue   61 LEU
Chi-restraints excluded: chain Y residue   11 ASP
Chi-restraints excluded: chain Y residue   49 ARG
Chi-restraints excluded: chain Y residue   66 VAL
Chi-restraints excluded: chain Z residue   47 GLU
Chi-restraints excluded: chain Z residue   50 SER
Chi-restraints excluded: chain Z residue   80 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 108 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 106 optimal weight:    0.5980
   chunk 27 optimal weight:   10.0000
   chunk 53 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.8784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.104216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.076318 restraints weight = 14840.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 2.16
r_work: 0.2893 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8719  Z= 0.158
  Angle     :  0.639   9.909  11826  Z= 0.318
  Chirality :  0.043   0.333   1457
  Planarity :  0.004   0.036   1489
  Dihedral  :  4.830  51.085   1266
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.52 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 29.43 %
    Favored  : 65.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.77 (0.25), residues: 1164
  helix:  2.21 (0.16), residues: 1033
  sheet: -2.33 (1.83), residues: 10
  loop : -1.21 (0.61), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N 588 
 TYR   0.007   0.001   TYR N 565 
 PHE   0.021   0.001   PHE Z  68 
 TRP   0.016   0.001   TRP N 378 
 HIS   0.006   0.001   HIS N 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 8719)
  covalent geometry    : angle       0.63915 (11826)
  hydrogen bonds       : bond        0.04838 (  834)
  hydrogen bonds       : angle       3.64632 ( 2496)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 196
  time to evaluate  : 0.226 
Fit side-chains
REVERT: N  426 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7255 (mt-10)
REVERT: N  453 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7517 (tmm-80)
REVERT: N  461 ASN cc_start: 0.7212 (p0) cc_final: 0.6483 (t0)
REVERT: N  550 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7554 (mm-30)
REVERT: P   49 ARG cc_start: 0.8080 (tpt170) cc_final: 0.7782 (tpp-160)
REVERT: P   79 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8103 (mmt90)
REVERT: Q   12 ARG cc_start: 0.6396 (tpt170) cc_final: 0.5897 (mmt180)
REVERT: T   10 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8001 (tm)
REVERT: T   49 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7538 (tpp80)
REVERT: U   56 LEU cc_start: 0.9005 (tp) cc_final: 0.8767 (tm)
REVERT: V   11 ASP cc_start: 0.8737 (p0) cc_final: 0.8432 (p0)
REVERT: V   47 GLU cc_start: 0.6207 (mm-30) cc_final: 0.5782 (mp0)
REVERT: V   63 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.7950 (mp0)
REVERT: W   10 LEU cc_start: 0.9223 (mm) cc_final: 0.8804 (tp)
REVERT: W   11 ASP cc_start: 0.8184 (p0) cc_final: 0.7667 (p0)
REVERT: W   12 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7284 (mtm-85)
REVERT: X   12 ARG cc_start: 0.8032 (pmm-80) cc_final: 0.7454 (mtm-85)
REVERT: Y   49 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8351 (tpp80)
REVERT: Z   47 GLU cc_start: 0.4497 (OUTLIER) cc_final: 0.3379 (mm-30)
  outliers start: 42
  outliers final: 27
  residues processed: 219
  average time/residue: 0.5392
  time to fit residues: 126.0947
Evaluate side-chains
  227 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 192
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  328 LYS
Chi-restraints excluded: chain N residue  332 LEU
Chi-restraints excluded: chain N residue  383 VAL
Chi-restraints excluded: chain N residue  422 VAL
Chi-restraints excluded: chain N residue  453 ARG
Chi-restraints excluded: chain N residue  558 ILE
Chi-restraints excluded: chain N residue  607 LEU
Chi-restraints excluded: chain O residue   10 LEU
Chi-restraints excluded: chain P residue   11 ASP
Chi-restraints excluded: chain P residue   50 SER
Chi-restraints excluded: chain P residue   79 ARG
Chi-restraints excluded: chain Q residue   19 MET
Chi-restraints excluded: chain Q residue   61 LEU
Chi-restraints excluded: chain R residue   54 THR
Chi-restraints excluded: chain S residue   50 SER
Chi-restraints excluded: chain S residue   51 ASN
Chi-restraints excluded: chain S residue   66 VAL
Chi-restraints excluded: chain T residue   10 LEU
Chi-restraints excluded: chain T residue   49 ARG
Chi-restraints excluded: chain U residue   66 VAL
Chi-restraints excluded: chain V residue   63 GLU
Chi-restraints excluded: chain V residue   66 VAL
Chi-restraints excluded: chain W residue   12 ARG
Chi-restraints excluded: chain W residue   51 ASN
Chi-restraints excluded: chain W residue   61 LEU
Chi-restraints excluded: chain X residue   47 GLU
Chi-restraints excluded: chain X residue   54 THR
Chi-restraints excluded: chain X residue   61 LEU
Chi-restraints excluded: chain X residue   67 ILE
Chi-restraints excluded: chain Y residue   11 ASP
Chi-restraints excluded: chain Y residue   49 ARG
Chi-restraints excluded: chain Y residue   66 VAL
Chi-restraints excluded: chain Z residue   47 GLU
Chi-restraints excluded: chain Z residue   50 SER
Chi-restraints excluded: chain Z residue   80 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 88 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 110 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 73 optimal weight:    0.6980
   chunk 67 optimal weight:    4.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
W  34 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.102349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.074387 restraints weight = 14931.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 2.15
r_work: 0.2852 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2738 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8719  Z= 0.192
  Angle     :  0.674  10.005  11826  Z= 0.337
  Chirality :  0.044   0.339   1457
  Planarity :  0.004   0.036   1489
  Dihedral  :  4.910  52.396   1266
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.04 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 29.79 %
    Favored  : 65.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.71 (0.25), residues: 1164
  helix:  2.16 (0.16), residues: 1034
  sheet: -2.38 (1.77), residues: 10
  loop : -1.14 (0.61), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG P  12 
 TYR   0.008   0.001   TYR N 565 
 PHE   0.024   0.001   PHE Z  68 
 TRP   0.016   0.001   TRP N 378 
 HIS   0.006   0.001   HIS N 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 8719)
  covalent geometry    : angle       0.67450 (11826)
  hydrogen bonds       : bond        0.05127 (  834)
  hydrogen bonds       : angle       3.71343 ( 2496)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 189
  time to evaluate  : 0.244 
Fit side-chains
REVERT: N  426 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7145 (mt-10)
REVERT: N  453 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7594 (tmm-80)
REVERT: N  461 ASN cc_start: 0.7249 (p0) cc_final: 0.6505 (t0)
REVERT: N  550 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7579 (mm-30)
REVERT: N  611 LEU cc_start: 0.9324 (mt) cc_final: 0.9112 (mm)
REVERT: N  627 GLU cc_start: 0.8902 (mp0) cc_final: 0.8581 (mp0)
REVERT: P   49 ARG cc_start: 0.8104 (tpt170) cc_final: 0.7808 (tpp-160)
REVERT: P   79 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8141 (mmt90)
REVERT: Q   12 ARG cc_start: 0.6498 (tpt170) cc_final: 0.5973 (mmt180)
REVERT: T   10 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8053 (tm)
REVERT: T   49 ARG cc_start: 0.8123 (tpp-160) cc_final: 0.7693 (tpp80)
REVERT: U   56 LEU cc_start: 0.9008 (tp) cc_final: 0.8753 (tm)
REVERT: V   11 ASP cc_start: 0.8737 (p0) cc_final: 0.8496 (p0)
REVERT: V   63 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.7948 (mp0)
REVERT: W   10 LEU cc_start: 0.9228 (mm) cc_final: 0.8816 (tp)
REVERT: W   11 ASP cc_start: 0.8287 (p0) cc_final: 0.7775 (p0)
REVERT: W   12 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7297 (mtm-85)
REVERT: X   12 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7494 (mtm-85)
REVERT: Y   49 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8361 (tpp80)
REVERT: Z   47 GLU cc_start: 0.4762 (OUTLIER) cc_final: 0.3761 (mm-30)
  outliers start: 40
  outliers final: 31
  residues processed: 213
  average time/residue: 0.5370
  time to fit residues: 122.1748
Evaluate side-chains
  230 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 191
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  328 LYS
Chi-restraints excluded: chain N residue  332 LEU
Chi-restraints excluded: chain N residue  353 VAL
Chi-restraints excluded: chain N residue  383 VAL
Chi-restraints excluded: chain N residue  422 VAL
Chi-restraints excluded: chain N residue  453 ARG
Chi-restraints excluded: chain N residue  487 LEU
Chi-restraints excluded: chain N residue  558 ILE
Chi-restraints excluded: chain N residue  607 LEU
Chi-restraints excluded: chain N residue  617 MET
Chi-restraints excluded: chain O residue   10 LEU
Chi-restraints excluded: chain P residue   79 ARG
Chi-restraints excluded: chain Q residue   19 MET
Chi-restraints excluded: chain Q residue   61 LEU
Chi-restraints excluded: chain R residue   54 THR
Chi-restraints excluded: chain S residue   50 SER
Chi-restraints excluded: chain S residue   51 ASN
Chi-restraints excluded: chain S residue   66 VAL
Chi-restraints excluded: chain T residue   10 LEU
Chi-restraints excluded: chain U residue   66 VAL
Chi-restraints excluded: chain V residue   54 THR
Chi-restraints excluded: chain V residue   63 GLU
Chi-restraints excluded: chain V residue   66 VAL
Chi-restraints excluded: chain V residue   72 ILE
Chi-restraints excluded: chain W residue   12 ARG
Chi-restraints excluded: chain W residue   51 ASN
Chi-restraints excluded: chain W residue   57 ILE
Chi-restraints excluded: chain W residue   61 LEU
Chi-restraints excluded: chain X residue   12 ARG
Chi-restraints excluded: chain X residue   47 GLU
Chi-restraints excluded: chain X residue   54 THR
Chi-restraints excluded: chain X residue   61 LEU
Chi-restraints excluded: chain X residue   67 ILE
Chi-restraints excluded: chain Y residue   11 ASP
Chi-restraints excluded: chain Y residue   49 ARG
Chi-restraints excluded: chain Y residue   66 VAL
Chi-restraints excluded: chain Z residue   47 GLU
Chi-restraints excluded: chain Z residue   50 SER
Chi-restraints excluded: chain Z residue   80 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 113 optimal weight:    0.7980
   chunk 46 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 108 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0070
   chunk 84 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 97 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   chunk 110 optimal weight:    0.9990
   overall best weight:    0.6800

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.105089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.077045 restraints weight = 14884.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 2.18
r_work: 0.2898 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2783 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8719  Z= 0.148
  Angle     :  0.650  10.279  11826  Z= 0.323
  Chirality :  0.043   0.346   1457
  Planarity :  0.004   0.035   1489
  Dihedral  :  4.869  49.934   1266
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.87 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 30.53 %
    Favored  : 64.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.84 (0.25), residues: 1164
  helix:  2.26 (0.16), residues: 1033
  sheet: -2.19 (1.78), residues: 10
  loop : -1.22 (0.61), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N 482 
 TYR   0.008   0.001   TYR N 565 
 PHE   0.022   0.001   PHE Z  68 
 TRP   0.021   0.001   TRP N 378 
 HIS   0.002   0.001   HIS N 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8719)
  covalent geometry    : angle       0.64963 (11826)
  hydrogen bonds       : bond        0.04686 (  834)
  hydrogen bonds       : angle       3.62412 ( 2496)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 197
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: N  426 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7533 (pt0)
REVERT: N  453 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7641 (tmm-80)
REVERT: N  461 ASN cc_start: 0.7193 (p0) cc_final: 0.6490 (t0)
REVERT: N  550 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7587 (mm-30)
REVERT: N  627 GLU cc_start: 0.8851 (mp0) cc_final: 0.8501 (mp0)
REVERT: P   49 ARG cc_start: 0.8041 (tpt170) cc_final: 0.7770 (tpp-160)
REVERT: P   79 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8066 (mmt90)
REVERT: T   10 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8011 (tm)
REVERT: T   49 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7499 (tpp-160)
REVERT: U   56 LEU cc_start: 0.9019 (tp) cc_final: 0.8790 (tm)
REVERT: V   11 ASP cc_start: 0.8687 (p0) cc_final: 0.8423 (p0)
REVERT: V   63 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.7934 (mp0)
REVERT: W   10 LEU cc_start: 0.9216 (mm) cc_final: 0.8793 (tp)
REVERT: W   11 ASP cc_start: 0.8258 (p0) cc_final: 0.7746 (p0)
REVERT: W   12 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7277 (mtm-85)
REVERT: X   12 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7473 (mtm-85)
REVERT: X   49 ARG cc_start: 0.8444 (tpt170) cc_final: 0.8099 (tpp-160)
REVERT: Z   47 GLU cc_start: 0.4641 (OUTLIER) cc_final: 0.3869 (mm-30)
  outliers start: 39
  outliers final: 24
  residues processed: 218
  average time/residue: 0.5253
  time to fit residues: 122.6084
Evaluate side-chains
  222 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 190
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  328 LYS
Chi-restraints excluded: chain N residue  332 LEU
Chi-restraints excluded: chain N residue  422 VAL
Chi-restraints excluded: chain N residue  453 ARG
Chi-restraints excluded: chain N residue  558 ILE
Chi-restraints excluded: chain N residue  607 LEU
Chi-restraints excluded: chain O residue   10 LEU
Chi-restraints excluded: chain P residue   72 ILE
Chi-restraints excluded: chain P residue   79 ARG
Chi-restraints excluded: chain Q residue   19 MET
Chi-restraints excluded: chain Q residue   61 LEU
Chi-restraints excluded: chain R residue   54 THR
Chi-restraints excluded: chain S residue   50 SER
Chi-restraints excluded: chain S residue   51 ASN
Chi-restraints excluded: chain S residue   66 VAL
Chi-restraints excluded: chain T residue   10 LEU
Chi-restraints excluded: chain T residue   49 ARG
Chi-restraints excluded: chain U residue   66 VAL
Chi-restraints excluded: chain V residue   54 THR
Chi-restraints excluded: chain V residue   63 GLU
Chi-restraints excluded: chain V residue   66 VAL
Chi-restraints excluded: chain V residue   72 ILE
Chi-restraints excluded: chain W residue   12 ARG
Chi-restraints excluded: chain W residue   57 ILE
Chi-restraints excluded: chain W residue   61 LEU
Chi-restraints excluded: chain X residue   12 ARG
Chi-restraints excluded: chain X residue   47 GLU
Chi-restraints excluded: chain X residue   54 THR
Chi-restraints excluded: chain Y residue   11 ASP
Chi-restraints excluded: chain Z residue   47 GLU
Chi-restraints excluded: chain Z residue   50 SER
Chi-restraints excluded: chain Z residue   80 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 101 optimal weight:    8.9990
   chunk 59 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 112 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0970
   chunk 25 optimal weight:    5.9990
   chunk 37 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 82 optimal weight:    0.5980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** Z  51 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 = 0.3505 r_free = 0.3505 target = 0.105374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.077349 restraints weight = 14928.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 2.18
r_work: 0.2903 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2789 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8719  Z= 0.150
  Angle     :  0.663  10.235  11826  Z= 0.331
  Chirality :  0.042   0.344   1457
  Planarity :  0.004   0.036   1489
  Dihedral  :  4.936  59.924   1266
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.87 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 31.38 %
    Favored  : 64.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.82 (0.25), residues: 1164
  helix:  2.26 (0.16), residues: 1033
  sheet: -2.39 (1.81), residues: 10
  loop : -1.29 (0.59), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N 482 
 TYR   0.007   0.001   TYR N 565 
 PHE   0.011   0.001   PHE N 552 
 TRP   0.022   0.001   TRP N 378 
 HIS   0.003   0.001   HIS N 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8719)
  covalent geometry    : angle       0.66264 (11826)
  hydrogen bonds       : bond        0.04680 (  834)
  hydrogen bonds       : angle       3.61233 ( 2496)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3635.57 seconds
wall clock time: 62 minutes 31.02 seconds (3751.02 seconds total)