Starting phenix.real_space_refine
on Fri Sep 11 00:34:08 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7n0b_24102/09_2026/7n0b_24102.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n0b_24102/09_2026/7n0b_24102.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7n0b_24102/09_2026/7n0b_24102.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7n0b_24102/09_2026/7n0b_24102.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n0b_24102/09_2026/7n0b_24102.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n0b_24102/09_2026/7n0b_24102.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n0b_24102/09_2026/7n0b_24102.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n0b_24102/09_2026/7n0b_24102.cif"
  }
  resolution = 3.9
  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=   0.003 sd=   0.084
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: 7
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      5      6.06       5
     P      39      5.49       5
     S      52      5.16       5
     C    3589      2.51       5
     N     995      2.21       5
     O    1193      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5875
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 955
          Classifications: {'peptide': 131}
          Link IDs: {'PTRANS': 7, 'TRANS': 123}
    Chain: "B"
      Number of atoms: 4089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 4089
          Classifications: {'peptide': 512}
          Link IDs: {'PTRANS': 26, 'TRANS': 485}
          Chain breaks: 1
    Chain: "T"
      Number of atoms: 419
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 419
          Classifications: {'RNAv2': 20}
          Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 12}
          Link IDs: {'rna3p': 19}
    Chain: "D"
      Number of atoms: 404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 404
          Classifications: {'RNAv2': 19}
          Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 8}
          Link IDs: {'rna3p': 18}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {' CA': 2, ' ZN': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    520  SG  CYS A  74      36.388  29.677  93.960  1.00 45.58           S
  ATOM    546  SG  CYS A  77      33.521  31.561  95.217  1.00 35.44           S
  ATOM    651  SG  CYS A  90      33.777  28.393  95.952  1.00 53.66           S
  ATOM    854  SG  CYS A 117      44.933  12.952 101.734  1.00 87.14           S
  ATOM    874  SG  CYS A 120      45.542  13.925 105.225  1.00 89.83           S
  ATOM    935  SG  CYS A 128      48.215  13.881 102.415  1.00 79.86           S
  ATOM    947  SG  CYS A 130      47.587  11.036 103.195  1.00 83.52           S
  ATOM   2581  SG  CYS B 207      37.217  26.751  62.636  1.00 32.38           S
  ATOM   2601  SG  CYS B 210      38.310  26.605  59.183  1.00 42.28           S
  ATOM   2722  SG  CYS B 226      35.594  28.831  60.379  1.00 33.72           S
  ATOM   3022  SG  CYS B 261      27.187  61.749  57.555  1.00 44.79           S
  ATOM   3152  SG  CYS B 279      30.047  59.367  59.050  1.00 18.04           S
  ATOM   4542  SG  CYS B 452      42.808  40.337  10.665  1.00 95.65           S
  ATOM   4698  SG  CYS B 484      41.023  39.224  13.041  1.00 96.43           S

  Time building chain proxies: 1.42, per 1000 atoms: 0.24
  Number of scatterers: 5875
  At special positions: 0
  Unit cell: (69.42, 91.848, 129.228, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      5     29.99
     Ca      2     19.99
     S      52     16.00
     P      39     15.00
     O    1193      8.00
     N     995      7.00
     C    3589      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: 0.36
  Conformation dependent library (CDL) restraints added in 321.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 201 "
        pdb="ZN    ZN A 201 " - pdb=" NE2 HIS A  83 "
        pdb="ZN    ZN A 201 " - pdb=" SG  CYS A  90 "
        pdb="ZN    ZN A 201 " - pdb=" SG  CYS A  77 "
        pdb="ZN    ZN A 201 " - pdb=" SG  CYS A  74 "
      pdb="  ZN A 202 "
        pdb="ZN    ZN A 202 " - pdb=" SG  CYS A 120 "
        pdb="ZN    ZN A 202 " - pdb=" SG  CYS A 130 "
        pdb="ZN    ZN A 202 " - pdb=" SG  CYS A 128 "
        pdb="ZN    ZN A 202 " - pdb=" SG  CYS A 117 "
      pdb="  ZN B 603 "
        pdb="ZN    ZN B 603 " - pdb=" ND1 HIS B 229 "
        pdb="ZN    ZN B 603 " - pdb=" SG  CYS B 226 "
        pdb="ZN    ZN B 603 " - pdb=" SG  CYS B 207 "
        pdb="ZN    ZN B 603 " - pdb=" SG  CYS B 210 "
      pdb="  ZN B 604 "
        pdb="ZN    ZN B 604 " - pdb=" NE2 HIS B 257 "
        pdb="ZN    ZN B 604 " - pdb=" ND1 HIS B 264 "
        pdb="ZN    ZN B 604 " - pdb=" SG  CYS B 261 "
        pdb="ZN    ZN B 604 " - pdb=" SG  CYS B 279 "
      pdb="  ZN B 605 "
        pdb="ZN    ZN B 605 " - pdb=" ND1 HIS B 487 "
        pdb="ZN    ZN B 605 " - pdb=" SG  CYS B 484 "
        pdb="ZN    ZN B 605 " - pdb=" SG  CYS B 452 "
      Number of angles added : 13


  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1202

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 8 sheets defined
      26.1% alpha, 12.0% beta
      18 base pairs and 28 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 19
      removed outlier: 3.876A  pdb=" N   PHE A  16 " --> pdb=" O   THR A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 33
      removed outlier: 3.586A  pdb=" N   ALA A  26 " --> pdb=" O   ASP A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 80
    Processing helix  chain 'A' and resid 85 through 89
      removed outlier: 4.219A  pdb=" N   PHE A  89 " --> pdb=" O   PRO A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 104
      No H-bonds generated for 'chain 'A' and resid 102 through 104'
    Processing helix  chain 'A' and resid 107 through 114
      removed outlier: 4.029A  pdb=" N   LYS A 113 " --> pdb=" O   GLY A 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.526A  pdb=" N   VAL B  29 " --> pdb=" O   HIS B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 155
    Processing helix  chain 'B' and resid 169 through 174
    Processing helix  chain 'B' and resid 189 through 196
    Processing helix  chain 'B' and resid 245 through 248
      removed outlier: 3.893A  pdb=" N   GLY B 248 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 245 through 248'
    Processing helix  chain 'B' and resid 270 through 287
      removed outlier: 3.863A  pdb=" N   MET B 276 " --> pdb=" O   CYS B 272 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA B 281 " --> pdb=" O   THR B 277 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   CYS B 285 " --> pdb=" O   ALA B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 325
      removed outlier: 3.596A  pdb=" N   ASN B 306 " --> pdb=" O   GLU B 302 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL B 317 " --> pdb=" O   GLN B 313 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   LYS B 318 " --> pdb=" O   HIS B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 374
    Processing helix  chain 'B' and resid 414 through 416
      No H-bonds generated for 'chain 'B' and resid 414 through 416'
    Processing helix  chain 'B' and resid 432 through 437
      removed outlier: 3.934A  pdb=" N   VAL B 437 " --> pdb=" O   SER B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 480
      removed outlier: 3.725A  pdb=" N   GLY B 480 " --> pdb=" O   ARG B 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 505
      removed outlier: 4.344A  pdb=" N   ASN B 489 " --> pdb=" O   ARG B 485 " (cutoff:3.500A)
      removed outlier: 5.235A  pdb=" N   GLU B 490 " --> pdb=" O   HIS B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 515 through 523
      removed outlier: 3.546A  pdb=" N   LEU B 519 " --> pdb=" O   THR B 516 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ASN B 521 " --> pdb=" O   ASN B 518 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 69
    Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55
      removed outlier: 4.256A  pdb=" N   TYR B 124 " --> pdb=" O   ILE B  55 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 116 through 118
      removed outlier: 5.648A  pdb=" N   CYS B  94 " --> pdb=" O   PRO B 106 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 223 through 225
      removed outlier: 3.712A  pdb=" N   THR B 223 " --> pdb=" O   SER B 218 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 364 through 365
      removed outlier: 3.721A  pdb=" N   LEU B 329 " --> pdb=" O   GLU B 347 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LYS B 349 " --> pdb=" O   LEU B 329 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL B 381 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 397 through 401
    Processing sheet with id=AA7, first strand: chain 'B' and resid 410 through 412
    Processing sheet with id=AA8, first strand: chain 'B' and resid 446 through 447
      removed outlier: 6.220A  pdb=" N   TYR B 446 " --> pdb=" O   ILE B 474 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    127 hydrogen bonds defined for protein.
    336 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      41 hydrogen bonds
      82 hydrogen bond angles
      0 basepair planarities
      18 basepair parallelities
      28 stacking parallelities
  Total time for adding SS restraints: 0.79

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1589
        1.33 -     1.46: 1648
        1.46 -     1.58: 2720
        1.58 -     1.70: 76
        1.70 -     1.83: 68
  Bond restraints: 6101
  Sorted by residual:
  bond pdb=" N   ARG B 212 "
       pdb=" CA  ARG B 212 "
    ideal  model  delta    sigma   weight residual
    1.453  1.494 -0.041 1.31e-02 5.83e+03 9.96e+00
  bond pdb=" ND1 HIS B 487 "
       pdb=" CE1 HIS B 487 "
    ideal  model  delta    sigma   weight residual
    1.321  1.352 -0.031 1.00e-02 1.00e+04 9.37e+00
  bond pdb=" CG  HIS B 487 "
       pdb=" ND1 HIS B 487 "
    ideal  model  delta    sigma   weight residual
    1.378  1.409 -0.031 1.10e-02 8.26e+03 7.95e+00
  bond pdb=" ND1 HIS B 264 "
       pdb=" CE1 HIS B 264 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.71e+00
  bond pdb=" N   VAL A  97 "
       pdb=" CA  VAL A  97 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.037 1.35e-02 5.49e+03 7.71e+00
  ... (remaining 6096 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 7881
        2.17 -     4.33: 509
        4.33 -     6.50: 62
        6.50 -     8.66: 11
        8.66 -    10.83: 7
  Bond angle restraints: 8470
  Sorted by residual:
  angle pdb=" N   VAL A  13 "
        pdb=" CA  VAL A  13 "
        pdb=" C   VAL A  13 "
      ideal   model   delta    sigma   weight residual
     112.96  102.13   10.83 1.00e+00 1.00e+00 1.17e+02
  angle pdb=" N   ASP B 273 "
        pdb=" CA  ASP B 273 "
        pdb=" C   ASP B 273 "
      ideal   model   delta    sigma   weight residual
     113.12  102.64   10.48 1.25e+00 6.40e-01 7.04e+01
  angle pdb=" N   ALA B 187 "
        pdb=" CA  ALA B 187 "
        pdb=" C   ALA B 187 "
      ideal   model   delta    sigma   weight residual
     111.07  118.72   -7.65 1.07e+00 8.73e-01 5.11e+01
  angle pdb=" CB  HIS B 487 "
        pdb=" CG  HIS B 487 "
        pdb=" CD2 HIS B 487 "
      ideal   model   delta    sigma   weight residual
     131.20  123.76    7.44 1.30e+00 5.92e-01 3.27e+01
  angle pdb=" CA  ALA B 187 "
        pdb=" C   ALA B 187 "
        pdb=" O   ALA B 187 "
      ideal   model   delta    sigma   weight residual
     120.82  114.82    6.00 1.05e+00 9.07e-01 3.26e+01
  ... (remaining 8465 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.99: 3039
       15.99 -    31.98: 314
       31.98 -    47.97: 103
       47.97 -    63.95: 40
       63.95 -    79.94: 8
  Dihedral angle restraints: 3504
    sinusoidal: 1632
      harmonic: 1872
  Sorted by residual:
  dihedral pdb=" O5'   C D  71 "
           pdb=" C5'   C D  71 "
           pdb=" C4'   C D  71 "
           pdb=" C3'   C D  71 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.77  -59.77     3      6.40e+00 2.44e-02 5.21e+01
  dihedral pdb=" O5'   A D  60 "
           pdb=" C5'   A D  60 "
           pdb=" C4'   A D  60 "
           pdb=" C3'   A D  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.83  -57.83     3      6.40e+00 2.44e-02 5.19e+01
  dihedral pdb=" O5'   C T  20 "
           pdb=" C5'   C T  20 "
           pdb=" C4'   C T  20 "
           pdb=" C3'   C T  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    5.83   54.17     3      6.40e+00 2.44e-02 5.09e+01
  ... (remaining 3501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 723
       0.063 -    0.126: 158
       0.126 -    0.190: 37
       0.190 -    0.253: 40
       0.253 -    0.316: 6
  Chirality restraints: 964
  Sorted by residual:
  chirality pdb=" CA  LEU B 185 "
            pdb=" N   LEU B 185 "
            pdb=" C   LEU B 185 "
            pdb=" CB  LEU B 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.50e+00
  chirality pdb=" CB  ILE B 231 "
            pdb=" CA  ILE B 231 "
            pdb=" CG1 ILE B 231 "
            pdb=" CG2 ILE B 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" P     C D  71 "
            pdb=" OP1   C D  71 "
            pdb=" OP2   C D  71 "
            pdb=" O5'   C D  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.45   -0.27 2.00e-01 2.50e+01 1.88e+00
  ... (remaining 961 not shown)

  Planarity restraints: 943
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A  83 "    0.100 2.00e-02 2.50e+03   7.39e-02 8.19e+01
        pdb=" CG  HIS A  83 "   -0.112 2.00e-02 2.50e+03
        pdb=" ND1 HIS A  83 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD2 HIS A  83 "   -0.046 2.00e-02 2.50e+03
        pdb=" CE1 HIS A  83 "    0.057 2.00e-02 2.50e+03
        pdb=" NE2 HIS A  83 "    0.050 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  76 "   -0.083 2.00e-02 2.50e+03   4.41e-02 3.89e+01
        pdb=" CG  TYR A  76 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  76 "    0.044 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  76 "    0.030 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  76 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  76 "    0.025 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  76 "    0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR A  76 "   -0.063 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 271 "    0.024 2.00e-02 2.50e+03   4.75e-02 2.26e+01
        pdb=" C   SER B 271 "   -0.082 2.00e-02 2.50e+03
        pdb=" O   SER B 271 "    0.031 2.00e-02 2.50e+03
        pdb=" N   CYS B 272 "    0.028 2.00e-02 2.50e+03
  ... (remaining 940 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 42
        2.52 -     3.11: 4151
        3.11 -     3.71: 9418
        3.71 -     4.30: 12840
        4.30 -     4.90: 20212
  Nonbonded interactions: 46663
  Sorted by model distance:
  nonbonded pdb="CA    CA B 601 "
            pdb=" O   HOH D 101 "
     model   vdw
     1.921 2.510
  nonbonded pdb=" OP1   C D  71 "
            pdb="CA    CA B 601 "
     model   vdw
     1.925 2.510
  nonbonded pdb=" OD2 ASP B  90 "
            pdb="CA    CA B 601 "
     model   vdw
     2.013 2.510
  nonbonded pdb=" OD2 ASP B 273 "
            pdb="CA    CA B 601 "
     model   vdw
     2.123 2.510
  nonbonded pdb=" OD1 ASP B  90 "
            pdb="CA    CA B 602 "
     model   vdw
     2.197 2.510
  ... (remaining 46658 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.230
  Find NCS groups from input model:        0.020
  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:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
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      :  0.013   0.482   6120  Z= 0.489
  Angle     :  1.242  25.170   8483  Z= 0.683
  Chirality :  0.074   0.316    964
  Planarity :  0.008   0.074    943
  Dihedral  : 15.723  79.943   2302
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  7.58 %
    Favored  : 92.06 %
  Cbeta Deviations :  0.17 %
  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: -3.60 (0.27), residues: 637
  helix: -3.30 (0.31), residues: 139
  sheet: -2.38 (0.82), residues: 37
  loop : -2.24 (0.25), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 163 
 TYR   0.083   0.003   TYR A  76 
 PHE   0.023   0.003   PHE A 110 
 TRP   0.024   0.003   TRP B 520 
 HIS   0.013   0.002   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00600 /  0.33 ( 6101)
  covalent geometry    : angle       1.13652 /  0.68 ( 8470)
  hydrogen bonds       : bond        0.19598 / 13.36 (  168)
  hydrogen bonds       : angle       8.15554 /  5.67 (  418)
  metal coordination   : bond        0.20815 / 14.65 (   19)
  metal coordination   : angle      12.84065 / 10.29 (   13)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 140
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASP cc_start: 0.7419 (m-30) cc_final: 0.6871 (m-30)
REVERT: A   98 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6814 (mp10)
REVERT: B   92 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7839 (mm-30)
REVERT: B  195 MET cc_start: 0.8486 (mtt) cc_final: 0.8129 (mtt)
REVERT: B  253 LEU cc_start: 0.7116 (tp) cc_final: 0.6789 (tp)
REVERT: B  348 TRP cc_start: 0.6564 (t-100) cc_final: 0.6026 (t-100)
REVERT: B  494 TYR cc_start: 0.8505 (t80) cc_final: 0.8234 (t80)
REVERT: B  509 TRP cc_start: 0.8565 (m100) cc_final: 0.8321 (m100)
  outliers start: 2
  outliers final: 0
  residues processed: 141
  average time/residue: 0.0928
  time to fit residues: 16.4834
Evaluate side-chains
  98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain B residue   92 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0670
   overall best weight:    0.7722

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  95 HIS
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 HIS
B 228 HIS
B 229 HIS
B 314 HIS
B 478 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.192350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.151931 restraints weight = 9422.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.149508 restraints weight = 8422.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.151203 restraints weight = 8024.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.151483 restraints weight = 5773.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.152100 restraints weight = 5599.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.023   1.755   6120  Z= 0.427
  Angle     :  0.723   9.286   8483  Z= 0.342
  Chirality :  0.048   0.258    964
  Planarity :  0.005   0.053    943
  Dihedral  : 13.206  76.732   1160
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.34 %
    Favored  : 82.13 %
  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: -2.53 (0.30), residues: 637
  helix: -2.05 (0.36), residues: 148
  sheet: -2.12 (0.63), residues: 58
  loop : -1.53 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  81 
 TYR   0.015   0.001   TYR B 447 
 PHE   0.016   0.002   PHE B  33 
 TRP   0.011   0.001   TRP B 348 
 HIS   0.005   0.001   HIS B 330 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.15 ( 6101)
  covalent geometry    : angle       0.71333 /  0.34 ( 8470)
  hydrogen bonds       : bond        0.04410 /  2.92 (  168)
  hydrogen bonds       : angle       5.38507 /  3.63 (  418)
  metal coordination   : bond        0.40317 / 26.68 (   19)
  metal coordination   : angle       3.10197 /  2.19 (   13)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8402 (mtpp) cc_final: 0.8162 (ttmm)
REVERT: A   40 ASN cc_start: 0.8202 (t0) cc_final: 0.7974 (t0)
REVERT: B  132 ASP cc_start: 0.7669 (t0) cc_final: 0.7422 (m-30)
REVERT: B  241 MET cc_start: 0.7001 (ptp) cc_final: 0.6739 (mtm)
REVERT: B  253 LEU cc_start: 0.7563 (tp) cc_final: 0.7274 (tp)
REVERT: B  254 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6645 (tm-30)
REVERT: B  445 PHE cc_start: 0.8289 (p90) cc_final: 0.7970 (p90)
REVERT: B  494 TYR cc_start: 0.8896 (t80) cc_final: 0.8595 (t80)
REVERT: B  509 TRP cc_start: 0.8806 (m100) cc_final: 0.8446 (m100)
REVERT: B  514 PHE cc_start: 0.7245 (t80) cc_final: 0.6981 (t80)
  outliers start: 14
  outliers final: 3
  residues processed: 116
  average time/residue: 0.0887
  time to fit residues: 13.0023
Evaluate side-chains
  94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  191 GLU
Chi-restraints excluded: chain B residue  254 GLN
Chi-restraints excluded: chain B residue  341 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 59 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 57 optimal weight:    6.9990
   chunk 23 optimal weight:    0.6980
   chunk 50 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 108 GLN
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.189733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.149961 restraints weight = 9285.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.149790 restraints weight = 9329.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.151017 restraints weight = 8811.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.152058 restraints weight = 5722.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.152661 restraints weight = 5108.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.212   6120  Z= 0.161
  Angle     :  0.729   8.780   8483  Z= 0.337
  Chirality :  0.048   0.269    964
  Planarity :  0.004   0.047    943
  Dihedral  : 11.917  75.745   1154
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 15.70 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.17 (0.31), residues: 637
  helix: -1.40 (0.40), residues: 146
  sheet: -1.92 (0.63), residues: 60
  loop : -1.43 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  78 
 TYR   0.027   0.002   TYR B 447 
 PHE   0.024   0.002   PHE B 133 
 TRP   0.023   0.001   TRP B 348 
 HIS   0.016   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 ( 6101)
  covalent geometry    : angle       0.70874 /  0.33 ( 8470)
  hydrogen bonds       : bond        0.03841 /  2.55 (  168)
  hydrogen bonds       : angle       4.95032 /  3.33 (  418)
  metal coordination   : bond        0.05071 /  3.33 (   19)
  metal coordination   : angle       4.41406 /  2.69 (   13)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.6356 (mtt) cc_final: 0.6125 (mtt)
REVERT: B   72 MET cc_start: 0.8629 (mmm) cc_final: 0.8288 (mtp)
REVERT: B  105 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7326 (mp)
REVERT: B  253 LEU cc_start: 0.7470 (tp) cc_final: 0.7167 (tt)
REVERT: B  315 MET cc_start: 0.7925 (tmm) cc_final: 0.7626 (tmm)
REVERT: B  348 TRP cc_start: 0.6929 (m-10) cc_final: 0.6313 (m-10)
REVERT: B  445 PHE cc_start: 0.8205 (p90) cc_final: 0.7981 (p90)
REVERT: B  494 TYR cc_start: 0.8793 (t80) cc_final: 0.8558 (t80)
  outliers start: 16
  outliers final: 12
  residues processed: 105
  average time/residue: 0.0807
  time to fit residues: 11.1433
Evaluate side-chains
  94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  229 HIS
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  330 HIS
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  444 PHE
Chi-restraints excluded: chain B residue  466 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 65 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 30 optimal weight:    0.4980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 330 HIS ** 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 = 0.4406 r_free = 0.4406 target = 0.197512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.157201 restraints weight = 9264.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.155405 restraints weight = 9185.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.156725 restraints weight = 9356.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.157624 restraints weight = 6502.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.158320 restraints weight = 5883.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.3400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.181   6120  Z= 0.131
  Angle     :  0.669   8.549   8483  Z= 0.308
  Chirality :  0.047   0.249    964
  Planarity :  0.004   0.045    943
  Dihedral  : 11.658  74.640   1154
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 18.05 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.91 (0.31), residues: 637
  helix: -1.11 (0.41), residues: 146
  sheet: -1.75 (0.61), residues: 61
  loop : -1.28 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 400 
 TYR   0.014   0.001   TYR A  27 
 PHE   0.019   0.002   PHE B 133 
 TRP   0.016   0.001   TRP B 509 
 HIS   0.018   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.12 ( 6101)
  covalent geometry    : angle       0.64838 /  0.31 ( 8470)
  hydrogen bonds       : bond        0.03434 /  2.27 (  168)
  hydrogen bonds       : angle       4.81349 /  3.26 (  418)
  metal coordination   : bond        0.04268 /  2.81 (   19)
  metal coordination   : angle       4.30183 /  2.62 (   13)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 VAL cc_start: 0.9237 (m) cc_final: 0.8936 (p)
REVERT: B   72 MET cc_start: 0.8612 (mmm) cc_final: 0.8398 (mtp)
REVERT: B  105 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7254 (mp)
REVERT: B  253 LEU cc_start: 0.7636 (tp) cc_final: 0.7415 (tt)
REVERT: B  315 MET cc_start: 0.8174 (tmm) cc_final: 0.7815 (tmm)
REVERT: B  494 TYR cc_start: 0.8834 (t80) cc_final: 0.8605 (t80)
  outliers start: 17
  outliers final: 10
  residues processed: 105
  average time/residue: 0.0772
  time to fit residues: 10.8586
Evaluate side-chains
  93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  229 HIS
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  444 PHE
Chi-restraints excluded: chain B residue  466 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0010
   chunk 33 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9980
   chunk 5 optimal weight:    0.2980
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.6586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  67 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.197698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.157284 restraints weight = 9332.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.154689 restraints weight = 8282.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.156566 restraints weight = 7849.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.156785 restraints weight = 5687.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.157280 restraints weight = 5592.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.4010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.3813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.170   6120  Z= 0.125
  Angle     :  0.656   8.273   8483  Z= 0.304
  Chirality :  0.047   0.237    964
  Planarity :  0.004   0.047    943
  Dihedral  : 11.577  73.762   1154
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 20.40 %
    Favored  : 77.26 %
  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: -1.68 (0.31), residues: 637
  helix: -0.95 (0.40), residues: 146
  sheet: -1.36 (0.61), residues: 59
  loop : -1.17 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 400 
 TYR   0.019   0.001   TYR B 447 
 PHE   0.024   0.002   PHE B 514 
 TRP   0.016   0.001   TRP B 509 
 HIS   0.018   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 ( 6101)
  covalent geometry    : angle       0.63715 /  0.30 ( 8470)
  hydrogen bonds       : bond        0.03393 /  2.23 (  168)
  hydrogen bonds       : angle       4.71224 /  3.20 (  418)
  metal coordination   : bond        0.04001 /  2.63 (   19)
  metal coordination   : angle       4.03037 /  2.44 (   13)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8564 (mtpp) cc_final: 0.8244 (ttmm)
REVERT: A   42 VAL cc_start: 0.8629 (t) cc_final: 0.8384 (p)
REVERT: A   66 GLU cc_start: 0.6320 (tp30) cc_final: 0.5942 (tp30)
REVERT: A  119 VAL cc_start: 0.9196 (m) cc_final: 0.8897 (p)
REVERT: B  241 MET cc_start: 0.6845 (ptp) cc_final: 0.6567 (mtm)
REVERT: B  253 LEU cc_start: 0.7726 (tp) cc_final: 0.7037 (tt)
REVERT: B  273 ASP cc_start: 0.8143 (t70) cc_final: 0.7685 (t0)
REVERT: B  315 MET cc_start: 0.8272 (tmm) cc_final: 0.7744 (tmm)
REVERT: B  392 TYR cc_start: 0.7910 (m-80) cc_final: 0.7647 (m-80)
REVERT: B  494 TYR cc_start: 0.8782 (t80) cc_final: 0.8573 (t80)
  outliers start: 13
  outliers final: 11
  residues processed: 97
  average time/residue: 0.0753
  time to fit residues: 9.9254
Evaluate side-chains
  94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  229 HIS
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  444 PHE
Chi-restraints excluded: chain B residue  466 VAL
Chi-restraints excluded: chain B residue  495 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 48 optimal weight:    0.4980
   chunk 18 optimal weight:    2.9990
   chunk 4 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0980
   chunk 53 optimal weight:    0.0770
   chunk 24 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.4338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 313 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.199475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.159404 restraints weight = 9207.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.157938 restraints weight = 9002.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.159728 restraints weight = 8809.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.160209 restraints weight = 6130.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.160744 restraints weight = 5832.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.4167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.167   6120  Z= 0.111
  Angle     :  0.633   8.444   8483  Z= 0.291
  Chirality :  0.046   0.222    964
  Planarity :  0.004   0.052    943
  Dihedral  : 11.468  73.037   1154
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 19.31 %
    Favored  : 77.26 %
  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: -1.46 (0.32), residues: 637
  helix: -0.78 (0.41), residues: 150
  sheet: -0.98 (0.61), residues: 59
  loop : -1.06 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 400 
 TYR   0.011   0.001   TYR B 447 
 PHE   0.029   0.002   PHE B 436 
 TRP   0.013   0.001   TRP B 348 
 HIS   0.019   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.10 ( 6101)
  covalent geometry    : angle       0.61457 /  0.29 ( 8470)
  hydrogen bonds       : bond        0.03222 /  2.13 (  168)
  hydrogen bonds       : angle       4.52483 /  3.06 (  418)
  metal coordination   : bond        0.03906 /  2.58 (   19)
  metal coordination   : angle       3.96705 /  2.40 (   13)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8333 (ttmm)
REVERT: A  119 VAL cc_start: 0.9221 (m) cc_final: 0.8929 (p)
REVERT: B  241 MET cc_start: 0.6767 (ptp) cc_final: 0.6535 (mtm)
REVERT: B  253 LEU cc_start: 0.7718 (tp) cc_final: 0.7475 (tp)
REVERT: B  273 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7565 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 105
  average time/residue: 0.0615
  time to fit residues: 8.9772
Evaluate side-chains
  99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  229 HIS
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  273 ASP
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  444 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 65 optimal weight:   10.0000
   chunk 41 optimal weight:    0.0670
   chunk 14 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.7522

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 114 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.197783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.157969 restraints weight = 9236.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.155447 restraints weight = 8600.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.157063 restraints weight = 8405.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.156995 restraints weight = 6387.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.157437 restraints weight = 6767.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.4456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.164   6120  Z= 0.132
  Angle     :  0.652   8.727   8483  Z= 0.302
  Chirality :  0.046   0.229    964
  Planarity :  0.004   0.053    943
  Dihedral  : 11.482  72.864   1154
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 21.48 %
    Favored  : 75.09 %
  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: -1.27 (0.32), residues: 637
  helix: -0.52 (0.42), residues: 144
  sheet: -0.99 (0.58), residues: 59
  loop : -0.95 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 400 
 TYR   0.021   0.001   TYR B 447 
 PHE   0.027   0.002   PHE B 436 
 TRP   0.025   0.002   TRP B 509 
 HIS   0.018   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 6101)
  covalent geometry    : angle       0.63319 /  0.30 ( 8470)
  hydrogen bonds       : bond        0.03275 /  2.16 (  168)
  hydrogen bonds       : angle       4.60609 /  3.11 (  418)
  metal coordination   : bond        0.03858 /  2.54 (   19)
  metal coordination   : angle       3.97166 /  2.43 (   13)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8336 (ttmm)
REVERT: A  119 VAL cc_start: 0.9156 (m) cc_final: 0.8858 (p)
REVERT: B  241 MET cc_start: 0.7025 (ptp) cc_final: 0.6700 (mtm)
REVERT: B  253 LEU cc_start: 0.7773 (tp) cc_final: 0.7168 (tt)
REVERT: B  273 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7720 (t0)
REVERT: B  519 LEU cc_start: 0.8503 (tp) cc_final: 0.8086 (pp)
  outliers start: 19
  outliers final: 15
  residues processed: 98
  average time/residue: 0.0710
  time to fit residues: 9.4558
Evaluate side-chains
  97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  229 HIS
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  273 ASP
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  444 PHE
Chi-restraints excluded: chain B residue  466 VAL
Chi-restraints excluded: chain B residue  495 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 26 optimal weight:    0.0670
   chunk 44 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 17 optimal weight:    8.9990
   chunk 9 optimal weight:    0.7980
   chunk 63 optimal weight:    6.9990
   chunk 66 optimal weight:   10.0000
   overall best weight:    0.6718

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.205176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.158298 restraints weight = 9353.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.157560 restraints weight = 7498.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.158931 restraints weight = 6941.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.159558 restraints weight = 4967.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.160170 restraints weight = 4715.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.4617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.163   6120  Z= 0.125
  Angle     :  0.657   8.675   8483  Z= 0.301
  Chirality :  0.046   0.218    964
  Planarity :  0.003   0.026    943
  Dihedral  : 11.494  72.725   1154
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 21.66 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.09 (0.33), residues: 637
  helix: -0.15 (0.43), residues: 140
  sheet: -1.41 (0.55), residues: 73
  loop : -0.78 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 400 
 TYR   0.009   0.001   TYR B 420 
 PHE   0.019   0.002   PHE B 436 
 TRP   0.026   0.002   TRP B 509 
 HIS   0.019   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 6101)
  covalent geometry    : angle       0.63874 /  0.30 ( 8470)
  hydrogen bonds       : bond        0.03229 /  2.15 (  168)
  hydrogen bonds       : angle       4.42070 /  3.04 (  418)
  metal coordination   : bond        0.03842 /  2.52 (   19)
  metal coordination   : angle       3.99229 /  2.45 (   13)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8611 (mtpp) cc_final: 0.8328 (ttmm)
REVERT: A  119 VAL cc_start: 0.9170 (m) cc_final: 0.8885 (p)
REVERT: B  241 MET cc_start: 0.6993 (ptp) cc_final: 0.6778 (ptp)
REVERT: B  253 LEU cc_start: 0.7744 (tp) cc_final: 0.7113 (tt)
REVERT: B  273 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7745 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 98
  average time/residue: 0.0750
  time to fit residues: 9.9071
Evaluate side-chains
  98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  229 HIS
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  273 ASP
Chi-restraints excluded: chain B residue  444 PHE
Chi-restraints excluded: chain B residue  466 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 7 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0980
   chunk 24 optimal weight:    0.0570
   chunk 65 optimal weight:   10.0000
   chunk 66 optimal weight:    9.9990
   chunk 59 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.6900

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 427 HIS ** 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 = 0.4419 r_free = 0.4419 target = 0.198550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.159608 restraints weight = 9232.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.158417 restraints weight = 9504.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.160168 restraints weight = 8089.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.160463 restraints weight = 5930.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.161341 restraints weight = 5816.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.4774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.161   6120  Z= 0.130
  Angle     :  0.668  10.285   8483  Z= 0.305
  Chirality :  0.046   0.217    964
  Planarity :  0.003   0.026    943
  Dihedral  : 11.500  72.598   1154
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 23.29 %
    Favored  : 73.65 %
  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: -0.99 (0.33), residues: 637
  helix: -0.04 (0.43), residues: 140
  sheet: -1.28 (0.55), residues: 75
  loop : -0.73 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 400 
 TYR   0.012   0.001   TYR A  27 
 PHE   0.026   0.002   PHE B 436 
 TRP   0.017   0.001   TRP B 509 
 HIS   0.018   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.12 ( 6101)
  covalent geometry    : angle       0.65049 /  0.30 ( 8470)
  hydrogen bonds       : bond        0.03278 /  2.19 (  168)
  hydrogen bonds       : angle       4.47636 /  3.10 (  418)
  metal coordination   : bond        0.03794 /  2.50 (   19)
  metal coordination   : angle       3.96272 /  2.43 (   13)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8613 (mtpp) cc_final: 0.8311 (ttmm)
REVERT: A  119 VAL cc_start: 0.9125 (m) cc_final: 0.8806 (p)
REVERT: B  253 LEU cc_start: 0.7718 (tp) cc_final: 0.7113 (tt)
REVERT: B  273 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7794 (t0)
  outliers start: 17
  outliers final: 16
  residues processed: 95
  average time/residue: 0.0723
  time to fit residues: 9.1875
Evaluate side-chains
  95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  229 HIS
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  273 ASP
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  444 PHE
Chi-restraints excluded: chain B residue  466 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 42 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 66 optimal weight:   10.0000
   chunk 8 optimal weight:    0.2980
   chunk 62 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0670
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.4718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 427 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.189688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.152925 restraints weight = 8961.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.150119 restraints weight = 10821.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.151921 restraints weight = 9648.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.151895 restraints weight = 7363.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.152353 restraints weight = 7986.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.4918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.162   6120  Z= 0.121
  Angle     :  0.684  10.460   8483  Z= 0.314
  Chirality :  0.046   0.209    964
  Planarity :  0.003   0.025    943
  Dihedral  : 11.489  72.494   1154
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 23.65 %
    Favored  : 73.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.90 (0.33), residues: 637
  helix:  0.17 (0.43), residues: 139
  sheet: -1.57 (0.59), residues: 64
  loop : -0.69 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 400 
 TYR   0.010   0.001   TYR B 494 
 PHE   0.019   0.002   PHE B 436 
 TRP   0.017   0.001   TRP B 348 
 HIS   0.019   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.12 ( 6101)
  covalent geometry    : angle       0.66715 /  0.31 ( 8470)
  hydrogen bonds       : bond        0.03227 /  2.16 (  168)
  hydrogen bonds       : angle       4.45206 /  3.09 (  418)
  metal coordination   : bond        0.03798 /  2.50 (   19)
  metal coordination   : angle       3.91345 /  2.38 (   13)

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8305 (tppp)
REVERT: A  119 VAL cc_start: 0.9020 (m) cc_final: 0.8673 (p)
REVERT: B  253 LEU cc_start: 0.7737 (tp) cc_final: 0.7163 (tt)
REVERT: B  476 ARG cc_start: 0.7328 (mpt180) cc_final: 0.6828 (mpt180)
  outliers start: 18
  outliers final: 15
  residues processed: 94
  average time/residue: 0.0781
  time to fit residues: 9.8975
Evaluate side-chains
  93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  229 HIS
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  444 PHE
Chi-restraints excluded: chain B residue  466 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 25 optimal weight:    0.0070
   chunk 6 optimal weight:    0.0870
   chunk 17 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   overall best weight:    0.4978

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.185370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.148369 restraints weight = 8941.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.147031 restraints weight = 12015.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.148568 restraints weight = 11477.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.149285 restraints weight = 7872.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.149971 restraints weight = 7361.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.5147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.161   6120  Z= 0.121
  Angle     :  0.667  10.096   8483  Z= 0.307
  Chirality :  0.046   0.224    964
  Planarity :  0.003   0.026    943
  Dihedral  : 11.461  72.364   1154
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 24.19 %
    Favored  : 73.29 %
  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: -0.82 (0.33), residues: 637
  helix:  0.30 (0.44), residues: 140
  sheet: -1.55 (0.60), residues: 64
  loop : -0.66 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 400 
 TYR   0.012   0.001   TYR A  27 
 PHE   0.017   0.001   PHE B 436 
 TRP   0.014   0.001   TRP B 348 
 HIS   0.019   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 ( 6101)
  covalent geometry    : angle       0.64931 /  0.30 ( 8470)
  hydrogen bonds       : bond        0.03190 /  2.14 (  168)
  hydrogen bonds       : angle       4.46224 /  3.08 (  418)
  metal coordination   : bond        0.03757 /  2.48 (   19)
  metal coordination   : angle       3.89981 /  2.35 (   13)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1076.51 seconds
wall clock time: 19 minutes 19.85 seconds (1159.85 seconds total)