Starting phenix.real_space_refine
on Tue Jan 13 14:13:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ysp_34079/01_2026/7ysp_34079.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ysp_34079/01_2026/7ysp_34079.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ysp_34079/01_2026/7ysp_34079.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ysp_34079/01_2026/7ysp_34079.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ysp_34079/01_2026/7ysp_34079.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ysp_34079/01_2026/7ysp_34079.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     S      48      5.16       5
     C    4278      2.51       5
     N    1162      2.21       5
     O    1317      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6810
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3374
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3374
          Classifications: {'peptide': 430}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3376
          Classifications: {'peptide': 430}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.79, per 1000 atoms: 0.26
  Number of scatterers: 6810
  At special positions: 0
  Unit cell: (108.712, 72.76, 73.616, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     P       5     15.00
     O    1317      8.00
     N    1162      7.00
     C    4278      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 293.1 milliseconds
  

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1594

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 10 sheets defined
      52.2% alpha, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 28
    Processing helix  chain 'A' and resid 47 through 51
    Processing helix  chain 'A' and resid 72 through 80
    Processing helix  chain 'A' and resid 88 through 90
      No H-bonds generated for 'chain 'A' and resid 88 through 90'
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 111 through 127
      removed outlier: 4.324A  pdb=" N   ASP A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 5.722A  pdb=" N   LEU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 161
      removed outlier: 4.344A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 196
      removed outlier: 4.705A  pdb=" N   GLU A 196 " --> pdb=" O   HIS A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 215
      removed outlier: 3.515A  pdb=" N   ILE A 209 " --> pdb=" O   ASP A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 4.920A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 260
    Processing helix  chain 'A' and resid 278 through 283
      removed outlier: 4.253A  pdb=" N   TYR A 282 " --> pdb=" O   GLU A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 4.124A  pdb=" N   PHE A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 324 through 337
      removed outlier: 3.624A  pdb=" N   THR A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 383
      No H-bonds generated for 'chain 'A' and resid 381 through 383'
    Processing helix  chain 'A' and resid 384 through 400
      removed outlier: 3.761A  pdb=" N   TRP A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 4.181A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 437
      removed outlier: 4.352A  pdb=" N   PHE A 418 " --> pdb=" O   GLU A 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 28
      removed outlier: 3.584A  pdb=" N   GLY B  13 " --> pdb=" O   ALA B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 48
      removed outlier: 4.301A  pdb=" N   LEU B  44 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   ARG B  48 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 72 through 81
      removed outlier: 3.730A  pdb=" N   ASP B  76 " --> pdb=" O   PRO B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 90
      No H-bonds generated for 'chain 'B' and resid 88 through 90'
    Processing helix  chain 'B' and resid 102 through 109
      removed outlier: 4.229A  pdb=" N   TYR B 108 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 128
      removed outlier: 3.683A  pdb=" N   LEU B 114 " --> pdb=" O   GLU B 110 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   SER B 128 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 161
    Processing helix  chain 'B' and resid 182 through 198
      removed outlier: 4.866A  pdb=" N   GLU B 196 " --> pdb=" O   HIS B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 215
    Processing helix  chain 'B' and resid 223 through 244
      removed outlier: 3.845A  pdb=" N   LEU B 230 " --> pdb=" O   ASP B 226 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   CYS B 241 " --> pdb=" O   GLY B 237 " (cutoff:3.500A)
      removed outlier: 5.137A  pdb=" N   LEU B 242 " --> pdb=" O   VAL B 238 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   PHE B 244 " --> pdb=" O   THR B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 260
    Processing helix  chain 'B' and resid 287 through 295
      removed outlier: 3.557A  pdb=" N   LEU B 291 " --> pdb=" O   THR B 287 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   MET B 295 " --> pdb=" O   LEU B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 339
      removed outlier: 3.692A  pdb=" N   VAL B 328 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 343
    Processing helix  chain 'B' and resid 384 through 401
      removed outlier: 3.710A  pdb=" N   PHE B 388 " --> pdb=" O   ILE B 384 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   ARG B 401 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 410
      removed outlier: 4.042A  pdb=" N   TYR B 408 " --> pdb=" O   PHE B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 438
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8
      removed outlier: 6.620A  pdb=" N   ILE A   5 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
      removed outlier: 8.542A  pdb=" N   PHE A 138 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   ILE A   7 " --> pdb=" O   PHE A 138 " (cutoff:3.500A)
      removed outlier: 9.532A  pdb=" N   SER A 140 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL A 137 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   HIS A 139 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   CYS A 200 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 69
      removed outlier: 6.625A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 315 through 316
      removed outlier: 6.294A  pdb=" N   CYS A 315 " --> pdb=" O   LYS A 352 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 320
      removed outlier: 6.090A  pdb=" N   TYR A 319 " --> pdb=" O   ASN A 356 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 8
      removed outlier: 6.423A  pdb=" N   VAL B   5 " --> pdb=" O   GLN B 136 " (cutoff:3.500A)
      removed outlier: 8.104A  pdb=" N   THR B 138 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ILE B   7 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
      removed outlier: 8.789A  pdb=" N   SER B 140 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 8
      removed outlier: 6.423A  pdb=" N   VAL B   5 " --> pdb=" O   GLN B 136 " (cutoff:3.500A)
      removed outlier: 8.104A  pdb=" N   THR B 138 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ILE B   7 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
      removed outlier: 8.789A  pdb=" N   SER B 140 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   SER B 170 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 55
    Processing sheet with id=AA9, first strand: chain 'B' and resid 67 through 69
      removed outlier: 5.974A  pdb=" N   LEU B  67 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 269 through 273
      removed outlier: 6.282A  pdb=" N   VAL B 315 " --> pdb=" O   LYS B 352 " (cutoff:3.500A)
      removed outlier: 8.156A  pdb=" N   ALA B 354 " --> pdb=" O   VAL B 315 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   ALA B 317 " --> pdb=" O   ALA B 354 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   CYS B 356 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   PHE B 319 " --> pdb=" O   CYS B 356 " (cutoff:3.500A)

    307 hydrogen bonds defined for protein.
    888 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: 0.70

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2258
        1.34 -     1.46: 1119
        1.46 -     1.57: 3505
        1.57 -     1.69: 8
        1.69 -     1.81: 76
  Bond restraints: 6966
  Sorted by residual:
  bond pdb=" C5  GDP B 501 "
       pdb=" C4  GDP B 501 "
    ideal  model  delta    sigma   weight residual
    1.490  1.470  0.020 2.00e-02 2.50e+03 1.01e+00
  bond pdb=" C   VAL A  62 "
       pdb=" O   VAL A  62 "
    ideal  model  delta    sigma   weight residual
    1.232  1.241 -0.009 8.90e-03 1.26e+04 9.49e-01
  bond pdb=" CA  GLU A 183 "
       pdb=" C   GLU A 183 "
    ideal  model  delta    sigma   weight residual
    1.522  1.532 -0.010 1.26e-02 6.30e+03 6.30e-01
  bond pdb=" CB  GLU B 125 "
       pdb=" CG  GLU B 125 "
    ideal  model  delta    sigma   weight residual
    1.520  1.541 -0.021 3.00e-02 1.11e+03 5.02e-01
  bond pdb=" C   GLU A 183 "
       pdb=" N   PRO A 184 "
    ideal  model  delta    sigma   weight residual
    1.335  1.344 -0.009 1.28e-02 6.10e+03 4.95e-01
  ... (remaining 6961 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 9204
        1.57 -     3.13: 211
        3.13 -     4.70: 29
        4.70 -     6.26: 13
        6.26 -     7.83: 5
  Bond angle restraints: 9462
  Sorted by residual:
  angle pdb=" N   ILE A 110 "
        pdb=" CA  ILE A 110 "
        pdb=" C   ILE A 110 "
      ideal   model   delta    sigma   weight residual
     113.53  109.75    3.78 9.80e-01 1.04e+00 1.49e+01
  angle pdb=" CB  ARG A 121 "
        pdb=" CG  ARG A 121 "
        pdb=" CD  ARG A 121 "
      ideal   model   delta    sigma   weight residual
     111.30  119.13   -7.83 2.30e+00 1.89e-01 1.16e+01
  angle pdb=" C   VAL B 328 "
        pdb=" N   ASP B 329 "
        pdb=" CA  ASP B 329 "
      ideal   model   delta    sigma   weight residual
     121.14  116.61    4.53 1.75e+00 3.27e-01 6.69e+00
  angle pdb=" N   MET B 149 "
        pdb=" CA  MET B 149 "
        pdb=" CB  MET B 149 "
      ideal   model   delta    sigma   weight residual
     110.12  113.65   -3.53 1.47e+00 4.63e-01 5.77e+00
  angle pdb=" CA  ILE A 110 "
        pdb=" C   ILE A 110 "
        pdb=" N   GLY A 111 "
      ideal   model   delta    sigma   weight residual
     119.31  116.68    2.63 1.15e+00 7.56e-01 5.23e+00
  ... (remaining 9457 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.25: 4067
       34.25 -    68.51: 62
       68.51 -   102.76: 11
      102.76 -   137.01: 2
      137.01 -   171.27: 2
  Dihedral angle restraints: 4144
    sinusoidal: 1659
      harmonic: 2485
  Sorted by residual:
  dihedral pdb=" C8  GTP A 501 "
           pdb=" C1' GTP A 501 "
           pdb=" N9  GTP A 501 "
           pdb=" O4' GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -84.14 -171.27     1      2.00e+01 2.50e-03 4.77e+01
  dihedral pdb=" O5' GTP A 501 "
           pdb=" O3A GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" PB  GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     274.12  134.17  139.95     1      2.00e+01 2.50e-03 4.24e+01
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  -36.72  105.99     1      2.00e+01 2.50e-03 3.06e+01
  ... (remaining 4141 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 662
       0.036 -    0.073: 249
       0.073 -    0.109: 97
       0.109 -    0.146: 24
       0.146 -    0.182: 2
  Chirality restraints: 1034
  Sorted by residual:
  chirality pdb=" CB  THR B 221 "
            pdb=" CA  THR B 221 "
            pdb=" OG1 THR B 221 "
            pdb=" CG2 THR B 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 8.28e-01
  chirality pdb=" CB  VAL B 238 "
            pdb=" CA  VAL B 238 "
            pdb=" CG1 VAL B 238 "
            pdb=" CG2 VAL B 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.54e-01
  chirality pdb=" CA  GLU B 125 "
            pdb=" N   GLU B 125 "
            pdb=" C   GLU B 125 "
            pdb=" CB  GLU B 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.20e-01
  ... (remaining 1031 not shown)

  Planarity restraints: 1233
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 432 "    0.010 2.00e-02 2.50e+03   1.05e-02 2.22e+00
        pdb=" CG  TYR A 432 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 432 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 432 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 432 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 432 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 432 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 432 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 269 "    0.024 5.00e-02 4.00e+02   3.56e-02 2.03e+00
        pdb=" N   PRO B 270 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 270 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 270 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  31 "   -0.023 5.00e-02 4.00e+02   3.42e-02 1.87e+00
        pdb=" N   PRO B  32 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1230 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 160
        2.65 -     3.21: 6965
        3.21 -     3.77: 12044
        3.77 -     4.34: 15753
        4.34 -     4.90: 24426
  Nonbonded interactions: 59348
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 122 "
            pdb=" OG  SER B 126 "
     model   vdw
     2.086 3.040
  nonbonded pdb=" O   LYS B 105 "
            pdb=" OG1 THR B 109 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   LEU A 269 "
            pdb=" OG  SER A 379 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OD1 ASN B 186 "
            pdb=" OH  TYR B 408 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OG1 THR A 271 "
            pdb=" O   ASN A 300 "
     model   vdw
     2.223 3.040
  ... (remaining 59343 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:             0.370
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.790
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
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      :  0.002   0.025   6966  Z= 0.110
  Angle     :  0.606   7.828   9462  Z= 0.306
  Chirality :  0.045   0.182   1034
  Planarity :  0.004   0.041   1233
  Dihedral  : 15.054 171.268   2550
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 18.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.29), residues: 854
  helix:  0.71 (0.26), residues: 380
  sheet: -0.82 (0.45), residues: 125
  loop :  0.05 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 121 
 TYR   0.026   0.001   TYR A 432 
 PHE   0.024   0.001   PHE A 255 
 TRP   0.024   0.002   TRP B  21 
 HIS   0.003   0.001   HIS B   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 6966)
  covalent geometry    : angle       0.60641 ( 9462)
  hydrogen bonds       : bond        0.14153 (  307)
  hydrogen bonds       : angle       5.97909 (  888)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 CYS cc_start: 0.8767 (m) cc_final: 0.8416 (m)
REVERT: A   52 PHE cc_start: 0.8187 (m-80) cc_final: 0.7930 (m-80)
REVERT: A  102 ASN cc_start: 0.9076 (t0) cc_final: 0.8455 (t0)
REVERT: A  120 ASP cc_start: 0.9082 (m-30) cc_final: 0.8819 (m-30)
REVERT: A  152 LEU cc_start: 0.9319 (tp) cc_final: 0.9073 (tp)
REVERT: A  186 ASN cc_start: 0.9334 (m110) cc_final: 0.9083 (m110)
REVERT: A  189 LEU cc_start: 0.9517 (mt) cc_final: 0.9265 (mt)
REVERT: A  313 MET cc_start: 0.6740 (tmm) cc_final: 0.6134 (tmm)
REVERT: A  398 MET cc_start: 0.9338 (mtm) cc_final: 0.8944 (mtm)
REVERT: B    1 MET cc_start: 0.7511 (mmp) cc_final: 0.7026 (mmm)
REVERT: B  137 LEU cc_start: 0.9224 (tp) cc_final: 0.8986 (tp)
REVERT: B  149 MET cc_start: 0.9281 (mpp) cc_final: 0.8880 (mpp)
REVERT: B  350 ASN cc_start: 0.8441 (p0) cc_final: 0.8059 (p0)
REVERT: B  425 MET cc_start: 0.9338 (ppp) cc_final: 0.8984 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.0620
  time to fit residues: 13.0580
Evaluate side-chains
  106 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    0.0030
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:   20.0000
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    2.5996

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 186 ASN
B 424 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.089752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.064030 restraints weight = 23008.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.066561 restraints weight = 15288.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.068458 restraints weight = 11540.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.069684 restraints weight = 9380.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.070854 restraints weight = 8146.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6966  Z= 0.152
  Angle     :  0.638   9.347   9462  Z= 0.321
  Chirality :  0.046   0.171   1034
  Planarity :  0.005   0.052   1233
  Dihedral  : 10.349 177.262    959
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 11.46 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.29), residues: 854
  helix:  0.81 (0.26), residues: 388
  sheet: -1.00 (0.45), residues: 131
  loop :  0.09 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 422 
 TYR   0.052   0.002   TYR A 432 
 PHE   0.019   0.001   PHE A 255 
 TRP   0.010   0.001   TRP B 103 
 HIS   0.003   0.001   HIS B  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6966)
  covalent geometry    : angle       0.63838 ( 9462)
  hydrogen bonds       : bond        0.04021 (  307)
  hydrogen bonds       : angle       4.94643 (  888)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 HIS cc_start: 0.8550 (OUTLIER) cc_final: 0.8195 (t-90)
REVERT: A  102 ASN cc_start: 0.9172 (t0) cc_final: 0.8509 (t0)
REVERT: A  120 ASP cc_start: 0.9143 (m-30) cc_final: 0.8923 (m-30)
REVERT: A  189 LEU cc_start: 0.9459 (mt) cc_final: 0.9240 (mt)
REVERT: A  313 MET cc_start: 0.7028 (tmm) cc_final: 0.6617 (tmm)
REVERT: A  398 MET cc_start: 0.9306 (mtm) cc_final: 0.8892 (mtm)
REVERT: B  149 MET cc_start: 0.9232 (mpp) cc_final: 0.8574 (mtt)
REVERT: B  269 MET cc_start: 0.8482 (tpt) cc_final: 0.8139 (mmt)
REVERT: B  301 MET cc_start: 0.9265 (mmp) cc_final: 0.8960 (mmp)
REVERT: B  350 ASN cc_start: 0.8617 (p0) cc_final: 0.8230 (p0)
REVERT: B  425 MET cc_start: 0.9349 (ppp) cc_final: 0.8957 (ppp)
REVERT: B  432 TYR cc_start: 0.8694 (m-80) cc_final: 0.8272 (t80)
  outliers start: 9
  outliers final: 7
  residues processed: 123
  average time/residue: 0.0541
  time to fit residues: 10.1065
Evaluate side-chains
  113 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  282 TYR
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  349 ASN
Chi-restraints excluded: chain B residue  376 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 83 optimal weight:    0.2980
   chunk 39 optimal weight:   10.0000
   chunk 26 optimal weight:    8.9990
   chunk 53 optimal weight:   40.0000
   chunk 59 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 82 optimal weight:    7.9990
   overall best weight:    2.2386

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.089408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.062198 restraints weight = 22771.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.064753 restraints weight = 15483.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.066695 restraints weight = 11793.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.067979 restraints weight = 9667.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.069000 restraints weight = 8406.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6966  Z= 0.133
  Angle     :  0.612  10.251   9462  Z= 0.304
  Chirality :  0.046   0.175   1034
  Planarity :  0.004   0.053   1233
  Dihedral  : 10.347 176.157    959
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 15.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 13.51 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.29), residues: 854
  helix:  0.94 (0.27), residues: 387
  sheet: -0.75 (0.46), residues: 122
  loop :  0.02 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 422 
 TYR   0.049   0.001   TYR A 432 
 PHE   0.019   0.001   PHE A 255 
 TRP   0.009   0.001   TRP B  21 
 HIS   0.003   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6966)
  covalent geometry    : angle       0.61223 ( 9462)
  hydrogen bonds       : bond        0.03722 (  307)
  hydrogen bonds       : angle       4.78996 (  888)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8963 (tt)
REVERT: A   88 HIS cc_start: 0.8550 (OUTLIER) cc_final: 0.8267 (t-90)
REVERT: A  102 ASN cc_start: 0.9200 (t0) cc_final: 0.8555 (t0)
REVERT: A  120 ASP cc_start: 0.9223 (m-30) cc_final: 0.8951 (m-30)
REVERT: A  189 LEU cc_start: 0.9474 (mt) cc_final: 0.9244 (mt)
REVERT: A  313 MET cc_start: 0.7108 (tmm) cc_final: 0.6311 (tmm)
REVERT: A  398 MET cc_start: 0.9377 (mtm) cc_final: 0.8943 (mtm)
REVERT: B  269 MET cc_start: 0.8579 (tpt) cc_final: 0.8086 (mmt)
REVERT: B  301 MET cc_start: 0.9224 (mmp) cc_final: 0.8985 (mmp)
REVERT: B  342 TYR cc_start: 0.9206 (m-80) cc_final: 0.8985 (m-80)
REVERT: B  350 ASN cc_start: 0.8643 (p0) cc_final: 0.8303 (p0)
REVERT: B  425 MET cc_start: 0.9400 (ppp) cc_final: 0.9036 (ppp)
  outliers start: 11
  outliers final: 7
  residues processed: 123
  average time/residue: 0.0596
  time to fit residues: 11.1617
Evaluate side-chains
  116 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  282 TYR
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  349 ASN
Chi-restraints excluded: chain B residue  376 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 32 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 82 optimal weight:    6.9990
   chunk 79 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 69 optimal weight:    9.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.089802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.062805 restraints weight = 22841.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.065448 restraints weight = 15413.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.067346 restraints weight = 11649.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.068836 restraints weight = 9554.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.069766 restraints weight = 8216.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6966  Z= 0.122
  Angle     :  0.610   8.570   9462  Z= 0.300
  Chirality :  0.045   0.169   1034
  Planarity :  0.004   0.052   1233
  Dihedral  : 10.366 174.679    959
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.78 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.29), residues: 854
  helix:  0.99 (0.26), residues: 388
  sheet: -0.79 (0.46), residues: 124
  loop :  0.04 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 422 
 TYR   0.048   0.001   TYR A 432 
 PHE   0.017   0.001   PHE A 255 
 TRP   0.008   0.001   TRP B 346 
 HIS   0.002   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6966)
  covalent geometry    : angle       0.61037 ( 9462)
  hydrogen bonds       : bond        0.03576 (  307)
  hydrogen bonds       : angle       4.65229 (  888)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9058 (tt)
REVERT: A   88 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.8294 (t-90)
REVERT: A  102 ASN cc_start: 0.9123 (t0) cc_final: 0.8472 (t0)
REVERT: A  120 ASP cc_start: 0.9299 (m-30) cc_final: 0.9016 (m-30)
REVERT: A  189 LEU cc_start: 0.9482 (mt) cc_final: 0.9257 (mt)
REVERT: A  313 MET cc_start: 0.7207 (tmm) cc_final: 0.6381 (tmm)
REVERT: A  398 MET cc_start: 0.9409 (mtm) cc_final: 0.8927 (mtm)
REVERT: B    1 MET cc_start: 0.7415 (mmp) cc_final: 0.7125 (mmp)
REVERT: B  200 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8445 (mm-30)
REVERT: B  269 MET cc_start: 0.8621 (tpt) cc_final: 0.8233 (mmt)
REVERT: B  301 MET cc_start: 0.9203 (mmp) cc_final: 0.8803 (mmp)
REVERT: B  350 ASN cc_start: 0.8641 (p0) cc_final: 0.8282 (p0)
REVERT: B  425 MET cc_start: 0.9449 (ppp) cc_final: 0.9066 (ppp)
REVERT: B  432 TYR cc_start: 0.8722 (m-80) cc_final: 0.8236 (t80)
  outliers start: 15
  outliers final: 9
  residues processed: 127
  average time/residue: 0.0608
  time to fit residues: 11.6471
Evaluate side-chains
  115 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  282 TYR
Chi-restraints excluded: chain A residue  326 LYS
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  349 ASN
Chi-restraints excluded: chain B residue  376 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 78 optimal weight:    7.9990
   chunk 37 optimal weight:    8.9990
   chunk 20 optimal weight:    8.9990
   chunk 5 optimal weight:    0.0980
   chunk 32 optimal weight:    0.0870
   chunk 16 optimal weight:   10.0000
   chunk 57 optimal weight:   40.0000
   chunk 31 optimal weight:    2.9990
   chunk 81 optimal weight:    7.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    3.0364

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

Flipped N/Q/H residues before XYZ refinement:
A 186 ASN
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** 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 = 0.3822 r_free = 0.3822 target = 0.089013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.061918 restraints weight = 23176.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.064395 restraints weight = 15596.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.066275 restraints weight = 11921.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.067581 restraints weight = 9765.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.068609 restraints weight = 8493.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6966  Z= 0.157
  Angle     :  0.633   9.383   9462  Z= 0.317
  Chirality :  0.045   0.181   1034
  Planarity :  0.004   0.054   1233
  Dihedral  : 10.425 174.785    959
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 17.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.19 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.29), residues: 854
  helix:  0.92 (0.27), residues: 387
  sheet: -0.74 (0.46), residues: 125
  loop :  0.01 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 422 
 TYR   0.048   0.001   TYR A 432 
 PHE   0.016   0.001   PHE A 255 
 TRP   0.008   0.001   TRP B 103 
 HIS   0.003   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 6966)
  covalent geometry    : angle       0.63289 ( 9462)
  hydrogen bonds       : bond        0.03665 (  307)
  hydrogen bonds       : angle       4.79513 (  888)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9040 (tt)
REVERT: A   88 HIS cc_start: 0.8681 (OUTLIER) cc_final: 0.8419 (t-90)
REVERT: A   98 ASP cc_start: 0.8802 (t70) cc_final: 0.8100 (t0)
REVERT: A  102 ASN cc_start: 0.9155 (t0) cc_final: 0.8544 (t0)
REVERT: A  120 ASP cc_start: 0.9341 (m-30) cc_final: 0.9089 (m-30)
REVERT: A  189 LEU cc_start: 0.9474 (mt) cc_final: 0.9261 (mt)
REVERT: A  313 MET cc_start: 0.7207 (tmm) cc_final: 0.6310 (tmm)
REVERT: A  398 MET cc_start: 0.9418 (mtm) cc_final: 0.8938 (mtm)
REVERT: B  149 MET cc_start: 0.9276 (mpp) cc_final: 0.9027 (mpp)
REVERT: B  200 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8513 (mm-30)
REVERT: B  269 MET cc_start: 0.8673 (tpt) cc_final: 0.8309 (mmt)
REVERT: B  301 MET cc_start: 0.9153 (mmp) cc_final: 0.8746 (mmp)
REVERT: B  350 ASN cc_start: 0.8623 (p0) cc_final: 0.8278 (p0)
REVERT: B  425 MET cc_start: 0.9458 (ppp) cc_final: 0.9088 (ppp)
REVERT: B  432 TYR cc_start: 0.8738 (m-80) cc_final: 0.8214 (t80)
  outliers start: 19
  outliers final: 15
  residues processed: 127
  average time/residue: 0.0601
  time to fit residues: 11.4962
Evaluate side-chains
  121 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  282 TYR
Chi-restraints excluded: chain A residue  326 LYS
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  349 ASN
Chi-restraints excluded: chain B residue  357 ASP
Chi-restraints excluded: chain B residue  376 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 59 optimal weight:    7.9990
   chunk 69 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   chunk 32 optimal weight:    0.0060
   chunk 71 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    1.5800

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

Flipped N/Q/H residues before XYZ refinement:
** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.090667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.063285 restraints weight = 22884.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.065965 restraints weight = 15404.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.067855 restraints weight = 11646.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.069389 restraints weight = 9542.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.070357 restraints weight = 8183.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6966  Z= 0.117
  Angle     :  0.627  13.108   9462  Z= 0.306
  Chirality :  0.045   0.175   1034
  Planarity :  0.004   0.050   1233
  Dihedral  : 10.427 173.482    959
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 15.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 17.87 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.29), residues: 854
  helix:  0.92 (0.27), residues: 388
  sheet: -0.67 (0.46), residues: 127
  loop : -0.03 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  84 
 TYR   0.048   0.001   TYR A 432 
 PHE   0.016   0.001   PHE A 255 
 TRP   0.008   0.001   TRP B 103 
 HIS   0.003   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6966)
  covalent geometry    : angle       0.62724 ( 9462)
  hydrogen bonds       : bond        0.03475 (  307)
  hydrogen bonds       : angle       4.70612 (  888)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9198 (tt)
REVERT: A   88 HIS cc_start: 0.8602 (OUTLIER) cc_final: 0.8340 (t-90)
REVERT: A   98 ASP cc_start: 0.8728 (t70) cc_final: 0.7946 (t70)
REVERT: A  102 ASN cc_start: 0.9161 (t0) cc_final: 0.8528 (t0)
REVERT: A  120 ASP cc_start: 0.9342 (m-30) cc_final: 0.9088 (m-30)
REVERT: A  189 LEU cc_start: 0.9475 (mt) cc_final: 0.9252 (mt)
REVERT: A  313 MET cc_start: 0.7234 (tmm) cc_final: 0.6302 (tmm)
REVERT: A  398 MET cc_start: 0.9368 (mtm) cc_final: 0.8862 (mtm)
REVERT: B  149 MET cc_start: 0.9281 (mpp) cc_final: 0.9073 (mpp)
REVERT: B  200 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8427 (mm-30)
REVERT: B  269 MET cc_start: 0.8615 (tpt) cc_final: 0.8225 (mmt)
REVERT: B  275 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6790 (pp)
REVERT: B  301 MET cc_start: 0.9165 (mmp) cc_final: 0.8686 (mmp)
REVERT: B  350 ASN cc_start: 0.8616 (p0) cc_final: 0.8286 (p0)
REVERT: B  425 MET cc_start: 0.9451 (ppp) cc_final: 0.9076 (ppp)
  outliers start: 22
  outliers final: 15
  residues processed: 134
  average time/residue: 0.0626
  time to fit residues: 12.5218
Evaluate side-chains
  125 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  282 TYR
Chi-restraints excluded: chain A residue  326 LYS
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  377 PHE
Chi-restraints excluded: chain B residue  413 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 50 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 30 optimal weight:   20.0000
   chunk 37 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0050
   chunk 53 optimal weight:   20.0000
   chunk 43 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   overall best weight:    1.7800

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

Flipped N/Q/H residues before XYZ refinement:
A 228 ASN
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** 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 = 0.3858 r_free = 0.3858 target = 0.090877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.065402 restraints weight = 23001.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.068147 restraints weight = 15086.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.070162 restraints weight = 11151.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.071499 restraints weight = 8926.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.072722 restraints weight = 7687.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6966  Z= 0.125
  Angle     :  0.657  12.804   9462  Z= 0.317
  Chirality :  0.046   0.180   1034
  Planarity :  0.004   0.051   1233
  Dihedral  : 10.455 173.123    959
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 19.51 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.29), residues: 854
  helix:  0.96 (0.27), residues: 387
  sheet: -0.54 (0.47), residues: 129
  loop : -0.07 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 322 
 TYR   0.047   0.001   TYR A 432 
 PHE   0.017   0.001   PHE A 169 
 TRP   0.008   0.001   TRP B 103 
 HIS   0.004   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6966)
  covalent geometry    : angle       0.65705 ( 9462)
  hydrogen bonds       : bond        0.03435 (  307)
  hydrogen bonds       : angle       4.67998 (  888)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 CYS cc_start: 0.8920 (m) cc_final: 0.8577 (m)
REVERT: A   23 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9166 (tt)
REVERT: A   27 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7447 (mt-10)
REVERT: A   88 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.8374 (t-90)
REVERT: A   98 ASP cc_start: 0.8753 (t70) cc_final: 0.8062 (t70)
REVERT: A  102 ASN cc_start: 0.9123 (t0) cc_final: 0.8519 (t0)
REVERT: A  120 ASP cc_start: 0.9362 (m-30) cc_final: 0.9104 (m-30)
REVERT: A  189 LEU cc_start: 0.9475 (mt) cc_final: 0.9226 (mt)
REVERT: A  313 MET cc_start: 0.7296 (tmm) cc_final: 0.6337 (tmm)
REVERT: A  319 TYR cc_start: 0.7502 (m-80) cc_final: 0.7131 (m-80)
REVERT: A  398 MET cc_start: 0.9382 (mtm) cc_final: 0.8855 (mtm)
REVERT: B  200 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8395 (mm-30)
REVERT: B  265 LEU cc_start: 0.8600 (mm) cc_final: 0.8199 (mm)
REVERT: B  269 MET cc_start: 0.8469 (tpt) cc_final: 0.8124 (mmt)
REVERT: B  275 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6757 (pp)
REVERT: B  301 MET cc_start: 0.9221 (mmp) cc_final: 0.8776 (mmp)
REVERT: B  350 ASN cc_start: 0.8675 (p0) cc_final: 0.8314 (p0)
REVERT: B  393 GLU cc_start: 0.9337 (pp20) cc_final: 0.9115 (pp20)
REVERT: B  425 MET cc_start: 0.9493 (ppp) cc_final: 0.9112 (ppp)
REVERT: B  432 TYR cc_start: 0.8723 (m-80) cc_final: 0.8176 (t80)
  outliers start: 22
  outliers final: 18
  residues processed: 133
  average time/residue: 0.0589
  time to fit residues: 11.8149
Evaluate side-chains
  132 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  349 ASN
Chi-restraints excluded: chain B residue  357 ASP
Chi-restraints excluded: chain B residue  377 PHE
Chi-restraints excluded: chain B residue  413 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 31 optimal weight:    8.9990
   chunk 30 optimal weight:   20.0000
   chunk 39 optimal weight:    6.9990
   chunk 84 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 79 optimal weight:    5.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 192 HIS
B 426 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.085525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.060605 restraints weight = 24390.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.063033 restraints weight = 16255.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.064777 restraints weight = 12202.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.066238 restraints weight = 9922.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.067098 restraints weight = 8462.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   6966  Z= 0.269
  Angle     :  0.730  11.597   9462  Z= 0.370
  Chirality :  0.049   0.282   1034
  Planarity :  0.005   0.053   1233
  Dihedral  : 10.588 177.195    959
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 22.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 19.51 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.29), residues: 854
  helix:  0.65 (0.26), residues: 385
  sheet: -0.71 (0.47), residues: 127
  loop : -0.05 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  84 
 TYR   0.044   0.002   TYR A 432 
 PHE   0.016   0.002   PHE A 202 
 TRP   0.013   0.002   TRP B 103 
 HIS   0.004   0.002   HIS B 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00553 ( 6966)
  covalent geometry    : angle       0.73012 ( 9462)
  hydrogen bonds       : bond        0.03999 (  307)
  hydrogen bonds       : angle       5.09352 (  888)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9249 (tt)
REVERT: A   88 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.8518 (t-90)
REVERT: A   98 ASP cc_start: 0.8732 (t70) cc_final: 0.8068 (t0)
REVERT: A  102 ASN cc_start: 0.9260 (t0) cc_final: 0.8700 (t0)
REVERT: A  313 MET cc_start: 0.7351 (tmm) cc_final: 0.6331 (tmm)
REVERT: A  398 MET cc_start: 0.9381 (mtm) cc_final: 0.8876 (mtm)
REVERT: B  269 MET cc_start: 0.8597 (tpt) cc_final: 0.8118 (tpt)
REVERT: B  301 MET cc_start: 0.9166 (mmp) cc_final: 0.8847 (mmp)
REVERT: B  350 ASN cc_start: 0.8734 (p0) cc_final: 0.8388 (p0)
REVERT: B  425 MET cc_start: 0.9502 (ppp) cc_final: 0.9134 (ppp)
  outliers start: 27
  outliers final: 18
  residues processed: 130
  average time/residue: 0.0577
  time to fit residues: 11.3181
Evaluate side-chains
  121 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  282 TYR
Chi-restraints excluded: chain A residue  326 LYS
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  349 ASN
Chi-restraints excluded: chain B residue  357 ASP
Chi-restraints excluded: chain B residue  377 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 45 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9990
   chunk 50 optimal weight:   20.0000
   chunk 64 optimal weight:    8.9990
   chunk 35 optimal weight:    7.9990
   chunk 78 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 192 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.086282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.059569 restraints weight = 23891.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.062013 restraints weight = 16060.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.063851 restraints weight = 12172.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.065203 restraints weight = 9990.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.066069 restraints weight = 8636.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6966  Z= 0.206
  Angle     :  0.727  12.274   9462  Z= 0.357
  Chirality :  0.048   0.199   1034
  Planarity :  0.005   0.052   1233
  Dihedral  : 10.627 177.132    959
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 20.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 20.87 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.29), residues: 854
  helix:  0.56 (0.26), residues: 385
  sheet: -0.93 (0.46), residues: 126
  loop : -0.09 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 322 
 TYR   0.047   0.002   TYR A 432 
 PHE   0.019   0.002   PHE A 255 
 TRP   0.021   0.002   TRP B  21 
 HIS   0.004   0.001   HIS B 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 6966)
  covalent geometry    : angle       0.72699 ( 9462)
  hydrogen bonds       : bond        0.03886 (  307)
  hydrogen bonds       : angle       5.10712 (  888)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9216 (tt)
REVERT: A   27 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7548 (mt-10)
REVERT: A   88 HIS cc_start: 0.8787 (OUTLIER) cc_final: 0.8570 (t-90)
REVERT: A   98 ASP cc_start: 0.8822 (t70) cc_final: 0.8146 (t70)
REVERT: A  102 ASN cc_start: 0.9189 (t0) cc_final: 0.8623 (t0)
REVERT: A  272 TYR cc_start: 0.8286 (t80) cc_final: 0.8056 (t80)
REVERT: A  313 MET cc_start: 0.7342 (tmm) cc_final: 0.6364 (tmm)
REVERT: A  398 MET cc_start: 0.9433 (mtm) cc_final: 0.8884 (mtm)
REVERT: B  269 MET cc_start: 0.8653 (tpt) cc_final: 0.8181 (tpt)
REVERT: B  296 PHE cc_start: 0.8791 (m-80) cc_final: 0.7993 (m-80)
REVERT: B  299 LYS cc_start: 0.9150 (pttm) cc_final: 0.8949 (pttm)
REVERT: B  301 MET cc_start: 0.9167 (mmp) cc_final: 0.8839 (mmp)
REVERT: B  350 ASN cc_start: 0.8769 (p0) cc_final: 0.8428 (p0)
REVERT: B  425 MET cc_start: 0.9524 (ppp) cc_final: 0.9156 (ppp)
REVERT: B  432 TYR cc_start: 0.8752 (m-80) cc_final: 0.8203 (t80)
  outliers start: 25
  outliers final: 20
  residues processed: 126
  average time/residue: 0.0584
  time to fit residues: 11.1234
Evaluate side-chains
  125 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  282 TYR
Chi-restraints excluded: chain A residue  326 LYS
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  349 ASN
Chi-restraints excluded: chain B residue  357 ASP
Chi-restraints excluded: chain B residue  377 PHE
Chi-restraints excluded: chain B residue  413 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 5 optimal weight:    0.0010
   chunk 57 optimal weight:   20.0000
   chunk 14 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 34 optimal weight:    8.9990
   chunk 37 optimal weight:   20.0000
   chunk 60 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.3590

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.089818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.062784 restraints weight = 22963.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.065453 restraints weight = 15477.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.067403 restraints weight = 11692.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.068672 restraints weight = 9554.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.069657 restraints weight = 8320.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6966  Z= 0.127
  Angle     :  0.734  13.946   9462  Z= 0.347
  Chirality :  0.048   0.215   1034
  Planarity :  0.004   0.052   1233
  Dihedral  : 10.587 174.644    959
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 22.24 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.29), residues: 854
  helix:  0.68 (0.27), residues: 386
  sheet: -0.76 (0.46), residues: 130
  loop : -0.07 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 322 
 TYR   0.048   0.001   TYR A 432 
 PHE   0.021   0.001   PHE A 255 
 TRP   0.021   0.002   TRP B  21 
 HIS   0.006   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6966)
  covalent geometry    : angle       0.73403 ( 9462)
  hydrogen bonds       : bond        0.03681 (  307)
  hydrogen bonds       : angle       4.96798 (  888)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9219 (tt)
REVERT: A   27 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7535 (mt-10)
REVERT: A   52 PHE cc_start: 0.7930 (m-80) cc_final: 0.7664 (m-80)
REVERT: A   98 ASP cc_start: 0.8754 (t70) cc_final: 0.8084 (t70)
REVERT: A  102 ASN cc_start: 0.9135 (t0) cc_final: 0.8521 (t0)
REVERT: A  167 LEU cc_start: 0.9149 (tt) cc_final: 0.8942 (tt)
REVERT: A  313 MET cc_start: 0.7382 (tmm) cc_final: 0.6504 (tmm)
REVERT: A  398 MET cc_start: 0.9295 (mtm) cc_final: 0.8766 (mtm)
REVERT: B  103 TRP cc_start: 0.7617 (t60) cc_final: 0.7216 (t-100)
REVERT: B  265 LEU cc_start: 0.8558 (mm) cc_final: 0.8271 (mm)
REVERT: B  269 MET cc_start: 0.8700 (tpt) cc_final: 0.8232 (tpt)
REVERT: B  301 MET cc_start: 0.9124 (mmp) cc_final: 0.8743 (mmp)
REVERT: B  350 ASN cc_start: 0.8630 (p0) cc_final: 0.8355 (p0)
REVERT: B  425 MET cc_start: 0.9488 (ppp) cc_final: 0.9110 (ppp)
REVERT: B  432 TYR cc_start: 0.8677 (m-80) cc_final: 0.8166 (t80)
  outliers start: 19
  outliers final: 16
  residues processed: 124
  average time/residue: 0.0580
  time to fit residues: 10.9211
Evaluate side-chains
  122 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  326 LYS
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  357 ASP
Chi-restraints excluded: chain B residue  377 PHE
Chi-restraints excluded: chain B residue  413 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 80 optimal weight:    0.0770
   chunk 28 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 37 optimal weight:   10.0000
   chunk 74 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    1.6144

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.089335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.062603 restraints weight = 23209.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.065267 restraints weight = 15615.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.067251 restraints weight = 11772.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.068689 restraints weight = 9574.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.069697 restraints weight = 8240.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6966  Z= 0.130
  Angle     :  0.739  13.314   9462  Z= 0.351
  Chirality :  0.048   0.223   1034
  Planarity :  0.004   0.052   1233
  Dihedral  : 10.582 173.534    959
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 16.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 22.51 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.29), residues: 854
  helix:  0.69 (0.27), residues: 386
  sheet: -0.75 (0.47), residues: 130
  loop : -0.09 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 322 
 TYR   0.047   0.001   TYR A 432 
 PHE   0.019   0.001   PHE A 255 
 TRP   0.019   0.002   TRP B  21 
 HIS   0.006   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6966)
  covalent geometry    : angle       0.73871 ( 9462)
  hydrogen bonds       : bond        0.03672 (  307)
  hydrogen bonds       : angle       4.97001 (  888)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1218.23 seconds
wall clock time: 21 minutes 56.04 seconds (1316.04 seconds total)