Starting phenix.real_space_refine
on Thu Jul 24 12:00:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n0b_24102/07_2025/7n0b_24102.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n0b_24102/07_2025/7n0b_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n0b_24102/07_2025/7n0b_24102.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n0b_24102/07_2025/7n0b_24102.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n0b_24102/07_2025/7n0b_24102.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n0b_24102/07_2025/7n0b_24102.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.45, per 1000 atoms: 0.76
  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: 1.63
  Conformation dependent library (CDL) restraints added in 811.2 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: 2.20
  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: 2.04

  Time building geometry restraints manager: 1.90 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: 3199
       18.54 -    37.08: 278
       37.08 -    55.61: 87
       55.61 -    74.15: 44
       74.15 -    92.69: 6
  Dihedral angle restraints: 3614
    sinusoidal: 1742
      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 3611 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:             0.640
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     22.270
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
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  : 16.966  92.688   2412
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.024   0.003   TRP B 520 
 HIS   0.013   0.002   HIS B 229 
 PHE   0.023   0.003   PHE A 110 
 TYR   0.083   0.003   TYR A  76 
 ARG   0.005   0.001   ARG B 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19598 (  168)
  hydrogen bonds       : angle       8.15554 (  418)
  metal coordination   : bond        0.20815 (   19)
  metal coordination   : angle      12.84065 (   13)
  covalent geometry    : bond        0.00596 ( 6101)
  covalent geometry    : angle       1.10353 ( 8470)

*********************** 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  : 0.555 
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: 0.7448 (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: 0.6790 (tp)
REVERT: B  348 TRP cc_start: 0.6563 (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: 0.2099
  time to fit residues: 36.9918
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  : 0.617 
-------------------------------------------------------------------------------
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 56 optimal weight:    7.9990
   chunk 50 optimal weight:    9.9990
   chunk 28 optimal weight:    0.4980
   chunk 17 optimal weight:    7.9990
   chunk 34 optimal weight:    0.8980
   chunk 27 optimal weight:    0.2980
   chunk 52 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4329 r_free = 0.4329 target = 0.191413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.151660 restraints weight = 9241.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.149051 restraints weight = 9644.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.150829 restraints weight = 8417.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.023   1.755   6120  Z= 0.429
  Angle     :  0.651   8.765   8483  Z= 0.330
  Chirality :  0.042   0.171    964
  Planarity :  0.005   0.053    943
  Dihedral  : 16.650  95.349   1270
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.98 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.30), residues: 637
  helix: -2.03 (0.37), residues: 148
  sheet: -2.14 (0.63), residues: 58
  loop : -1.54 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 348 
 HIS   0.005   0.001   HIS B 330 
 PHE   0.015   0.002   PHE B 111 
 TYR   0.014   0.001   TYR B 447 
 ARG   0.003   0.000   ARG B  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04476 (  168)
  hydrogen bonds       : angle       5.41175 (  418)
  metal coordination   : bond        0.40304 (   19)
  metal coordination   : angle       3.16221 (   13)
  covalent geometry    : bond        0.00342 ( 6101)
  covalent geometry    : angle       0.63980 ( 8470)

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

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

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

  1274 Ramachandran restraints generated.
    637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8454 (mtpp) cc_final: 0.8208 (ttmm)
REVERT: A   40 ASN cc_start: 0.8215 (t0) cc_final: 0.7976 (t0)
REVERT: B  132 ASP cc_start: 0.7680 (t0) cc_final: 0.7410 (m-30)
REVERT: B  241 MET cc_start: 0.6923 (ptp) cc_final: 0.6703 (mtm)
REVERT: B  253 LEU cc_start: 0.7569 (tp) cc_final: 0.7291 (tp)
REVERT: B  254 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6636 (tm-30)
REVERT: B  445 PHE cc_start: 0.8236 (p90) cc_final: 0.7962 (p90)
REVERT: B  447 TYR cc_start: 0.7275 (t80) cc_final: 0.6826 (t80)
REVERT: B  494 TYR cc_start: 0.8843 (t80) cc_final: 0.8581 (t80)
REVERT: B  509 TRP cc_start: 0.8787 (m100) cc_final: 0.8444 (m100)
REVERT: B  514 PHE cc_start: 0.7245 (t80) cc_final: 0.7006 (t80)
  outliers start: 15
  outliers final: 5
  residues processed: 116
  average time/residue: 0.2182
  time to fit residues: 31.7678
Evaluate side-chains
  95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
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 25 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0370
   chunk 19 optimal weight:    0.0570
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.4976

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4343 r_free = 0.4343 target = 0.193182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.152598 restraints weight = 9382.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.150555 restraints weight = 8633.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.152342 restraints weight = 8206.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.211   6120  Z= 0.123
  Angle     :  0.607  10.164   8483  Z= 0.302
  Chirality :  0.040   0.136    964
  Planarity :  0.004   0.048    943
  Dihedral  : 16.291  95.129   1264
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.25 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.31), residues: 637
  helix: -1.49 (0.40), residues: 145
  sheet: -1.72 (0.65), residues: 58
  loop : -1.39 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 292 
 HIS   0.018   0.001   HIS B 229 
 PHE   0.022   0.002   PHE B 377 
 TYR   0.018   0.001   TYR B 351 
 ARG   0.005   0.000   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03639 (  168)
  hydrogen bonds       : angle       4.91193 (  418)
  metal coordination   : bond        0.04944 (   19)
  metal coordination   : angle       4.44675 (   13)
  covalent geometry    : bond        0.00248 ( 6101)
  covalent geometry    : angle       0.58170 ( 8470)

*********************** 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: 16
    poor density    : 97
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8390 (mtpp) cc_final: 0.8141 (ttmm)
REVERT: B   72 MET cc_start: 0.8564 (mmm) cc_final: 0.8168 (mtp)
REVERT: B  132 ASP cc_start: 0.7850 (t0) cc_final: 0.7565 (m-30)
REVERT: B  253 LEU cc_start: 0.7491 (tp) cc_final: 0.7205 (tt)
REVERT: B  445 PHE cc_start: 0.8254 (p90) cc_final: 0.7961 (p90)
REVERT: B  494 TYR cc_start: 0.8834 (t80) cc_final: 0.8600 (t80)
REVERT: B  509 TRP cc_start: 0.8776 (m100) cc_final: 0.8546 (m100)
  outliers start: 16
  outliers final: 9
  residues processed: 111
  average time/residue: 0.2139
  time to fit residues: 31.3556
Evaluate side-chains
  95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain B residue  229 HIS
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  330 HIS
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  466 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 45 optimal weight:    0.4980
   chunk 2 optimal weight:    0.1980
   chunk 21 optimal weight:    0.0980
   chunk 63 optimal weight:    4.9990
   chunk 48 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 6 optimal weight:    0.1980
   overall best weight:    0.3580

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

Flipped N/Q/H residues before XYZ refinement:
B  67 ASN
B 104 ASN
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 313 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.201002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.160809 restraints weight = 9365.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.158768 restraints weight = 8534.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.160893 restraints weight = 8050.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.179   6120  Z= 0.111
  Angle     :  0.578   8.526   8483  Z= 0.285
  Chirality :  0.040   0.196    964
  Planarity :  0.004   0.046    943
  Dihedral  : 16.037  95.139   1264
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.87 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.31), residues: 637
  helix: -1.27 (0.40), residues: 148
  sheet: -1.60 (0.66), residues: 48
  loop : -1.36 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 348 
 HIS   0.019   0.001   HIS B 229 
 PHE   0.021   0.002   PHE B 133 
 TYR   0.014   0.001   TYR B 447 
 ARG   0.004   0.000   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03157 (  168)
  hydrogen bonds       : angle       4.79542 (  418)
  metal coordination   : bond        0.04173 (   19)
  metal coordination   : angle       4.17953 (   13)
  covalent geometry    : bond        0.00226 ( 6101)
  covalent geometry    : angle       0.55430 ( 8470)

*********************** 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
  115 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8343 (mtpp) cc_final: 0.8093 (ttmm)
REVERT: A   42 VAL cc_start: 0.8825 (t) cc_final: 0.8538 (p)
REVERT: A   66 GLU cc_start: 0.6416 (tp30) cc_final: 0.5936 (tp30)
REVERT: A  119 VAL cc_start: 0.9228 (m) cc_final: 0.8926 (p)
REVERT: B   90 ASP cc_start: 0.7126 (t70) cc_final: 0.6888 (t0)
REVERT: B  253 LEU cc_start: 0.7539 (tp) cc_final: 0.7026 (tt)
REVERT: B  273 ASP cc_start: 0.7838 (t70) cc_final: 0.7278 (t0)
REVERT: B  509 TRP cc_start: 0.8737 (m100) cc_final: 0.8512 (m100)
  outliers start: 12
  outliers final: 9
  residues processed: 112
  average time/residue: 0.1813
  time to fit residues: 26.9264
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  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ASP
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  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  466 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 59 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0970
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 114 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.196887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.155772 restraints weight = 9086.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.153937 restraints weight = 8804.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.155333 restraints weight = 9405.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.3725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.170   6120  Z= 0.146
  Angle     :  0.594   8.352   8483  Z= 0.296
  Chirality :  0.041   0.137    964
  Planarity :  0.004   0.050    943
  Dihedral  : 15.962  94.985   1264
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 19.68 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.31), residues: 637
  helix: -0.87 (0.42), residues: 148
  sheet: -1.25 (0.61), residues: 58
  loop : -1.22 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 348 
 HIS   0.018   0.001   HIS B 229 
 PHE   0.025   0.002   PHE B 217 
 TYR   0.014   0.001   TYR B 494 
 ARG   0.005   0.000   ARG B 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03257 (  168)
  hydrogen bonds       : angle       4.77384 (  418)
  metal coordination   : bond        0.04037 (   19)
  metal coordination   : angle       4.14966 (   13)
  covalent geometry    : bond        0.00320 ( 6101)
  covalent geometry    : angle       0.57225 ( 8470)

*********************** 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
  102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 VAL cc_start: 0.9211 (m) cc_final: 0.8904 (p)
REVERT: B  253 LEU cc_start: 0.7498 (tp) cc_final: 0.6897 (tt)
REVERT: B  392 TYR cc_start: 0.7984 (m-80) cc_final: 0.7757 (m-80)
REVERT: B  509 TRP cc_start: 0.8759 (m100) cc_final: 0.8527 (m100)
  outliers start: 15
  outliers final: 11
  residues processed: 98
  average time/residue: 0.1842
  time to fit residues: 24.2316
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  : 0.585 
-------------------------------------------------------------------------------
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   79 CYS
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  229 HIS
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  439 LEU
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 9 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 66 optimal weight:   20.0000
   chunk 23 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 47 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0470
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    4.9990
   overall best weight:    1.7484

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 108 GLN
** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.192281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.152216 restraints weight = 8966.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.149943 restraints weight = 9301.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.151218 restraints weight = 10350.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.4000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.170   6120  Z= 0.209
  Angle     :  0.648   8.391   8483  Z= 0.321
  Chirality :  0.042   0.196    964
  Planarity :  0.004   0.055    943
  Dihedral  : 16.051  94.676   1264
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 20.04 %
    Favored  : 76.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.32), residues: 637
  helix: -0.65 (0.42), residues: 145
  sheet: -1.40 (0.57), residues: 75
  loop : -1.00 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  86 
 HIS   0.018   0.002   HIS B 229 
 PHE   0.020   0.002   PHE B 133 
 TYR   0.013   0.002   TYR A  27 
 ARG   0.003   0.001   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03582 (  168)
  hydrogen bonds       : angle       4.84324 (  418)
  metal coordination   : bond        0.04143 (   19)
  metal coordination   : angle       4.38696 (   13)
  covalent geometry    : bond        0.00472 ( 6101)
  covalent geometry    : angle       0.62533 ( 8470)

*********************** 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: 18
    poor density    : 88
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 GLU cc_start: 0.6378 (tp30) cc_final: 0.5756 (tp30)
REVERT: A  119 VAL cc_start: 0.9149 (m) cc_final: 0.8845 (p)
REVERT: B  241 MET cc_start: 0.7001 (mtm) cc_final: 0.6703 (mtm)
REVERT: B  315 MET cc_start: 0.8134 (tmm) cc_final: 0.7912 (tmm)
  outliers start: 18
  outliers final: 13
  residues processed: 101
  average time/residue: 0.1888
  time to fit residues: 25.7382
Evaluate side-chains
  93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ASP
Chi-restraints excluded: chain A residue   40 ASN
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  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  466 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 1 optimal weight:    0.4980
   chunk 6 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
B  82 HIS
B 104 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.200368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.153625 restraints weight = 9200.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.152595 restraints weight = 7415.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.153950 restraints weight = 6711.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.4191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.167   6120  Z= 0.154
  Angle     :  0.609   8.959   8483  Z= 0.300
  Chirality :  0.040   0.129    964
  Planarity :  0.004   0.055    943
  Dihedral  : 15.982  94.642   1264
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 21.48 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.32), residues: 637
  helix: -0.56 (0.43), residues: 148
  sheet: -1.25 (0.59), residues: 64
  loop : -0.97 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 509 
 HIS   0.018   0.001   HIS B 229 
 PHE   0.029   0.002   PHE A  68 
 TYR   0.016   0.001   TYR A  27 
 ARG   0.003   0.000   ARG B 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03353 (  168)
  hydrogen bonds       : angle       4.64480 (  418)
  metal coordination   : bond        0.03989 (   19)
  metal coordination   : angle       4.16041 (   13)
  covalent geometry    : bond        0.00342 ( 6101)
  covalent geometry    : angle       0.58726 ( 8470)

*********************** 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
  103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8370 (ttmm)
REVERT: A  119 VAL cc_start: 0.9125 (m) cc_final: 0.8814 (p)
REVERT: B  188 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7917 (t70)
  outliers start: 16
  outliers final: 13
  residues processed: 98
  average time/residue: 0.1890
  time to fit residues: 24.7378
Evaluate side-chains
  89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
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  169 MET
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0370
   chunk 1 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0170
   chunk 62 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.4096

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.198262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.159205 restraints weight = 9058.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.157219 restraints weight = 9628.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.159277 restraints weight = 9251.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.4483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.165   6120  Z= 0.117
  Angle     :  0.604  10.670   8483  Z= 0.297
  Chirality :  0.040   0.133    964
  Planarity :  0.004   0.054    943
  Dihedral  : 15.830  94.290   1264
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.33), residues: 637
  helix: -0.31 (0.43), residues: 148
  sheet: -1.27 (0.57), residues: 71
  loop : -0.82 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 509 
 HIS   0.019   0.001   HIS B 229 
 PHE   0.025   0.002   PHE A  68 
 TYR   0.009   0.001   TYR B 494 
 ARG   0.006   0.000   ARG B 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03158 (  168)
  hydrogen bonds       : angle       4.52165 (  418)
  metal coordination   : bond        0.03863 (   19)
  metal coordination   : angle       3.92827 (   13)
  covalent geometry    : bond        0.00250 ( 6101)
  covalent geometry    : angle       0.58479 ( 8470)

*********************** 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
  105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.8635 (mtpp) cc_final: 0.8350 (ttmm)
REVERT: A  119 VAL cc_start: 0.9136 (m) cc_final: 0.8841 (p)
REVERT: B   95 HIS cc_start: 0.8381 (OUTLIER) cc_final: 0.7950 (m-70)
REVERT: B  447 TYR cc_start: 0.6050 (t80) cc_final: 0.5811 (t80)
REVERT: B  476 ARG cc_start: 0.7525 (mtt180) cc_final: 0.7146 (mmt180)
REVERT: B  495 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8099 (mm)
REVERT: B  523 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.5769 (m-10)
  outliers start: 17
  outliers final: 13
  residues processed: 102
  average time/residue: 0.1979
  time to fit residues: 27.1476
Evaluate side-chains
  93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ASP
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  229 HIS
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  444 PHE
Chi-restraints excluded: chain B residue  466 VAL
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  523 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 66 optimal weight:   20.0000
   chunk 10 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 39 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 59 optimal weight:   20.0000
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.202699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.154498 restraints weight = 9129.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.152015 restraints weight = 7755.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.153279 restraints weight = 8634.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.4666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.163   6120  Z= 0.142
  Angle     :  0.620  10.096   8483  Z= 0.303
  Chirality :  0.041   0.186    964
  Planarity :  0.004   0.036    943
  Dihedral  : 15.828  93.957   1264
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 23.47 %
    Favored  : 73.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.33), residues: 637
  helix: -0.26 (0.42), residues: 147
  sheet: -1.37 (0.56), residues: 66
  loop : -0.81 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 509 
 HIS   0.018   0.001   HIS B 229 
 PHE   0.036   0.002   PHE B 436 
 TYR   0.015   0.001   TYR A  27 
 ARG   0.005   0.000   ARG B 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03216 (  168)
  hydrogen bonds       : angle       4.54634 (  418)
  metal coordination   : bond        0.03866 (   19)
  metal coordination   : angle       4.03667 (   13)
  covalent geometry    : bond        0.00316 ( 6101)
  covalent geometry    : angle       0.59960 ( 8470)

*********************** 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
  97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 VAL cc_start: 0.9140 (m) cc_final: 0.8845 (p)
REVERT: B   95 HIS cc_start: 0.8525 (OUTLIER) cc_final: 0.8112 (m-70)
REVERT: B  188 HIS cc_start: 0.8024 (OUTLIER) cc_final: 0.7772 (t70)
REVERT: B  476 ARG cc_start: 0.7578 (mtt180) cc_final: 0.7366 (mmt180)
REVERT: B  523 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.5984 (m-10)
  outliers start: 16
  outliers final: 12
  residues processed: 94
  average time/residue: 0.1888
  time to fit residues: 23.9632
Evaluate side-chains
  93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  188 HIS
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  523 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0040
   chunk 46 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   chunk 30 optimal weight:    0.1980
   chunk 60 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.6398

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.187263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.150156 restraints weight = 8731.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.146770 restraints weight = 11704.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.148734 restraints weight = 11876.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.4825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.163   6120  Z= 0.123
  Angle     :  0.607  10.316   8483  Z= 0.295
  Chirality :  0.040   0.165    964
  Planarity :  0.004   0.035    943
  Dihedral  : 15.766  93.477   1264
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 23.47 %
    Favored  : 73.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.33), residues: 637
  helix: -0.14 (0.42), residues: 146
  sheet: -1.44 (0.57), residues: 67
  loop : -0.82 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 509 
 HIS   0.019   0.001   HIS B 229 
 PHE   0.020   0.002   PHE A  68 
 TYR   0.010   0.001   TYR B 392 
 ARG   0.006   0.000   ARG B 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03070 (  168)
  hydrogen bonds       : angle       4.41235 (  418)
  metal coordination   : bond        0.03827 (   19)
  metal coordination   : angle       3.95928 (   13)
  covalent geometry    : bond        0.00269 ( 6101)
  covalent geometry    : angle       0.58690 ( 8470)

********************** 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
  100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 VAL cc_start: 0.8990 (m) cc_final: 0.8639 (p)
REVERT: B   95 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.8035 (m-70)
REVERT: B  122 THR cc_start: 0.7749 (m) cc_final: 0.7394 (m)
REVERT: B  311 LYS cc_start: 0.7769 (ptpt) cc_final: 0.7561 (ptpp)
  outliers start: 17
  outliers final: 13
  residues processed: 97
  average time/residue: 0.1854
  time to fit residues: 24.0075
Evaluate side-chains
  96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 HIS
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   79 CYS
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   95 HIS
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  229 HIS
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  444 PHE
Chi-restraints excluded: chain B residue  466 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0980
   chunk 38 optimal weight:   10.0000
   chunk 66 optimal weight:   20.0000
   chunk 36 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0270
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4203 r_free = 0.4203 target = 0.187163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.150023 restraints weight = 8882.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.146719 restraints weight = 11512.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.148584 restraints weight = 10660.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.163   6120  Z= 0.121
  Angle     :  0.608  10.263   8483  Z= 0.296
  Chirality :  0.040   0.175    964
  Planarity :  0.003   0.033    943
  Dihedral  : 15.724  93.144   1264
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 24.19 %
    Favored  : 73.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.33), residues: 637
  helix: -0.01 (0.43), residues: 146
  sheet: -1.42 (0.57), residues: 72
  loop : -0.77 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 509 
 HIS   0.019   0.001   HIS B 229 
 PHE   0.020   0.002   PHE B 436 
 TYR   0.013   0.001   TYR A  27 
 ARG   0.006   0.000   ARG B 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03056 (  168)
  hydrogen bonds       : angle       4.29688 (  418)
  metal coordination   : bond        0.03819 (   19)
  metal coordination   : angle       3.91932 (   13)
  covalent geometry    : bond        0.00261 ( 6101)
  covalent geometry    : angle       0.58920 ( 8470)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2211.21 seconds
wall clock time: 39 minutes 52.60 seconds (2392.60 seconds total)