Starting phenix.real_space_refine
on Thu Jul  2 02:55:19 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7n0b_24102/07_2026/7n0b_24102.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n0b_24102/07_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n0b_24102/07_2026/7n0b_24102.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n0b_24102/07_2026/7n0b_24102.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7n0b_24102/07_2026/7n0b_24102.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7n0b_24102/07_2026/7n0b_24102.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n0b_24102/07_2026/7n0b_24102.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n0b_24102/07_2026/7n0b_24102.map"
  }
  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-dev-6108/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: {'RNA': 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: {'RNA': 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: 0.50
  Conformation dependent library (CDL) restraints added in 315.3 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: 0.65
  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: 0.99

  Time building geometry restraints manager: 0.67 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: 7952
        2.17 -     4.33: 439
        4.33 -     6.50: 61
        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 -    18.54: 3157
       18.54 -    37.08: 271
       37.08 -    55.61: 64
       55.61 -    74.15: 6
       74.15 -    92.69: 6
  Dihedral angle restraints: 3504
    sinusoidal: 1632
      harmonic: 1872
  Sorted by residual:
  dihedral pdb=" CA  HIS B 268 "
           pdb=" C   HIS B 268 "
           pdb=" N   VAL B 269 "
           pdb=" CA  VAL B 269 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.33   22.67     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" CA  TYR B 237 "
           pdb=" C   TYR B 237 "
           pdb=" N   ASN B 238 "
           pdb=" CA  ASN B 238 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.66  -20.34     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" C   PHE B 190 "
           pdb=" N   PHE B 190 "
           pdb=" CA  PHE B 190 "
           pdb=" CB  PHE B 190 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.08    9.48     0      2.50e+00 1.60e-01 1.44e+01
  ... (remaining 3501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 762
       0.063 -    0.126: 158
       0.126 -    0.190: 37
       0.190 -    0.253: 5
       0.253 -    0.316: 2
  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=" CA  PHE B 190 "
            pdb=" N   PHE B 190 "
            pdb=" C   PHE B 190 "
            pdb=" CB  PHE B 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.55e+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:             0.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     8.210
  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:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.270
-------------------------------------------------------------------------------
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     :  1.212  25.170   8483  Z= 0.682
  Chirality :  0.058   0.316    964
  Planarity :  0.008   0.074    943
  Dihedral  : 14.675  92.688   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        0.00596 /  0.33 ( 6101)
  covalent geometry    : angle       1.10353 /  0.67 ( 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  : 0.205 
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: 0.0910
  time to fit residues: 16.3254
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  : 0.199 
-------------------------------------------------------------------------------
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:    0.0970
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4339 r_free = 0.4339 target = 0.192489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.152690 restraints weight = 9438.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.151351 restraints weight = 9587.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.152971 restraints weight = 9057.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.154022 restraints weight = 6126.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.155416 restraints weight = 5318.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.023   1.752   6120  Z= 0.423
  Angle     :  0.637   8.886   8483  Z= 0.323
  Chirality :  0.041   0.162    964
  Planarity :  0.005   0.053    943
  Dihedral  : 11.983  95.597   1160
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.80 %
    Favored  : 82.49 %
  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: -2.52 (0.30), residues: 637
  helix: -2.04 (0.36), residues: 148
  sheet: -2.11 (0.63), residues: 58
  loop : -1.52 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  81 
 TYR   0.012   0.001   TYR A  30 
 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        0.00306 /  0.14 ( 6101)
  covalent geometry    : angle       0.62760 /  0.32 ( 8470)
  hydrogen bonds       : bond        0.04230 /  2.82 (  168)
  hydrogen bonds       : angle       5.32390 /  3.59 (  418)
  metal coordination   : bond        0.40217 / 26.62 (   19)
  metal coordination   : angle       2.92031 /  1.98 (   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
  123 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8167 (ttmm)
REVERT: A   40 ASN cc_start: 0.8167 (t0) cc_final: 0.7958 (t0)
REVERT: B   72 MET cc_start: 0.8484 (mmm) cc_final: 0.7894 (mmm)
REVERT: B  132 ASP cc_start: 0.7691 (t0) cc_final: 0.7439 (m-30)
REVERT: B  241 MET cc_start: 0.7060 (ptp) cc_final: 0.6760 (mtm)
REVERT: B  253 LEU cc_start: 0.7571 (tp) cc_final: 0.7285 (tp)
REVERT: B  254 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6674 (tm-30)
REVERT: B  445 PHE cc_start: 0.8247 (p90) cc_final: 0.7940 (p90)
REVERT: B  447 TYR cc_start: 0.7229 (t80) cc_final: 0.6834 (t80)
REVERT: B  494 TYR cc_start: 0.8856 (t80) cc_final: 0.8597 (t80)
REVERT: B  509 TRP cc_start: 0.8786 (m100) cc_final: 0.8393 (m100)
REVERT: B  514 PHE cc_start: 0.7188 (t80) cc_final: 0.6974 (t80)
  outliers start: 15
  outliers final: 4
  residues processed: 118
  average time/residue: 0.0900
  time to fit residues: 13.5786
Evaluate side-chains
  95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 CYS
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:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9980
   chunk 59 optimal weight:   20.0000
   chunk 33 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0010
   chunk 23 optimal weight:    0.5980
   chunk 50 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    0.8388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4404 r_free = 0.4404 target = 0.197220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.157548 restraints weight = 9139.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.155939 restraints weight = 9614.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.156874 restraints weight = 11031.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.158440 restraints weight = 6947.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.158896 restraints weight = 5635.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.2943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.222   6120  Z= 0.143
  Angle     :  0.613   9.557   8483  Z= 0.307
  Chirality :  0.040   0.137    964
  Planarity :  0.004   0.049    943
  Dihedral  : 11.669  95.408   1154
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 15.70 %
    Favored  : 81.23 %
  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: -2.22 (0.31), residues: 637
  helix: -1.53 (0.39), residues: 149
  sheet: -1.92 (0.62), residues: 60
  loop : -1.43 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  78 
 TYR   0.018   0.001   TYR B 351 
 PHE   0.024   0.002   PHE B 133 
 TRP   0.024   0.002   TRP B 348 
 HIS   0.016   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 ( 6101)
  covalent geometry    : angle       0.58626 /  0.30 ( 8470)
  hydrogen bonds       : bond        0.03687 /  2.46 (  168)
  hydrogen bonds       : angle       4.94869 /  3.38 (  418)
  metal coordination   : bond        0.05241 /  3.44 (   19)
  metal coordination   : angle       4.65525 /  2.79 (   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
  113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8215 (ttmm)
REVERT: A   44 MET cc_start: 0.6386 (mtt) cc_final: 0.6158 (mtt)
REVERT: A   66 GLU cc_start: 0.6233 (tp30) cc_final: 0.5870 (tp30)
REVERT: B  241 MET cc_start: 0.6841 (ptp) cc_final: 0.6553 (mtm)
REVERT: B  253 LEU cc_start: 0.7596 (tp) cc_final: 0.7257 (tt)
REVERT: B  276 MET cc_start: 0.7964 (mmm) cc_final: 0.6908 (mmm)
REVERT: B  348 TRP cc_start: 0.7011 (m-10) cc_final: 0.6369 (m-10)
REVERT: B  445 PHE cc_start: 0.8275 (p90) cc_final: 0.8011 (p90)
REVERT: B  494 TYR cc_start: 0.8885 (t80) cc_final: 0.8676 (t80)
REVERT: B  509 TRP cc_start: 0.8732 (m100) cc_final: 0.8082 (m100)
  outliers start: 17
  outliers final: 9
  residues processed: 109
  average time/residue: 0.0750
  time to fit residues: 10.6723
Evaluate side-chains
  92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 7 optimal weight:    0.0980
   chunk 46 optimal weight:    0.0970
   chunk 51 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 3 optimal weight:    0.2980
   chunk 30 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0570
   overall best weight:    0.2296

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  67 ASN
B 104 ASN
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.208363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.160743 restraints weight = 9373.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.159440 restraints weight = 6820.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.161249 restraints weight = 6765.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.161797 restraints weight = 4630.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.162667 restraints weight = 4439.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.180   6120  Z= 0.108
  Angle     :  0.580   8.453   8483  Z= 0.285
  Chirality :  0.039   0.176    964
  Planarity :  0.004   0.048    943
  Dihedral  : 11.364  95.047   1154
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.87 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.31), residues: 637
  helix: -1.36 (0.40), residues: 148
  sheet: -1.56 (0.68), residues: 48
  loop : -1.36 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  78 
 TYR   0.013   0.001   TYR A  27 
 PHE   0.018   0.001   PHE B 133 
 TRP   0.009   0.001   TRP B 348 
 HIS   0.019   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00215 /  0.10 ( 6101)
  covalent geometry    : angle       0.55882 /  0.28 ( 8470)
  hydrogen bonds       : bond        0.03140 /  2.06 (  168)
  hydrogen bonds       : angle       4.65738 /  3.18 (  418)
  metal coordination   : bond        0.04188 /  2.77 (   19)
  metal coordination   : angle       3.99213 /  2.34 (   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
  116 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8331 (mtpp) cc_final: 0.8114 (ttmm)
REVERT: A   42 VAL cc_start: 0.8718 (t) cc_final: 0.8505 (p)
REVERT: A   66 GLU cc_start: 0.6401 (tp30) cc_final: 0.5842 (tp30)
REVERT: A  119 VAL cc_start: 0.9206 (m) cc_final: 0.8985 (p)
REVERT: B  276 MET cc_start: 0.7883 (mmm) cc_final: 0.7073 (mmt)
  outliers start: 15
  outliers final: 12
  residues processed: 111
  average time/residue: 0.0713
  time to fit residues: 10.4643
Evaluate side-chains
  99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   64 ASP
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  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  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:   10.0000
   chunk 36 optimal weight:    0.7980
   chunk 53 optimal weight:    0.4980
   chunk 38 optimal weight:    0.0070
   chunk 33 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.6198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 313 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.205950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.158072 restraints weight = 9458.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.156577 restraints weight = 7189.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.158209 restraints weight = 8091.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.158601 restraints weight = 5179.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.159768 restraints weight = 4796.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.3793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.169   6120  Z= 0.119
  Angle     :  0.571   9.673   8483  Z= 0.282
  Chirality :  0.039   0.136    964
  Planarity :  0.004   0.054    943
  Dihedral  : 11.243  95.052   1154
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 19.86 %
    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: -1.74 (0.31), residues: 637
  helix: -1.11 (0.41), residues: 148
  sheet: -1.22 (0.61), residues: 59
  loop : -1.19 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  78 
 TYR   0.008   0.001   TYR B 447 
 PHE   0.026   0.002   PHE B 217 
 TRP   0.004   0.001   TRP B 247 
 HIS   0.019   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.11 ( 6101)
  covalent geometry    : angle       0.55048 /  0.28 ( 8470)
  hydrogen bonds       : bond        0.03064 /  2.02 (  168)
  hydrogen bonds       : angle       4.64965 /  3.17 (  418)
  metal coordination   : bond        0.03963 /  2.61 (   19)
  metal coordination   : angle       3.90850 /  2.28 (   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
  106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8486 (mtpp) cc_final: 0.8224 (ttmm)
REVERT: A   66 GLU cc_start: 0.6541 (tp30) cc_final: 0.6001 (tp30)
REVERT: A  119 VAL cc_start: 0.9213 (m) cc_final: 0.8984 (p)
REVERT: B  241 MET cc_start: 0.6697 (mtm) cc_final: 0.6455 (mtm)
REVERT: B  273 ASP cc_start: 0.8025 (t70) cc_final: 0.7239 (t0)
REVERT: B  276 MET cc_start: 0.7951 (mmm) cc_final: 0.6696 (mmm)
REVERT: B  494 TYR cc_start: 0.8751 (t80) cc_final: 0.8527 (t80)
REVERT: B  509 TRP cc_start: 0.8740 (m100) cc_final: 0.8058 (m100)
  outliers start: 16
  outliers final: 11
  residues processed: 101
  average time/residue: 0.0663
  time to fit residues: 8.9961
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  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain A residue   97 VAL
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  125 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  444 PHE
Chi-restraints excluded: chain B residue  466 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0970
   chunk 48 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0770
   chunk 21 optimal weight:    0.4980
   chunk 53 optimal weight:    0.0170
   chunk 24 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.3174

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 108 GLN ** 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 = 0.4192 r_free = 0.4192 target = 0.186966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.148523 restraints weight = 9035.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.145846 restraints weight = 12031.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.147296 restraints weight = 11913.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.147541 restraints weight = 8449.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.148047 restraints weight = 8115.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.4108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.166   6120  Z= 0.105
  Angle     :  0.545   8.658   8483  Z= 0.270
  Chirality :  0.039   0.131    964
  Planarity :  0.004   0.054    943
  Dihedral  : 11.091  94.394   1154
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 20.04 %
    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: -1.41 (0.32), residues: 637
  helix: -0.58 (0.43), residues: 142
  sheet: -1.06 (0.58), residues: 66
  loop : -1.06 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 400 
 TYR   0.011   0.001   TYR A  27 
 PHE   0.021   0.001   PHE B 217 
 TRP   0.011   0.001   TRP B 348 
 HIS   0.019   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00217 /  0.10 ( 6101)
  covalent geometry    : angle       0.52453 /  0.27 ( 8470)
  hydrogen bonds       : bond        0.02833 /  1.88 (  168)
  hydrogen bonds       : angle       4.37829 /  2.97 (  418)
  metal coordination   : bond        0.03864 /  2.56 (   19)
  metal coordination   : angle       3.84950 /  2.29 (   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
  106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8247 (mtpp) cc_final: 0.7969 (ttmm)
REVERT: A   66 GLU cc_start: 0.5946 (tp30) cc_final: 0.5679 (tp30)
REVERT: A  119 VAL cc_start: 0.8902 (m) cc_final: 0.8616 (p)
REVERT: B  241 MET cc_start: 0.6560 (mtm) cc_final: 0.6289 (mtm)
REVERT: B  273 ASP cc_start: 0.7687 (t70) cc_final: 0.7011 (t0)
REVERT: B  276 MET cc_start: 0.7679 (mmm) cc_final: 0.6763 (mmt)
  outliers start: 15
  outliers final: 11
  residues processed: 101
  average time/residue: 0.0703
  time to fit residues: 9.6958
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  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   64 ASP
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  125 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  444 PHE
Chi-restraints excluded: chain B residue  495 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 29 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 15 optimal weight:    8.9990
   chunk 62 optimal weight:    6.9990
   chunk 65 optimal weight:   10.0000
   chunk 41 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 114 ASN
B  82 HIS
B 108 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.200930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.153650 restraints weight = 9233.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.151541 restraints weight = 7997.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.152994 restraints weight = 7483.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.153596 restraints weight = 5448.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.154262 restraints weight = 5100.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.4248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.163   6120  Z= 0.187
  Angle     :  0.633   9.054   8483  Z= 0.315
  Chirality :  0.041   0.127    964
  Planarity :  0.004   0.053    943
  Dihedral  : 11.233  94.690   1154
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 21.30 %
    Favored  : 75.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.32), residues: 637
  helix: -0.63 (0.42), residues: 147
  sheet: -1.32 (0.54), residues: 74
  loop : -0.94 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 400 
 TYR   0.010   0.002   TYR B 420 
 PHE   0.017   0.002   PHE B 217 
 TRP   0.014   0.002   TRP B 348 
 HIS   0.018   0.002   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00421 /  0.18 ( 6101)
  covalent geometry    : angle       0.61189 /  0.31 ( 8470)
  hydrogen bonds       : bond        0.03309 /  2.21 (  168)
  hydrogen bonds       : angle       4.72385 /  3.19 (  418)
  metal coordination   : bond        0.03957 /  2.58 (   19)
  metal coordination   : angle       4.22169 /  2.60 (   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
  100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 VAL cc_start: 0.9212 (m) cc_final: 0.8958 (p)
REVERT: B  188 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.7779 (t70)
REVERT: B  273 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7659 (t0)
REVERT: B  509 TRP cc_start: 0.8861 (m100) cc_final: 0.8335 (m100)
  outliers start: 18
  outliers final: 13
  residues processed: 94
  average time/residue: 0.0687
  time to fit residues: 8.7660
Evaluate side-chains
  92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
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  120 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  188 HIS
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  439 LEU
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:    0.7980
   chunk 44 optimal weight:    5.9990
   chunk 51 optimal weight:    0.2980
   chunk 31 optimal weight:    0.0010
   chunk 28 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 17 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 66 optimal weight:   20.0000
   overall best weight:    0.6190

-------------------------------------------------------------------------------
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 = 0.4150 r_free = 0.4150 target = 0.182903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.145108 restraints weight = 9089.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.143973 restraints weight = 11721.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.145137 restraints weight = 11739.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.146169 restraints weight = 7909.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.146554 restraints weight = 6939.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.4470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.164   6120  Z= 0.120
  Angle     :  0.585   8.511   8483  Z= 0.286
  Chirality :  0.040   0.190    964
  Planarity :  0.004   0.053    943
  Dihedral  : 11.142  94.616   1154
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 22.20 %
    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: -1.12 (0.33), residues: 637
  helix: -0.18 (0.44), residues: 141
  sheet: -1.30 (0.56), residues: 73
  loop : -0.83 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 400 
 TYR   0.010   0.001   TYR B 420 
 PHE   0.017   0.001   PHE B 217 
 TRP   0.011   0.001   TRP B 348 
 HIS   0.018   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.11 ( 6101)
  covalent geometry    : angle       0.56387 /  0.28 ( 8470)
  hydrogen bonds       : bond        0.02929 /  1.95 (  168)
  hydrogen bonds       : angle       4.48477 /  3.03 (  418)
  metal coordination   : bond        0.03861 /  2.54 (   19)
  metal coordination   : angle       4.01277 /  2.47 (   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
  99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8518 (mtpp) cc_final: 0.8236 (ttmm)
REVERT: A   66 GLU cc_start: 0.6231 (tp30) cc_final: 0.6015 (tp30)
REVERT: A  119 VAL cc_start: 0.9039 (m) cc_final: 0.8754 (p)
REVERT: B  273 ASP cc_start: 0.7907 (t70) cc_final: 0.7505 (t0)
  outliers start: 16
  outliers final: 14
  residues processed: 92
  average time/residue: 0.0674
  time to fit residues: 8.3644
Evaluate side-chains
  94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  439 LEU
Chi-restraints excluded: chain B residue  444 PHE
Chi-restraints excluded: chain B residue  495 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 7 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 65 optimal weight:   10.0000
   chunk 66 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0030
   chunk 40 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.9992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 104 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.185043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.146999 restraints weight = 8960.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.145209 restraints weight = 12268.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.146362 restraints weight = 13615.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.148029 restraints weight = 8518.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.148480 restraints weight = 6838.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.4530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.162   6120  Z= 0.146
  Angle     :  0.598   8.723   8483  Z= 0.295
  Chirality :  0.040   0.136    964
  Planarity :  0.004   0.053    943
  Dihedral  : 11.143  94.673   1154
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 22.20 %
    Favored  : 74.73 %
  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: -1.05 (0.33), residues: 637
  helix: -0.09 (0.44), residues: 141
  sheet: -1.32 (0.57), residues: 73
  loop : -0.78 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 400 
 TYR   0.013   0.001   TYR A  27 
 PHE   0.015   0.002   PHE B 217 
 TRP   0.020   0.001   TRP B 348 
 HIS   0.018   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.14 ( 6101)
  covalent geometry    : angle       0.57734 /  0.29 ( 8470)
  hydrogen bonds       : bond        0.03102 /  2.06 (  168)
  hydrogen bonds       : angle       4.46730 /  3.03 (  418)
  metal coordination   : bond        0.03849 /  2.52 (   19)
  metal coordination   : angle       4.00532 /  2.47 (   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
  98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8541 (mtpp) cc_final: 0.8236 (ttmm)
REVERT: A  119 VAL cc_start: 0.8972 (m) cc_final: 0.8676 (p)
REVERT: B  241 MET cc_start: 0.6718 (mtm) cc_final: 0.6486 (mtm)
REVERT: B  273 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7489 (t0)
REVERT: B  476 ARG cc_start: 0.7407 (mpt180) cc_final: 0.7133 (mpt180)
  outliers start: 17
  outliers final: 14
  residues processed: 90
  average time/residue: 0.0689
  time to fit residues: 8.4381
Evaluate side-chains
  91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
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  439 LEU
Chi-restraints excluded: chain B residue  444 PHE
Chi-restraints excluded: chain B residue  495 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0770
   chunk 32 optimal weight:    0.4980
   chunk 66 optimal weight:   20.0000
   chunk 8 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.8140

-------------------------------------------------------------------------------
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 = 0.4145 r_free = 0.4145 target = 0.182275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.144566 restraints weight = 9124.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.142879 restraints weight = 12481.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.144534 restraints weight = 11872.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.145752 restraints weight = 7748.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.146276 restraints weight = 6681.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.4726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.162   6120  Z= 0.131
  Angle     :  0.585   8.639   8483  Z= 0.290
  Chirality :  0.040   0.141    964
  Planarity :  0.004   0.054    943
  Dihedral  : 11.086  94.641   1154
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 22.38 %
    Favored  : 74.55 %
  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: -0.94 (0.33), residues: 637
  helix:  0.07 (0.44), residues: 141
  sheet: -1.18 (0.57), residues: 75
  loop : -0.75 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 400 
 TYR   0.010   0.001   TYR B 420 
 PHE   0.015   0.002   PHE B 217 
 TRP   0.016   0.001   TRP B 348 
 HIS   0.018   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 6101)
  covalent geometry    : angle       0.56437 /  0.29 ( 8470)
  hydrogen bonds       : bond        0.02997 /  1.99 (  168)
  hydrogen bonds       : angle       4.38317 /  2.97 (  418)
  metal coordination   : bond        0.03838 /  2.51 (   19)
  metal coordination   : angle       3.96529 /  2.43 (   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
  104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8282 (ttmm)
REVERT: A  119 VAL cc_start: 0.9085 (m) cc_final: 0.8805 (p)
REVERT: B  273 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7604 (t0)
REVERT: B  476 ARG cc_start: 0.7589 (mpt180) cc_final: 0.7355 (mpt180)
REVERT: B  509 TRP cc_start: 0.8623 (m100) cc_final: 0.8209 (m100)
  outliers start: 17
  outliers final: 16
  residues processed: 96
  average time/residue: 0.0694
  time to fit residues: 8.8966
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  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
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  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  439 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 17 optimal weight:    0.4980
   chunk 60 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 7 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 64 optimal weight:    8.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 = 0.4196 r_free = 0.4196 target = 0.187062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.149173 restraints weight = 8858.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.147418 restraints weight = 11339.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.148750 restraints weight = 11355.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.149810 restraints weight = 7705.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.150323 restraints weight = 6788.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.4842

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     :  0.590   8.792   8483  Z= 0.292
  Chirality :  0.040   0.195    964
  Planarity :  0.003   0.027    943
  Dihedral  : 10.980  94.161   1154
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 23.47 %
    Favored  : 73.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.89 (0.33), residues: 637
  helix:  0.17 (0.44), residues: 141
  sheet: -1.24 (0.56), residues: 75
  loop : -0.72 (0.32), residues: 421

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   0.016   0.001   PHE B 217 
 TRP   0.016   0.001   TRP B 348 
 HIS   0.019   0.001   HIS B 229 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.11 ( 6101)
  covalent geometry    : angle       0.56978 /  0.29 ( 8470)
  hydrogen bonds       : bond        0.02941 /  1.95 (  168)
  hydrogen bonds       : angle       4.32062 /  2.92 (  418)
  metal coordination   : bond        0.03820 /  2.51 (   19)
  metal coordination   : angle       3.91119 /  2.38 (   13)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1023.44 seconds
wall clock time: 18 minutes 29.74 seconds (1109.74 seconds total)