Starting phenix.real_space_refine
on Sat May 10 21:16:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pjn_17713/05_2025/8pjn_17713.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pjn_17713/05_2025/8pjn_17713.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pjn_17713/05_2025/8pjn_17713.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pjn_17713/05_2025/8pjn_17713.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pjn_17713/05_2025/8pjn_17713.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pjn_17713/05_2025/8pjn_17713.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P       7      5.49       5
     S      51      5.16       5
     C    4382      2.51       5
     N    1231      2.21       5
     O    1244      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6917
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "b"
      Number of atoms: 2134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 296, 2134
          Classifications: {'peptide': 296}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 11, 'TRANS': 284}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 173
          Unresolved non-hydrogen angles: 213
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 13, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 127
    Chain: "2"
      Number of atoms: 1212
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1212
          Classifications: {'peptide': 156}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 11, 'TRANS': 144}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 83
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 43
    Chain: "i"
      Number of atoms: 3017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 395, 3017
          Classifications: {'peptide': 395}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 17, 'TRANS': 377}
          Unresolved non-hydrogen bonds: 141
          Unresolved non-hydrogen angles: 172
          Unresolved non-hydrogen dihedrals: 112
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 15, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 9}
          Unresolved non-hydrogen planarities: 114
    Chain: "u"
      Number of atoms: 552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 552
          Classifications: {'peptide': 76}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 36
    Chain: "b"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "i"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1865  SG  CYS b 354      34.319  76.743  20.414  1.00 38.66           S
  ATOM   2005  SG  CYS b 374      34.034  73.285  21.978  1.00 43.27           S
  ATOM   2030  SG  CYS b 377      32.056  76.493  23.338  1.00 44.14           S
  ATOM   5669  SG  CYS i 302      63.822  66.968  20.941  1.00 25.69           S
  ATOM   5746  SG  CYS i 314      65.272  68.705  24.005  1.00 25.97           S
  ATOM   5766  SG  CYS i 317      66.348  69.591  20.248  1.00 26.45           S

  Time building chain proxies: 4.60, per 1000 atoms: 0.67
  Number of scatterers: 6917
  At special positions: 0
  Unit cell: (123.395, 110.63, 105.524, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      51     16.00
     P       7     15.00
     O    1244      8.00
     N    1231      7.00
     C    4382      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.80
  Conformation dependent library (CDL) restraints added in 930.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN b 501 "
        pdb="ZN    ZN b 501 " - pdb=" ND1 HIS b 356 "
        pdb="ZN    ZN b 501 " - pdb=" SG  CYS b 354 "
        pdb="ZN    ZN b 501 " - pdb=" SG  CYS b 374 "
        pdb="ZN    ZN b 501 " - pdb=" SG  CYS b 377 "
      pdb="  ZN i 401 "
        pdb="ZN    ZN i 401 " - pdb=" NE2 HIS b 331 "
        pdb="ZN    ZN i 401 " - pdb=" SG  CYS i 302 "
        pdb="ZN    ZN i 401 " - pdb=" SG  CYS i 317 "
        pdb="ZN    ZN i 401 " - pdb=" SG  CYS i 314 "
      Number of angles added : 6


  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1752

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 6 sheets defined
      62.2% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'b' and resid 1 through 46
      removed outlier: 3.613A  pdb=" N   GLU b  10 " --> pdb=" O   THR b   6 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE b  43 " --> pdb=" O   LEU b  39 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LEU b  44 " --> pdb=" O   LYS b  40 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN b  45 " --> pdb=" O   HIS b  41 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   SER b  46 " --> pdb=" O   GLU b  42 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 54 through 81
      removed outlier: 4.273A  pdb=" N   LEU b  59 " --> pdb=" O   GLY b  55 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   VAL b  60 " --> pdb=" O   THR b  56 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   HIS b  79 " --> pdb=" O   LEU b  75 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LYS b  80 " --> pdb=" O   ALA b  76 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 82 through 97
      removed outlier: 4.091A  pdb=" N   VAL b  86 " --> pdb=" O   ILE b  82 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER b  87 " --> pdb=" O   HIS b  83 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 112 through 129
      removed outlier: 4.487A  pdb=" N   ARG b 116 " --> pdb=" O   ALA b 112 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   LEU b 117 " --> pdb=" O   ASP b 113 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 131 through 143
      removed outlier: 3.506A  pdb=" N   GLU b 141 " --> pdb=" O   GLU b 137 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 147 through 165
      Proline residue:  b 153  - end of helix
      removed outlier: 3.726A  pdb=" N   GLU b 156 " --> pdb=" O   GLU b 152 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LEU b 157 " --> pdb=" O   PRO b 153 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 262 through 275
    Processing helix  chain 'b' and resid 280 through 306
      Proline residue:  b 294  - end of helix
      removed outlier: 5.124A  pdb=" N   ASN b 298 " --> pdb=" O   PRO b 294 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 325 through 329
      removed outlier: 3.734A  pdb=" N   TRP b 329 " --> pdb=" O   LYS b 326 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 360 through 366
    Processing helix  chain '2' and resid 8 through 21
    Processing helix  chain '2' and resid 88 through 93
    Processing helix  chain '2' and resid 100 through 108
    Processing helix  chain '2' and resid 108 through 115
    Processing helix  chain '2' and resid 123 through 133
      removed outlier: 3.679A  pdb=" N   HIS 2 132 " --> pdb=" O   ALA 2 128 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 133 through 148
    Processing helix  chain 'i' and resid 6 through 18
    Processing helix  chain 'i' and resid 19 through 60
      Proline residue:  i  25  - end of helix
      removed outlier: 3.660A  pdb=" N   VAL i  50 " --> pdb=" O   HIS i  46 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   SER i  59 " --> pdb=" O   GLU i  55 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   GLY i  60 " --> pdb=" O   LYS i  56 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 64 through 108
      removed outlier: 4.260A  pdb=" N   SER i  69 " --> pdb=" O   ASP i  65 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   LEU i  70 " --> pdb=" O   SER i  66 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 109 through 111
      No H-bonds generated for 'chain 'i' and resid 109 through 111'
    Processing helix  chain 'i' and resid 116 through 137
    Processing helix  chain 'i' and resid 138 through 150
      removed outlier: 3.588A  pdb=" N   ALA i 142 " --> pdb=" O   TYR i 138 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 157 through 172
    Processing helix  chain 'i' and resid 176 through 185
    Processing helix  chain 'i' and resid 185 through 192
    Processing helix  chain 'i' and resid 195 through 211
      removed outlier: 3.711A  pdb=" N   SER i 199 " --> pdb=" O   CYS i 195 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 213 through 225
    Processing helix  chain 'i' and resid 226 through 229
      removed outlier: 7.472A  pdb=" N   GLU i 229 " --> pdb=" O   SER i 226 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'i' and resid 226 through 229'
    Processing helix  chain 'i' and resid 230 through 241
    Processing helix  chain 'i' and resid 242 through 245
    Processing helix  chain 'i' and resid 251 through 259
      removed outlier: 4.928A  pdb=" N   LEU i 257 " --> pdb=" O   PRO i 253 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ASP i 259 " --> pdb=" O   LYS i 255 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 261 through 278
      removed outlier: 3.517A  pdb=" N   MET i 265 " --> pdb=" O   ALA i 261 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 284 through 298
    Processing helix  chain 'i' and resid 299 through 304
      removed outlier: 3.970A  pdb=" N   LYS i 304 " --> pdb=" O   GLN i 301 " (cutoff:3.500A)
    Processing helix  chain 'i' and resid 314 through 317
    Processing helix  chain 'i' and resid 318 through 325
    Processing helix  chain 'i' and resid 364 through 371
    Processing helix  chain 'i' and resid 386 through 390
    Processing helix  chain 'u' and resid 22 through 34
    Processing helix  chain 'u' and resid 37 through 39
      No H-bonds generated for 'chain 'u' and resid 37 through 39'
    Processing helix  chain 'u' and resid 55 through 60
      removed outlier: 3.650A  pdb=" N   TYR u  59 " --> pdb=" O   THR u  55 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'b' and resid 357 through 359
    Processing sheet with id=AA2, first strand: chain 'b' and resid 372 through 373
    Processing sheet with id=AA3, first strand: chain '2' and resid 25 through 27
    Processing sheet with id=AA4, first strand: chain 'i' and resid 361 through 363
    Processing sheet with id=AA5, first strand: chain 'i' and resid 376 through 377
    Processing sheet with id=AA6, first strand: chain 'u' and resid 12 through 16
      removed outlier: 4.064A  pdb=" N   SER u  65 " --> pdb=" O   GLN u   2 " (cutoff:3.500A)

    413 hydrogen bonds defined for protein.
    1203 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.98

  Time building geometry restraints manager: 2.05 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1253
        1.33 -     1.45: 1623
        1.45 -     1.57: 4086
        1.57 -     1.69: 7
        1.69 -     1.81: 75
  Bond restraints: 7044
  Sorted by residual:
  bond pdb=" O2P SEP 2 171 "
       pdb=" P   SEP 2 171 "
    ideal  model  delta    sigma   weight residual
    1.610  1.508  0.102 2.00e-02 2.50e+03 2.59e+01
  bond pdb=" O2P SEP 2 168 "
       pdb=" P   SEP 2 168 "
    ideal  model  delta    sigma   weight residual
    1.610  1.509  0.101 2.00e-02 2.50e+03 2.55e+01
  bond pdb=" O1P SEP 2 168 "
       pdb=" P   SEP 2 168 "
    ideal  model  delta    sigma   weight residual
    1.610  1.511  0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" O3P SEP 2 168 "
       pdb=" P   SEP 2 168 "
    ideal  model  delta    sigma   weight residual
    1.610  1.512  0.098 2.00e-02 2.50e+03 2.40e+01
  bond pdb=" O1P SEP 2 169 "
       pdb=" P   SEP 2 169 "
    ideal  model  delta    sigma   weight residual
    1.610  1.513  0.097 2.00e-02 2.50e+03 2.35e+01
  ... (remaining 7039 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 9148
        1.73 -     3.47: 339
        3.47 -     5.20: 68
        5.20 -     6.93: 3
        6.93 -     8.67: 8
  Bond angle restraints: 9566
  Sorted by residual:
  angle pdb=" N   CYS i 178 "
        pdb=" CA  CYS i 178 "
        pdb=" C   CYS i 178 "
      ideal   model   delta    sigma   weight residual
     111.28  106.48    4.80 1.09e+00 8.42e-01 1.94e+01
  angle pdb=" C   TYR b  35 "
        pdb=" N   THR b  36 "
        pdb=" CA  THR b  36 "
      ideal   model   delta    sigma   weight residual
     120.28  114.56    5.72 1.44e+00 4.82e-01 1.58e+01
  angle pdb=" N   ASN b 368 "
        pdb=" CA  ASN b 368 "
        pdb=" C   ASN b 368 "
      ideal   model   delta    sigma   weight residual
     112.72  108.52    4.20 1.14e+00 7.69e-01 1.36e+01
  angle pdb=" CA  GLU b  31 "
        pdb=" C   GLU b  31 "
        pdb=" O   GLU b  31 "
      ideal   model   delta    sigma   weight residual
     121.00  117.41    3.59 1.05e+00 9.07e-01 1.17e+01
  angle pdb=" N   ILE 2 145 "
        pdb=" CA  ILE 2 145 "
        pdb=" C   ILE 2 145 "
      ideal   model   delta    sigma   weight residual
     110.72  107.32    3.40 1.01e+00 9.80e-01 1.13e+01
  ... (remaining 9561 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 3872
       17.47 -    34.93: 338
       34.93 -    52.40: 60
       52.40 -    69.86: 18
       69.86 -    87.33: 5
  Dihedral angle restraints: 4293
    sinusoidal: 1598
      harmonic: 2695
  Sorted by residual:
  dihedral pdb=" CA  PRO b 294 "
           pdb=" C   PRO b 294 "
           pdb=" N   ALA b 295 "
           pdb=" CA  ALA b 295 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.18   18.82     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  ASP i 216 "
           pdb=" CB  ASP i 216 "
           pdb=" CG  ASP i 216 "
           pdb=" OD1 ASP i 216 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.97   59.97     1      2.00e+01 2.50e-03 1.20e+01
  dihedral pdb=" CA  GLN i  17 "
           pdb=" C   GLN i  17 "
           pdb=" N   GLU i  18 "
           pdb=" CA  GLU i  18 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.08  -16.92     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 4290 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 782
       0.039 -    0.078: 218
       0.078 -    0.117: 90
       0.117 -    0.156: 17
       0.156 -    0.195: 7
  Chirality restraints: 1114
  Sorted by residual:
  chirality pdb=" CA  PHE b 367 "
            pdb=" N   PHE b 367 "
            pdb=" C   PHE b 367 "
            pdb=" CB  PHE b 367 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.19 2.00e-01 2.50e+01 9.49e-01
  chirality pdb=" CA  ILE 2 145 "
            pdb=" N   ILE 2 145 "
            pdb=" C   ILE 2 145 "
            pdb=" CB  ILE 2 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.65e-01
  chirality pdb=" CA  MET b 366 "
            pdb=" N   MET b 366 "
            pdb=" C   MET b 366 "
            pdb=" CB  MET b 366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.43e-01
  ... (remaining 1111 not shown)

  Planarity restraints: 1216
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG b 340 "    0.248 9.50e-02 1.11e+02   1.11e-01 7.61e+00
        pdb=" NE  ARG b 340 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG b 340 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG b 340 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG b 340 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR b  71 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" C   THR b  71 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   THR b  71 "    0.014 2.00e-02 2.50e+03
        pdb=" N   VAL b  72 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS b  69 "    0.009 2.00e-02 2.50e+03   1.88e-02 3.54e+00
        pdb=" C   LYS b  69 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   LYS b  69 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ASP b  70 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1213 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1339
        2.78 -     3.31: 6503
        3.31 -     3.84: 10731
        3.84 -     4.37: 11829
        4.37 -     4.90: 21585
  Nonbonded interactions: 51987
  Sorted by model distance:
  nonbonded pdb=" OG  SER i 194 "
            pdb=" OD2 ASP i 273 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OD2 ASP i 126 "
            pdb=" OG  SER i 149 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O2P SEP 2 171 "
            pdb=" OG  SER i 187 "
     model   vdw
     2.363 3.040
  nonbonded pdb=" O   PHE b 334 "
            pdb=" OG  SER i 336 "
     model   vdw
     2.373 3.040
  nonbonded pdb=" OE2 GLU i 167 "
            pdb=" NH1 ARG i 271 "
     model   vdw
     2.393 3.120
  ... (remaining 51982 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.960
  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:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     20.400
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:3.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
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      :  0.007   0.102   7053  Z= 0.395
  Angle     :  0.748   8.666   9572  Z= 0.434
  Chirality :  0.045   0.195   1114
  Planarity :  0.006   0.111   1216
  Dihedral  : 14.181  87.330   2541
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.29), residues: 901
  helix:  2.01 (0.24), residues: 494
  sheet:  0.82 (0.74), residues: 51
  loop : -1.31 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP i 181 
 HIS   0.007   0.001   HIS i 183 
 PHE   0.012   0.001   PHE 2  63 
 TYR   0.011   0.001   TYR 2 130 
 ARG   0.002   0.000   ARG i 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14965 (  413)
  hydrogen bonds       : angle       4.92542 ( 1203)
  metal coordination   : bond        0.02261 (    8)
  metal coordination   : angle       5.68416 (    6)
  covalent geometry    : bond        0.00678 ( 7044)
  covalent geometry    : angle       0.73444 ( 9566)
  Misc. bond           : bond        0.08212 (    1)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.733 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1755
  time to fit residues: 26.7874
Evaluate side-chains
  94 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0050
   chunk 37 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 36 optimal weight:    0.1980
   chunk 70 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 81 optimal weight:    3.9990
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
b 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.131834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.112134 restraints weight = 9278.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.53
r_work: 0.3108 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.0857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7053  Z= 0.109
  Angle     :  0.488   6.119   9572  Z= 0.247
  Chirality :  0.038   0.153   1114
  Planarity :  0.004   0.049   1216
  Dihedral  :  4.036  30.879   1010
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  5.65 %
    Favored  : 93.04 %
  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:  1.53 (0.29), residues: 901
  helix:  2.51 (0.23), residues: 505
  sheet:  0.62 (0.72), residues: 59
  loop : -1.36 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP i 120 
 HIS   0.003   0.001   HIS i 105 
 PHE   0.011   0.001   PHE 2  63 
 TYR   0.010   0.001   TYR 2  61 
 ARG   0.003   0.000   ARG i 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04584 (  413)
  hydrogen bonds       : angle       3.70465 ( 1203)
  metal coordination   : bond        0.00447 (    8)
  metal coordination   : angle       1.10835 (    6)
  covalent geometry    : bond        0.00234 ( 7044)
  covalent geometry    : angle       0.48734 ( 9566)
  Misc. bond           : bond        0.00077 (    1)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.721 
Fit side-chains
  outliers start: 9
  outliers final: 7
  residues processed: 106
  average time/residue: 0.1744
  time to fit residues: 25.7563
Evaluate side-chains
  103 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   53 LEU
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain i residue  209 ILE
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain u residue   14 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3361 r_free = 0.3361 target = 0.123354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.101336 restraints weight = 9657.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 1.75
r_work: 0.2904 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.1136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7053  Z= 0.137
  Angle     :  0.500   6.496   9572  Z= 0.252
  Chirality :  0.039   0.160   1114
  Planarity :  0.004   0.056   1216
  Dihedral  :  4.112  30.238   1010
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  9.57 %
    Favored  : 88.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.30), residues: 901
  helix:  2.64 (0.23), residues: 505
  sheet:  0.51 (0.71), residues: 59
  loop : -1.30 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP i 181 
 HIS   0.004   0.001   HIS i 105 
 PHE   0.012   0.001   PHE 2  63 
 TYR   0.010   0.001   TYR i 275 
 ARG   0.006   0.000   ARG i 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04931 (  413)
  hydrogen bonds       : angle       3.74315 ( 1203)
  metal coordination   : bond        0.00479 (    8)
  metal coordination   : angle       1.68314 (    6)
  covalent geometry    : bond        0.00325 ( 7044)
  covalent geometry    : angle       0.49872 ( 9566)
  Misc. bond           : bond        0.00035 (    1)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.729 
Fit side-chains
  outliers start: 12
  outliers final: 10
  residues processed: 112
  average time/residue: 0.1534
  time to fit residues: 24.4278
Evaluate side-chains
  113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   53 LEU
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain i residue   57 THR
Chi-restraints excluded: chain i residue  136 CYS
Chi-restraints excluded: chain i residue  184 ASP
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain u residue   14 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
b 305 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.126682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.106470 restraints weight = 9580.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 1.55
r_work: 0.2915 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2795 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7053  Z= 0.129
  Angle     :  0.486   6.735   9572  Z= 0.246
  Chirality :  0.039   0.155   1114
  Planarity :  0.004   0.058   1216
  Dihedral  :  4.130  31.732   1010
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 11.30 %
    Favored  : 86.52 %
  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:  1.72 (0.30), residues: 901
  helix:  2.72 (0.23), residues: 505
  sheet:  0.47 (0.70), residues: 59
  loop : -1.32 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP i 120 
 HIS   0.004   0.001   HIS i 105 
 PHE   0.010   0.001   PHE 2  63 
 TYR   0.010   0.001   TYR i 275 
 ARG   0.007   0.000   ARG i 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04739 (  413)
  hydrogen bonds       : angle       3.68829 ( 1203)
  metal coordination   : bond        0.00446 (    8)
  metal coordination   : angle       1.42552 (    6)
  covalent geometry    : bond        0.00307 ( 7044)
  covalent geometry    : angle       0.48483 ( 9566)
  Misc. bond           : bond        0.00032 (    1)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.816 
Fit side-chains
REVERT: i  153 ASP cc_start: 0.8968 (t0) cc_final: 0.8450 (t0)
REVERT: i  240 MET cc_start: 0.8831 (mmt) cc_final: 0.8221 (mmt)
  outliers start: 15
  outliers final: 13
  residues processed: 110
  average time/residue: 0.1558
  time to fit residues: 24.4530
Evaluate side-chains
  113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   53 LEU
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain b residue  358 ILE
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain i residue   57 THR
Chi-restraints excluded: chain i residue  136 CYS
Chi-restraints excluded: chain i residue  184 ASP
Chi-restraints excluded: chain i residue  208 LEU
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain u residue   14 THR
Chi-restraints excluded: chain u residue   66 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 80 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0670
   chunk 53 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
b 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.121943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.101012 restraints weight = 9590.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 1.73
r_work: 0.2914 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2786 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7053  Z= 0.114
  Angle     :  0.474   6.942   9572  Z= 0.240
  Chirality :  0.038   0.151   1114
  Planarity :  0.004   0.060   1216
  Dihedral  :  4.080  33.033   1010
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 12.17 %
    Favored  : 85.07 %
  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:  1.77 (0.30), residues: 901
  helix:  2.75 (0.23), residues: 505
  sheet:  0.48 (0.70), residues: 59
  loop : -1.29 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP i 120 
 HIS   0.003   0.001   HIS i 105 
 PHE   0.013   0.001   PHE i 225 
 TYR   0.009   0.001   TYR i 275 
 ARG   0.007   0.000   ARG i 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04445 (  413)
  hydrogen bonds       : angle       3.62245 ( 1203)
  metal coordination   : bond        0.00392 (    8)
  metal coordination   : angle       1.30282 (    6)
  covalent geometry    : bond        0.00261 ( 7044)
  covalent geometry    : angle       0.47255 ( 9566)
  Misc. bond           : bond        0.00034 (    1)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.730 
Fit side-chains
REVERT: 2   60 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7829 (mttm)
REVERT: i  153 ASP cc_start: 0.8959 (t0) cc_final: 0.8415 (t0)
  outliers start: 19
  outliers final: 16
  residues processed: 111
  average time/residue: 0.1496
  time to fit residues: 23.7182
Evaluate side-chains
  118 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   53 LEU
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain b residue  358 ILE
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain i residue   57 THR
Chi-restraints excluded: chain i residue  136 CYS
Chi-restraints excluded: chain i residue  184 ASP
Chi-restraints excluded: chain i residue  208 LEU
Chi-restraints excluded: chain i residue  209 ILE
Chi-restraints excluded: chain i residue  257 LEU
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain u residue   14 THR
Chi-restraints excluded: chain u residue   66 THR
Chi-restraints excluded: chain u residue   67 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0770
   chunk 73 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.7538

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

Flipped N/Q/H residues before XYZ refinement:
b  73 GLN
b 346 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.122169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.100013 restraints weight = 9706.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 1.73
r_work: 0.2907 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7053  Z= 0.119
  Angle     :  0.477   6.490   9572  Z= 0.242
  Chirality :  0.039   0.151   1114
  Planarity :  0.004   0.057   1216
  Dihedral  :  4.094  34.570   1010
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 12.46 %
    Favored  : 84.64 %
  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:  1.82 (0.30), residues: 901
  helix:  2.79 (0.23), residues: 505
  sheet:  0.57 (0.71), residues: 53
  loop : -1.25 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP i 120 
 HIS   0.003   0.001   HIS i 105 
 PHE   0.008   0.001   PHE 2  63 
 TYR   0.010   0.001   TYR i 275 
 ARG   0.006   0.000   ARG i 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04464 (  413)
  hydrogen bonds       : angle       3.59562 ( 1203)
  metal coordination   : bond        0.00399 (    8)
  metal coordination   : angle       1.23657 (    6)
  covalent geometry    : bond        0.00276 ( 7044)
  covalent geometry    : angle       0.47581 ( 9566)
  Misc. bond           : bond        0.00031 (    1)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.832 
Fit side-chains
REVERT: b   31 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8254 (tm-30)
REVERT: b   73 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8339 (mt0)
REVERT: 2   60 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7837 (mttm)
REVERT: i  153 ASP cc_start: 0.8960 (t0) cc_final: 0.8405 (t0)
REVERT: i  240 MET cc_start: 0.8806 (mmt) cc_final: 0.8457 (mmt)
REVERT: u   70 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8185 (m)
  outliers start: 20
  outliers final: 15
  residues processed: 111
  average time/residue: 0.1527
  time to fit residues: 24.3123
Evaluate side-chains
  120 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   53 LEU
Chi-restraints excluded: chain b residue   73 GLN
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain b residue  358 ILE
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain i residue   57 THR
Chi-restraints excluded: chain i residue  136 CYS
Chi-restraints excluded: chain i residue  184 ASP
Chi-restraints excluded: chain i residue  208 LEU
Chi-restraints excluded: chain i residue  209 ILE
Chi-restraints excluded: chain i residue  257 LEU
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain u residue   14 THR
Chi-restraints excluded: chain u residue   66 THR
Chi-restraints excluded: chain u residue   70 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0980
   chunk 6 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 28 optimal weight:    0.2980
   chunk 84 optimal weight:    6.9990
   chunk 27 optimal weight:    8.9990
   chunk 79 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
b  73 GLN
b 346 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.122908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.100954 restraints weight = 9578.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 1.69
r_work: 0.2925 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.1407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7053  Z= 0.103
  Angle     :  0.464   7.327   9572  Z= 0.235
  Chirality :  0.038   0.147   1114
  Planarity :  0.004   0.057   1216
  Dihedral  :  4.038  34.472   1010
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 13.33 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.90 (0.30), residues: 901
  helix:  2.86 (0.23), residues: 505
  sheet:  0.64 (0.72), residues: 53
  loop : -1.23 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP i 120 
 HIS   0.003   0.000   HIS i 105 
 PHE   0.011   0.001   PHE i 225 
 TYR   0.008   0.001   TYR i 275 
 ARG   0.006   0.000   ARG i 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04157 (  413)
  hydrogen bonds       : angle       3.52882 ( 1203)
  metal coordination   : bond        0.00328 (    8)
  metal coordination   : angle       1.06813 (    6)
  covalent geometry    : bond        0.00226 ( 7044)
  covalent geometry    : angle       0.46300 ( 9566)
  Misc. bond           : bond        0.00038 (    1)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.796 
Fit side-chains
REVERT: b   73 GLN cc_start: 0.8430 (mt0) cc_final: 0.8209 (mp10)
REVERT: 2   60 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7825 (mttm)
REVERT: i  153 ASP cc_start: 0.8935 (t0) cc_final: 0.8379 (t0)
REVERT: i  240 MET cc_start: 0.8760 (mmt) cc_final: 0.8424 (mmt)
REVERT: u   70 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8239 (m)
  outliers start: 20
  outliers final: 15
  residues processed: 114
  average time/residue: 0.1564
  time to fit residues: 25.6898
Evaluate side-chains
  119 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   53 LEU
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain b residue  358 ILE
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain 2 residue   79 ILE
Chi-restraints excluded: chain i residue   57 THR
Chi-restraints excluded: chain i residue  136 CYS
Chi-restraints excluded: chain i residue  184 ASP
Chi-restraints excluded: chain i residue  208 LEU
Chi-restraints excluded: chain i residue  257 LEU
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain u residue   14 THR
Chi-restraints excluded: chain u residue   67 LEU
Chi-restraints excluded: chain u residue   70 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0020
   chunk 39 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 83 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
b 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.121044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.098714 restraints weight = 9803.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 1.72
r_work: 0.2920 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7053  Z= 0.117
  Angle     :  0.483   7.014   9572  Z= 0.245
  Chirality :  0.038   0.149   1114
  Planarity :  0.004   0.057   1216
  Dihedral  :  4.051  35.613   1010
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 13.19 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.87 (0.30), residues: 901
  helix:  2.81 (0.23), residues: 508
  sheet:  0.71 (0.73), residues: 53
  loop : -1.23 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP i 120 
 HIS   0.003   0.001   HIS i 105 
 PHE   0.011   0.001   PHE i 225 
 TYR   0.009   0.001   TYR i 275 
 ARG   0.007   0.000   ARG i 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04321 (  413)
  hydrogen bonds       : angle       3.54581 ( 1203)
  metal coordination   : bond        0.00462 (    8)
  metal coordination   : angle       1.31855 (    6)
  covalent geometry    : bond        0.00270 ( 7044)
  covalent geometry    : angle       0.48203 ( 9566)
  Misc. bond           : bond        0.00028 (    1)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.734 
Fit side-chains
REVERT: b   31 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8329 (tm-30)
REVERT: b   73 GLN cc_start: 0.8444 (mt0) cc_final: 0.8197 (mp10)
REVERT: 2   60 LYS cc_start: 0.8073 (mmtt) cc_final: 0.7871 (mttm)
REVERT: i  153 ASP cc_start: 0.8960 (t0) cc_final: 0.8353 (t0)
REVERT: i  240 MET cc_start: 0.8810 (mmt) cc_final: 0.8455 (mmt)
REVERT: u   70 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8356 (m)
  outliers start: 21
  outliers final: 18
  residues processed: 113
  average time/residue: 0.1620
  time to fit residues: 25.9923
Evaluate side-chains
  124 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   53 LEU
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain b residue  305 GLN
Chi-restraints excluded: chain b residue  357 ILE
Chi-restraints excluded: chain b residue  358 ILE
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain i residue   57 THR
Chi-restraints excluded: chain i residue  136 CYS
Chi-restraints excluded: chain i residue  184 ASP
Chi-restraints excluded: chain i residue  208 LEU
Chi-restraints excluded: chain i residue  257 LEU
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain i residue  355 MET
Chi-restraints excluded: chain u residue   14 THR
Chi-restraints excluded: chain u residue   66 THR
Chi-restraints excluded: chain u residue   67 LEU
Chi-restraints excluded: chain u residue   70 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 88 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 86 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3306 r_free = 0.3306 target = 0.119506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.097459 restraints weight = 9795.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 1.67
r_work: 0.2893 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2768 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7053  Z= 0.133
  Angle     :  0.504   6.846   9572  Z= 0.258
  Chirality :  0.039   0.151   1114
  Planarity :  0.004   0.056   1216
  Dihedral  :  4.154  38.292   1010
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 13.48 %
    Favored  : 83.33 %
  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:  1.82 (0.30), residues: 901
  helix:  2.77 (0.23), residues: 508
  sheet:  0.68 (0.72), residues: 53
  loop : -1.26 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP i 181 
 HIS   0.003   0.001   HIS i 105 
 PHE   0.016   0.001   PHE i 225 
 TYR   0.010   0.001   TYR i 275 
 ARG   0.007   0.000   ARG i 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04628 (  413)
  hydrogen bonds       : angle       3.59807 ( 1203)
  metal coordination   : bond        0.00490 (    8)
  metal coordination   : angle       1.53013 (    6)
  covalent geometry    : bond        0.00315 ( 7044)
  covalent geometry    : angle       0.50283 ( 9566)
  Misc. bond           : bond        0.00034 (    1)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.770 
Fit side-chains
REVERT: b   73 GLN cc_start: 0.8471 (mt0) cc_final: 0.8143 (mp10)
REVERT: 2   60 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7897 (mttm)
REVERT: i  153 ASP cc_start: 0.8981 (t0) cc_final: 0.8369 (t0)
REVERT: i  240 MET cc_start: 0.8879 (mmt) cc_final: 0.8257 (mmt)
REVERT: u   70 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8232 (m)
  outliers start: 22
  outliers final: 20
  residues processed: 111
  average time/residue: 0.1568
  time to fit residues: 24.9298
Evaluate side-chains
  123 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   53 LEU
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain b residue  305 GLN
Chi-restraints excluded: chain b residue  357 ILE
Chi-restraints excluded: chain b residue  358 ILE
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   64 LYS
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain i residue   57 THR
Chi-restraints excluded: chain i residue  136 CYS
Chi-restraints excluded: chain i residue  184 ASP
Chi-restraints excluded: chain i residue  208 LEU
Chi-restraints excluded: chain i residue  209 ILE
Chi-restraints excluded: chain i residue  257 LEU
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain i residue  355 MET
Chi-restraints excluded: chain u residue   14 THR
Chi-restraints excluded: chain u residue   66 THR
Chi-restraints excluded: chain u residue   67 LEU
Chi-restraints excluded: chain u residue   70 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 78 optimal weight:    0.3980
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
b 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.119966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.097834 restraints weight = 9920.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 1.69
r_work: 0.2907 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2781 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7053  Z= 0.126
  Angle     :  0.502   6.856   9572  Z= 0.257
  Chirality :  0.039   0.150   1114
  Planarity :  0.004   0.055   1216
  Dihedral  :  4.155  39.387   1010
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 13.62 %
    Favored  : 83.48 %
  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:  1.83 (0.30), residues: 901
  helix:  2.79 (0.23), residues: 507
  sheet:  0.69 (0.73), residues: 53
  loop : -1.26 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP i 120 
 HIS   0.003   0.001   HIS i 105 
 PHE   0.012   0.001   PHE i 225 
 TYR   0.009   0.001   TYR i 275 
 ARG   0.007   0.000   ARG i 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04524 (  413)
  hydrogen bonds       : angle       3.58307 ( 1203)
  metal coordination   : bond        0.00486 (    8)
  metal coordination   : angle       1.49794 (    6)
  covalent geometry    : bond        0.00296 ( 7044)
  covalent geometry    : angle       0.50036 ( 9566)
  Misc. bond           : bond        0.00040 (    1)

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

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

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1802 Ramachandran restraints generated.
    901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.796 
Fit side-chains
REVERT: b   31 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8267 (tm-30)
REVERT: b   73 GLN cc_start: 0.8474 (mt0) cc_final: 0.8172 (mp10)
REVERT: 2   60 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7904 (mttm)
REVERT: i  153 ASP cc_start: 0.8979 (t0) cc_final: 0.8350 (t0)
REVERT: i  240 MET cc_start: 0.8779 (mmt) cc_final: 0.8172 (mmt)
REVERT: u   70 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8216 (m)
  outliers start: 20
  outliers final: 19
  residues processed: 109
  average time/residue: 0.1790
  time to fit residues: 28.4828
Evaluate side-chains
  121 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain b residue   53 LEU
Chi-restraints excluded: chain b residue   78 ASP
Chi-restraints excluded: chain b residue  274 LEU
Chi-restraints excluded: chain b residue  305 GLN
Chi-restraints excluded: chain b residue  357 ILE
Chi-restraints excluded: chain b residue  358 ILE
Chi-restraints excluded: chain 2 residue   53 VAL
Chi-restraints excluded: chain 2 residue   64 LYS
Chi-restraints excluded: chain 2 residue   68 ILE
Chi-restraints excluded: chain i residue   57 THR
Chi-restraints excluded: chain i residue  136 CYS
Chi-restraints excluded: chain i residue  184 ASP
Chi-restraints excluded: chain i residue  208 LEU
Chi-restraints excluded: chain i residue  257 LEU
Chi-restraints excluded: chain i residue  313 ASP
Chi-restraints excluded: chain i residue  355 MET
Chi-restraints excluded: chain u residue   14 THR
Chi-restraints excluded: chain u residue   66 THR
Chi-restraints excluded: chain u residue   67 LEU
Chi-restraints excluded: chain u residue   70 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0060
   chunk 69 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 50 optimal weight:    0.3980
   chunk 40 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
b 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.121048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.099029 restraints weight = 9756.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 1.68
r_work: 0.2926 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7053  Z= 0.114
  Angle     :  0.486   6.882   9572  Z= 0.248
  Chirality :  0.038   0.148   1114
  Planarity :  0.004   0.054   1216
  Dihedral  :  4.098  40.204   1010
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 14.20 %
    Favored  : 82.75 %
  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:  1.88 (0.30), residues: 901
  helix:  2.82 (0.23), residues: 508
  sheet:  0.72 (0.73), residues: 53
  loop : -1.24 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP i 120 
 HIS   0.003   0.001   HIS i 105 
 PHE   0.011   0.001   PHE i 225 
 TYR   0.008   0.001   TYR i 275 
 ARG   0.007   0.000   ARG i 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04247 (  413)
  hydrogen bonds       : angle       3.51658 ( 1203)
  metal coordination   : bond        0.00444 (    8)
  metal coordination   : angle       1.42609 (    6)
  covalent geometry    : bond        0.00261 ( 7044)
  covalent geometry    : angle       0.48506 ( 9566)
  Misc. bond           : bond        0.00044 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3922.51 seconds
wall clock time: 68 minutes 39.93 seconds (4119.93 seconds total)