Starting phenix.real_space_refine
on Tue Mar  3 13:51:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y58_33612/03_2026/7y58_33612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y58_33612/03_2026/7y58_33612.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y58_33612/03_2026/7y58_33612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y58_33612/03_2026/7y58_33612.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y58_33612/03_2026/7y58_33612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y58_33612/03_2026/7y58_33612.cif"
  }
  resolution = 3.8
  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=   0.023
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: 4
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    3639      2.51       5
     N     913      2.21       5
     O    1019      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5606
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 510, 3833
          Classifications: {'peptide': 510}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 489}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "B"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 902
          Classifications: {'peptide': 118}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 115}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 871
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 871
          Classifications: {'peptide': 115}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 111}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 1.51, per 1000 atoms: 0.27
  Number of scatterers: 5606
  At special positions: 0
  Unit cell: (72.297, 93.072, 116.34, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      35     16.00
     O    1019      8.00
     N     913      7.00
     C    3639      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  34 " - pdb=" SG  CYS B 106 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  34 " - pdb=" SG  CYS C 106 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 287.8 milliseconds
  

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1360

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 5 sheets defined
      59.2% alpha, 7.4% 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 16 through 32
      removed outlier: 3.905A  pdb=" N   ALA A  20 " --> pdb=" O   LYS A  16 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   SER A  27 " --> pdb=" O   VAL A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 41
    Processing helix  chain 'A' and resid 41 through 49
    Processing helix  chain 'A' and resid 53 through 70
      removed outlier: 3.673A  pdb=" N   LEU A  57 " --> pdb=" O   GLY A  53 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   VAL A  60 " --> pdb=" O   GLN A  56 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   TYR A  63 " --> pdb=" O   ILE A  59 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   SER A  64 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 82
      removed outlier: 3.609A  pdb=" N   SER A  75 " --> pdb=" O   ILE A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 101
      removed outlier: 3.712A  pdb=" N   ILE A 101 " --> pdb=" O   VAL A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 123
      removed outlier: 4.054A  pdb=" N   ILE A 111 " --> pdb=" O   ALA A 107 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LEU A 123 " --> pdb=" O   ILE A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 136
      removed outlier: 3.524A  pdb=" N   SER A 130 " --> pdb=" O   PRO A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 170
      removed outlier: 3.747A  pdb=" N   THR A 144 " --> pdb=" O   LYS A 140 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   VAL A 148 " --> pdb=" O   THR A 144 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TRP A 149 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   ALA A 157 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   VAL A 158 " --> pdb=" O   SER A 154 " (cutoff:3.500A)
      Proline residue:  A 161  - end of helix
      removed outlier: 3.817A  pdb=" N   GLN A 170 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 179
      removed outlier: 3.641A  pdb=" N   LEU A 178 " --> pdb=" O   HIS A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 192
      removed outlier: 4.026A  pdb=" N   PHE A 183 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE A 186 " --> pdb=" O   PRO A 182 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ALA A 187 " --> pdb=" O   PHE A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 234
    Processing helix  chain 'A' and resid 238 through 261
      removed outlier: 4.020A  pdb=" N   SER A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 272
    Processing helix  chain 'A' and resid 273 through 304
      removed outlier: 3.583A  pdb=" N   GLY A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   PHE A 284 " --> pdb=" O   THR A 280 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   MET A 285 " --> pdb=" O   ILE A 281 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ALA A 289 " --> pdb=" O   MET A 285 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   MET A 290 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   LEU A 295 " --> pdb=" O   ALA A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 315
    Processing helix  chain 'A' and resid 316 through 338
      removed outlier: 3.990A  pdb=" N   ALA A 320 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      Proline residue:  A 328  - end of helix
      Proline residue:  A 331  - end of helix
      removed outlier: 3.584A  pdb=" N   ARG A 336 " --> pdb=" O   GLY A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 360
      removed outlier: 3.566A  pdb=" N   VAL A 342 " --> pdb=" O   GLY A 338 " (cutoff:3.500A)
      Proline residue:  A 344  - end of helix
      removed outlier: 3.672A  pdb=" N   ILE A 347 " --> pdb=" O   LEU A 343 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   MET A 357 " --> pdb=" O   GLY A 353 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   TYR A 358 " --> pdb=" O   MET A 354 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   PHE A 360 " --> pdb=" O   ILE A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 391
      removed outlier: 4.283A  pdb=" N   LEU A 375 " --> pdb=" O   LEU A 371 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   LEU A 383 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 4.865A  pdb=" N   ALA A 384 " --> pdb=" O   MET A 380 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   VAL A 385 " --> pdb=" O   ALA A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 434
      removed outlier: 4.158A  pdb=" N   ALA A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   VAL A 405 " --> pdb=" O   ASN A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 439
      removed outlier: 3.873A  pdb=" N   SER A 439 " --> pdb=" O   SER A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 454
    Processing helix  chain 'A' and resid 454 through 466
    Processing helix  chain 'A' and resid 468 through 504
      removed outlier: 3.684A  pdb=" N   ASN A 472 " --> pdb=" O   LYS A 468 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 8
      removed outlier: 3.886A  pdb=" N   GLN B   6 " --> pdb=" O   ALA B  24 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   THR B  78 " --> pdb=" O   ASP B  73 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ASP B  73 " --> pdb=" O   THR B  78 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 48
      removed outlier: 3.607A  pdb=" N   TYR B 114 " --> pdb=" O   GLY B  98 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 52
    Processing sheet with id=AA4, first strand: chain 'C' and resid 22 through 24
      removed outlier: 3.814A  pdb=" N   CYS C  23 " --> pdb=" O   VAL C  81 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 59 through 62
      removed outlier: 4.016A  pdb=" N   ALA C  50 " --> pdb=" O   TRP C  37 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   CYS C  34 " --> pdb=" O   ASP C 101 " (cutoff:3.500A)

    325 hydrogen bonds defined for protein.
    957 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: 0.92

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 885
        1.29 -     1.42: 1477
        1.42 -     1.55: 3296
        1.55 -     1.68: 0
        1.68 -     1.82: 62
  Bond restraints: 5720
  Sorted by residual:
  bond pdb=" CA  ILE A 151 "
       pdb=" C   ILE A 151 "
    ideal  model  delta    sigma   weight residual
    1.524  1.435  0.089 1.22e-02 6.72e+03 5.26e+01
  bond pdb=" C   ILE A 151 "
       pdb=" O   ILE A 151 "
    ideal  model  delta    sigma   weight residual
    1.237  1.160  0.077 1.13e-02 7.83e+03 4.62e+01
  bond pdb=" CA  ILE A 151 "
       pdb=" CB  ILE A 151 "
    ideal  model  delta    sigma   weight residual
    1.540  1.471  0.068 1.17e-02 7.31e+03 3.39e+01
  bond pdb=" CA  ILE A 155 "
       pdb=" C   ILE A 155 "
    ideal  model  delta    sigma   weight residual
    1.521  1.444  0.077 1.45e-02 4.76e+03 2.78e+01
  bond pdb=" CA  ILE A 155 "
       pdb=" CB  ILE A 155 "
    ideal  model  delta    sigma   weight residual
    1.545  1.476  0.069 1.45e-02 4.76e+03 2.23e+01
  ... (remaining 5715 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.04: 7694
        4.04 -     8.07: 55
        8.07 -    12.11: 6
       12.11 -    16.15: 0
       16.15 -    20.18: 1
  Bond angle restraints: 7756
  Sorted by residual:
  angle pdb=" C   ARG C  32 "
        pdb=" CA  ARG C  32 "
        pdb=" CB  ARG C  32 "
      ideal   model   delta    sigma   weight residual
     110.42  130.60  -20.18 1.99e+00 2.53e-01 1.03e+02
  angle pdb=" N   ILE A 155 "
        pdb=" CA  ILE A 155 "
        pdb=" C   ILE A 155 "
      ideal   model   delta    sigma   weight residual
     112.76  103.59    9.17 1.27e+00 6.20e-01 5.21e+01
  angle pdb=" C   LEU C  19 "
        pdb=" N   ARG C  20 "
        pdb=" CA  ARG C  20 "
      ideal   model   delta    sigma   weight residual
     121.87  110.57   11.30 1.64e+00 3.72e-01 4.75e+01
  angle pdb=" N   ILE A 151 "
        pdb=" CA  ILE A 151 "
        pdb=" C   ILE A 151 "
      ideal   model   delta    sigma   weight residual
     110.42  104.18    6.24 9.60e-01 1.09e+00 4.23e+01
  angle pdb=" C   GLN C  40 "
        pdb=" CA  GLN C  40 "
        pdb=" CB  GLN C  40 "
      ideal   model   delta    sigma   weight residual
     109.68   98.56   11.12 1.98e+00 2.55e-01 3.15e+01
  ... (remaining 7751 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 2907
       17.94 -    35.88: 342
       35.88 -    53.82: 104
       53.82 -    71.76: 19
       71.76 -    89.70: 9
  Dihedral angle restraints: 3381
    sinusoidal: 1259
      harmonic: 2122
  Sorted by residual:
  dihedral pdb=" CD  ARG C  32 "
           pdb=" NE  ARG C  32 "
           pdb=" CZ  ARG C  32 "
           pdb=" NH1 ARG C  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   71.16  -71.16     1      1.00e+01 1.00e-02 6.50e+01
  dihedral pdb=" C   ARG C  32 "
           pdb=" N   ARG C  32 "
           pdb=" CA  ARG C  32 "
           pdb=" CB  ARG C  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.39   16.79     0      2.50e+00 1.60e-01 4.51e+01
  dihedral pdb=" CB  CYS C  34 "
           pdb=" SG  CYS C  34 "
           pdb=" SG  CYS C 106 "
           pdb=" CB  CYS C 106 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  148.32  -55.32     1      1.00e+01 1.00e-02 4.14e+01
  ... (remaining 3378 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 873
       0.098 -    0.197: 31
       0.197 -    0.295: 2
       0.295 -    0.393: 3
       0.393 -    0.491: 1
  Chirality restraints: 910
  Sorted by residual:
  chirality pdb=" CA  ARG C  32 "
            pdb=" N   ARG C  32 "
            pdb=" C   ARG C  32 "
            pdb=" CB  ARG C  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 6.03e+00
  chirality pdb=" CA  GLU B  89 "
            pdb=" N   GLU B  89 "
            pdb=" C   GLU B  89 "
            pdb=" CB  GLU B  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.87   -0.36 2.00e-01 2.50e+01 3.28e+00
  chirality pdb=" CA  ILE C  41 "
            pdb=" N   ILE C  41 "
            pdb=" C   ILE C  41 "
            pdb=" CB  ILE C  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.74   -0.31 2.00e-01 2.50e+01 2.36e+00
  ... (remaining 907 not shown)

  Planarity restraints: 959
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  32 "    1.028 9.50e-02 1.11e+02   4.61e-01 1.28e+02
        pdb=" NE  ARG C  32 "   -0.063 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  32 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  32 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  32 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  46 "   -0.672 9.50e-02 1.11e+02   3.01e-01 5.52e+01
        pdb=" NE  ARG C  46 "    0.040 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  46 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  46 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  46 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C  39 "   -0.017 2.00e-02 2.50e+03   3.28e-02 1.08e+01
        pdb=" C   ARG C  39 "    0.057 2.00e-02 2.50e+03
        pdb=" O   ARG C  39 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLN C  40 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 956 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 74
        2.63 -     3.20: 5413
        3.20 -     3.77: 8635
        3.77 -     4.33: 10937
        4.33 -     4.90: 18186
  Nonbonded interactions: 43245
  Sorted by model distance:
  nonbonded pdb=" O   ARG C  32 "
            pdb=" CE1 TYR C  53 "
     model   vdw
     2.068 3.340
  nonbonded pdb=" O   TYR A 315 "
            pdb=" OH  TYR A 366 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OE2 GLU A 473 "
            pdb=" N   GLY B  55 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OD1 ASP B 111 "
            pdb=" N   PHE B 112 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" NE  ARG C  69 "
            pdb=" OG  SER C  87 "
     model   vdw
     2.279 3.120
  ... (remaining 43240 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:             2.920
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.190
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
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      :  0.005   0.089   5724  Z= 0.322
  Angle     :  0.884  20.185   7764  Z= 0.498
  Chirality :  0.050   0.491    910
  Planarity :  0.018   0.461    959
  Dihedral  : 18.111  89.698   2009
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.99 %
    Favored  : 90.01 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 24.87 %
    Favored  : 71.74 %
  Cbeta Deviations :  0.44 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.32), residues: 731
  helix:  0.64 (0.27), residues: 399
  sheet: -2.12 (0.55), residues: 83
  loop : -3.19 (0.35), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  67 
 TYR   0.018   0.002   TYR A 410 
 PHE   0.013   0.001   PHE A 288 
 TRP   0.015   0.001   TRP A 300 
 HIS   0.002   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 5720)
  covalent geometry    : angle       0.88414 ( 7756)
  SS BOND              : bond        0.00136 (    4)
  SS BOND              : angle       0.80662 (    8)
  hydrogen bonds       : bond        0.16589 (  325)
  hydrogen bonds       : angle       6.15983 (  957)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A  233 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7638 (tp30)
REVERT: A  380 MET cc_start: 0.7942 (tpp) cc_final: 0.7530 (tpp)
REVERT: A  393 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7958 (mt-10)
REVERT: A  409 MET cc_start: 0.7100 (mmp) cc_final: 0.6704 (mmm)
REVERT: C   73 SER cc_start: 0.8697 (t) cc_final: 0.8468 (p)
REVERT: C   95 MET cc_start: 0.7206 (tpt) cc_final: 0.6510 (ttp)
REVERT: C   97 TYR cc_start: 0.7300 (m-80) cc_final: 0.6798 (m-80)
  outliers start: 20
  outliers final: 7
  residues processed: 165
  average time/residue: 0.0668
  time to fit residues: 14.7276
Evaluate side-chains
  123 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue   60 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0770
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0870
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.4716

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

Flipped N/Q/H residues before XYZ refinement:
A 302 GLN
** A 401 ASN ** 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 = 0.3954 r_free = 0.3954 target = 0.172024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.137213 restraints weight = 7796.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.141706 restraints weight = 4350.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.144734 restraints weight = 2959.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.146548 restraints weight = 2281.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.147977 restraints weight = 1934.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5724  Z= 0.146
  Angle     :  0.675   7.238   7764  Z= 0.341
  Chirality :  0.040   0.129    910
  Planarity :  0.005   0.065    959
  Dihedral  :  6.484  54.173    801
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.80 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 23.35 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.32), residues: 731
  helix:  1.12 (0.26), residues: 414
  sheet: -1.60 (0.59), residues: 84
  loop : -2.95 (0.38), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  32 
 TYR   0.024   0.002   TYR B  95 
 PHE   0.014   0.001   PHE A  94 
 TRP   0.016   0.001   TRP A  81 
 HIS   0.004   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 5720)
  covalent geometry    : angle       0.67531 ( 7756)
  SS BOND              : bond        0.00135 (    4)
  SS BOND              : angle       0.63995 (    8)
  hydrogen bonds       : bond        0.05303 (  325)
  hydrogen bonds       : angle       4.62909 (  957)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 119
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A   81 TRP cc_start: 0.7745 (t-100) cc_final: 0.7412 (t60)
REVERT: A   99 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6881 (tt)
REVERT: A  183 PHE cc_start: 0.6589 (OUTLIER) cc_final: 0.6078 (t80)
REVERT: A  233 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7610 (tp30)
REVERT: A  285 MET cc_start: 0.7478 (mmt) cc_final: 0.7206 (mmp)
REVERT: A  288 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.6840 (t80)
REVERT: A  409 MET cc_start: 0.7938 (mmp) cc_final: 0.7416 (mmm)
REVERT: A  430 ARG cc_start: 0.8351 (ttp-110) cc_final: 0.8039 (ttm-80)
REVERT: C   73 SER cc_start: 0.8520 (t) cc_final: 0.8214 (p)
REVERT: C   95 MET cc_start: 0.7530 (tpt) cc_final: 0.6607 (ttt)
REVERT: C   97 TYR cc_start: 0.7323 (m-80) cc_final: 0.6450 (m-80)
  outliers start: 28
  outliers final: 12
  residues processed: 135
  average time/residue: 0.0601
  time to fit residues: 11.3174
Evaluate side-chains
  128 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue   60 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 65 optimal weight:    6.9990
   chunk 34 optimal weight:    0.1980
   chunk 57 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.160676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.125958 restraints weight = 7754.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.130238 restraints weight = 4363.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.133113 restraints weight = 2978.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.135075 restraints weight = 2303.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.136033 restraints weight = 1933.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   5724  Z= 0.213
  Angle     :  0.714   7.235   7764  Z= 0.366
  Chirality :  0.042   0.151    910
  Planarity :  0.005   0.052    959
  Dihedral  :  6.195  53.158    798
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.34 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  6.77 %
    Allowed  : 23.69 %
    Favored  : 69.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.32), residues: 731
  helix:  0.90 (0.26), residues: 413
  sheet: -1.47 (0.58), residues: 88
  loop : -3.15 (0.38), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 114 
 TYR   0.018   0.002   TYR B  95 
 PHE   0.018   0.002   PHE A 288 
 TRP   0.021   0.001   TRP A  81 
 HIS   0.003   0.002   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 5720)
  covalent geometry    : angle       0.71411 ( 7756)
  SS BOND              : bond        0.00548 (    4)
  SS BOND              : angle       0.45874 (    8)
  hydrogen bonds       : bond        0.05936 (  325)
  hydrogen bonds       : angle       4.61134 (  957)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 114
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A   81 TRP cc_start: 0.7834 (t-100) cc_final: 0.7495 (t60)
REVERT: A   99 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6771 (tt)
REVERT: A  183 PHE cc_start: 0.6809 (OUTLIER) cc_final: 0.5997 (t80)
REVERT: A  233 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7623 (tp30)
REVERT: A  285 MET cc_start: 0.7835 (mmt) cc_final: 0.7475 (mmp)
REVERT: A  288 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.7059 (t80)
REVERT: A  409 MET cc_start: 0.7901 (mmp) cc_final: 0.7346 (mmm)
REVERT: A  430 ARG cc_start: 0.8377 (ttp-110) cc_final: 0.7992 (ttm-80)
REVERT: A  434 ASP cc_start: 0.8081 (t0) cc_final: 0.7759 (t0)
REVERT: B   29 ARG cc_start: 0.8622 (mtp85) cc_final: 0.8325 (mtm180)
REVERT: C   73 SER cc_start: 0.8414 (t) cc_final: 0.8144 (p)
REVERT: C   95 MET cc_start: 0.7472 (tpt) cc_final: 0.6639 (ttt)
REVERT: C   97 TYR cc_start: 0.7415 (m-80) cc_final: 0.6443 (m-80)
  outliers start: 40
  outliers final: 21
  residues processed: 143
  average time/residue: 0.0598
  time to fit residues: 11.8643
Evaluate side-chains
  132 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 MET
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue   60 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 16 optimal weight:    0.2980
   chunk 62 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 71 optimal weight:    5.9990
   chunk 69 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.166050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.131341 restraints weight = 7824.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.135790 restraints weight = 4397.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.138731 restraints weight = 2987.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.140807 restraints weight = 2302.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.141974 restraints weight = 1926.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5724  Z= 0.151
  Angle     :  0.649   6.824   7764  Z= 0.329
  Chirality :  0.040   0.169    910
  Planarity :  0.005   0.052    959
  Dihedral  :  5.980  52.791    796
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.52 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 24.70 %
    Favored  : 70.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.32), residues: 731
  helix:  1.19 (0.26), residues: 400
  sheet: -0.94 (0.62), residues: 73
  loop : -2.91 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 430 
 TYR   0.018   0.002   TYR B  95 
 PHE   0.012   0.001   PHE A 288 
 TRP   0.015   0.001   TRP A  81 
 HIS   0.003   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 5720)
  covalent geometry    : angle       0.64872 ( 7756)
  SS BOND              : bond        0.00175 (    4)
  SS BOND              : angle       0.44344 (    8)
  hydrogen bonds       : bond        0.05097 (  325)
  hydrogen bonds       : angle       4.35430 (  957)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.7763 (mptt) cc_final: 0.7286 (mtmm)
REVERT: A   40 MET cc_start: 0.7346 (ttm) cc_final: 0.7068 (ttm)
REVERT: A   81 TRP cc_start: 0.7712 (t-100) cc_final: 0.7355 (t60)
REVERT: A   99 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6723 (tt)
REVERT: A  183 PHE cc_start: 0.6762 (OUTLIER) cc_final: 0.6055 (t80)
REVERT: A  233 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7651 (tp30)
REVERT: A  285 MET cc_start: 0.7765 (mmt) cc_final: 0.7438 (mmp)
REVERT: A  288 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6875 (t80)
REVERT: A  358 TYR cc_start: 0.8616 (t80) cc_final: 0.8411 (t80)
REVERT: A  409 MET cc_start: 0.7866 (mmp) cc_final: 0.7368 (mmm)
REVERT: A  434 ASP cc_start: 0.7908 (t0) cc_final: 0.7673 (t0)
REVERT: C   73 SER cc_start: 0.8452 (t) cc_final: 0.8175 (p)
REVERT: C   95 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6321 (ttp)
REVERT: C   97 TYR cc_start: 0.7508 (m-80) cc_final: 0.6999 (m-80)
  outliers start: 31
  outliers final: 18
  residues processed: 134
  average time/residue: 0.0627
  time to fit residues: 11.5562
Evaluate side-chains
  132 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   95 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 55 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
B 120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.161603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.126192 restraints weight = 7982.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.130397 restraints weight = 4520.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.133338 restraints weight = 3112.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.135235 restraints weight = 2410.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.136383 restraints weight = 2032.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062   5724  Z= 0.248
  Angle     :  0.726   7.175   7764  Z= 0.376
  Chirality :  0.043   0.212    910
  Planarity :  0.005   0.054    959
  Dihedral  :  6.283  53.186    796
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.89 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  7.45 %
    Allowed  : 23.52 %
    Favored  : 69.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.89 (0.32), residues: 731
  helix:  0.84 (0.26), residues: 408
  sheet: -1.23 (0.60), residues: 80
  loop : -2.91 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 430 
 TYR   0.017   0.002   TYR A 410 
 PHE   0.021   0.002   PHE A 288 
 TRP   0.021   0.002   TRP A  81 
 HIS   0.003   0.002   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 ( 5720)
  covalent geometry    : angle       0.72628 ( 7756)
  SS BOND              : bond        0.00320 (    4)
  SS BOND              : angle       0.35780 (    8)
  hydrogen bonds       : bond        0.05958 (  325)
  hydrogen bonds       : angle       4.60548 (  957)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 113
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 LYS cc_start: 0.7777 (mptt) cc_final: 0.7307 (mtmm)
REVERT: A   99 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6798 (tt)
REVERT: A  183 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6226 (t80)
REVERT: A  233 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7634 (tp30)
REVERT: A  285 MET cc_start: 0.7903 (mmt) cc_final: 0.7543 (mmp)
REVERT: A  288 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.7116 (t80)
REVERT: A  321 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8258 (mm)
REVERT: A  380 MET cc_start: 0.7392 (tpp) cc_final: 0.6734 (tpp)
REVERT: A  409 MET cc_start: 0.7855 (mmp) cc_final: 0.7391 (mmm)
REVERT: A  434 ASP cc_start: 0.7979 (t0) cc_final: 0.7733 (t0)
REVERT: C   73 SER cc_start: 0.8384 (t) cc_final: 0.8168 (p)
REVERT: C   95 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6435 (ttp)
REVERT: C   97 TYR cc_start: 0.7626 (m-80) cc_final: 0.7085 (m-80)
  outliers start: 44
  outliers final: 31
  residues processed: 142
  average time/residue: 0.0645
  time to fit residues: 12.5622
Evaluate side-chains
  145 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 109
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  416 PHE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   95 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 52 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 120 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.163286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.129494 restraints weight = 7655.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.133749 restraints weight = 4169.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.136695 restraints weight = 2785.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.138535 restraints weight = 2117.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.139913 restraints weight = 1770.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5724  Z= 0.158
  Angle     :  0.658   6.745   7764  Z= 0.332
  Chirality :  0.040   0.171    910
  Planarity :  0.005   0.052    959
  Dihedral  :  6.106  52.829    796
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.80 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 26.40 %
    Favored  : 67.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.32), residues: 731
  helix:  1.06 (0.26), residues: 406
  sheet: -1.17 (0.67), residues: 61
  loop : -2.82 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  32 
 TYR   0.017   0.002   TYR B  95 
 PHE   0.013   0.001   PHE A 284 
 TRP   0.015   0.001   TRP A  81 
 HIS   0.002   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 5720)
  covalent geometry    : angle       0.65842 ( 7756)
  SS BOND              : bond        0.00135 (    4)
  SS BOND              : angle       0.39312 (    8)
  hydrogen bonds       : bond        0.05146 (  325)
  hydrogen bonds       : angle       4.40103 (  957)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 112
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.7743 (mptt) cc_final: 0.7227 (mtmm)
REVERT: A   81 TRP cc_start: 0.7838 (t-100) cc_final: 0.7291 (t60)
REVERT: A   99 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6734 (tt)
REVERT: A  183 PHE cc_start: 0.6916 (OUTLIER) cc_final: 0.6137 (t80)
REVERT: A  233 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7649 (tp30)
REVERT: A  285 MET cc_start: 0.7753 (mmt) cc_final: 0.7413 (mmp)
REVERT: A  288 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6909 (t80)
REVERT: A  321 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8114 (mm)
REVERT: A  380 MET cc_start: 0.7351 (tpp) cc_final: 0.6989 (tpp)
REVERT: A  409 MET cc_start: 0.7733 (mmp) cc_final: 0.7287 (mmm)
REVERT: A  434 ASP cc_start: 0.7944 (t0) cc_final: 0.7698 (t0)
REVERT: B   29 ARG cc_start: 0.8465 (mtp85) cc_final: 0.8170 (mtm180)
REVERT: C   73 SER cc_start: 0.8504 (t) cc_final: 0.8228 (p)
REVERT: C   95 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6344 (ttp)
REVERT: C   97 TYR cc_start: 0.7600 (m-80) cc_final: 0.7059 (m-80)
  outliers start: 34
  outliers final: 23
  residues processed: 134
  average time/residue: 0.0629
  time to fit residues: 11.6484
Evaluate side-chains
  135 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   95 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 55 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 120 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.161499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.127272 restraints weight = 7711.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.131576 restraints weight = 4208.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.134537 restraints weight = 2817.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.136454 restraints weight = 2141.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.137615 restraints weight = 1787.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5724  Z= 0.162
  Angle     :  0.656   6.784   7764  Z= 0.331
  Chirality :  0.041   0.159    910
  Planarity :  0.005   0.052    959
  Dihedral  :  6.093  53.906    796
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  8.21 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 27.75 %
    Favored  : 66.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.32), residues: 731
  helix:  1.09 (0.26), residues: 406
  sheet: -1.42 (0.57), residues: 85
  loop : -2.74 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  32 
 TYR   0.016   0.002   TYR B  95 
 PHE   0.013   0.001   PHE A 284 
 TRP   0.032   0.002   TRP A 173 
 HIS   0.003   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 5720)
  covalent geometry    : angle       0.65589 ( 7756)
  SS BOND              : bond        0.00149 (    4)
  SS BOND              : angle       0.38747 (    8)
  hydrogen bonds       : bond        0.05108 (  325)
  hydrogen bonds       : angle       4.36235 (  957)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 113
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.7748 (mptt) cc_final: 0.7224 (mtmm)
REVERT: A   81 TRP cc_start: 0.7837 (t-100) cc_final: 0.7325 (t60)
REVERT: A   99 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6752 (tt)
REVERT: A  183 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.6145 (t80)
REVERT: A  233 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7659 (tp30)
REVERT: A  285 MET cc_start: 0.7756 (mmt) cc_final: 0.7413 (mmp)
REVERT: A  288 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6920 (t80)
REVERT: A  321 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8133 (mm)
REVERT: A  337 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7960 (m-10)
REVERT: A  358 TYR cc_start: 0.8710 (t80) cc_final: 0.8466 (t80)
REVERT: A  380 MET cc_start: 0.7417 (tpp) cc_final: 0.6891 (tpp)
REVERT: A  409 MET cc_start: 0.7756 (mmp) cc_final: 0.7300 (mmm)
REVERT: A  434 ASP cc_start: 0.7891 (t0) cc_final: 0.7650 (t0)
REVERT: C   73 SER cc_start: 0.8510 (t) cc_final: 0.8245 (p)
REVERT: C   95 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6333 (ttp)
REVERT: C   97 TYR cc_start: 0.7585 (m-80) cc_final: 0.7128 (m-80)
  outliers start: 34
  outliers final: 25
  residues processed: 136
  average time/residue: 0.0590
  time to fit residues: 11.1793
Evaluate side-chains
  137 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 106
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  337 PHE
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  382 SER
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   95 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 69 optimal weight:    8.9990
   chunk 19 optimal weight:    0.0470
   chunk 65 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0370
   chunk 56 optimal weight:    0.0970
   chunk 51 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.2954

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.170271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.136351 restraints weight = 7655.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.140702 restraints weight = 4213.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.143694 restraints weight = 2826.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.145456 restraints weight = 2158.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.146784 restraints weight = 1810.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.3413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5724  Z= 0.121
  Angle     :  0.625   7.173   7764  Z= 0.311
  Chirality :  0.040   0.144    910
  Planarity :  0.004   0.046    959
  Dihedral  :  5.919  58.828    796
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  7.25 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 29.44 %
    Favored  : 66.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.29 (0.33), residues: 731
  helix:  1.34 (0.26), residues: 406
  sheet: -1.44 (0.57), residues: 85
  loop : -2.46 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 109 
 TYR   0.015   0.001   TYR B  95 
 PHE   0.014   0.001   PHE A 284 
 TRP   0.015   0.001   TRP A 173 
 HIS   0.002   0.000   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5720)
  covalent geometry    : angle       0.62529 ( 7756)
  SS BOND              : bond        0.00076 (    4)
  SS BOND              : angle       0.50599 (    8)
  hydrogen bonds       : bond        0.04425 (  325)
  hydrogen bonds       : angle       4.18024 (  957)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.7757 (mptt) cc_final: 0.7228 (mtmm)
REVERT: A   81 TRP cc_start: 0.7770 (t-100) cc_final: 0.7270 (t60)
REVERT: A   99 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6717 (tt)
REVERT: A  183 PHE cc_start: 0.6736 (OUTLIER) cc_final: 0.5967 (t80)
REVERT: A  233 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7654 (tp30)
REVERT: A  288 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6808 (t80)
REVERT: A  358 TYR cc_start: 0.8586 (t80) cc_final: 0.8342 (t80)
REVERT: A  380 MET cc_start: 0.7280 (tpp) cc_final: 0.6767 (tpp)
REVERT: A  409 MET cc_start: 0.7785 (mmp) cc_final: 0.7298 (mmm)
REVERT: A  434 ASP cc_start: 0.7910 (t0) cc_final: 0.7696 (t0)
REVERT: B   29 ARG cc_start: 0.8401 (mtp85) cc_final: 0.8114 (mtm180)
REVERT: C   73 SER cc_start: 0.8537 (t) cc_final: 0.8291 (p)
REVERT: C   95 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6279 (ttp)
REVERT: C   97 TYR cc_start: 0.7559 (m-80) cc_final: 0.6872 (m-80)
  outliers start: 25
  outliers final: 18
  residues processed: 127
  average time/residue: 0.0652
  time to fit residues: 11.2394
Evaluate side-chains
  135 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   95 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 120 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.165592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.130065 restraints weight = 7853.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.134376 restraints weight = 4403.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.137219 restraints weight = 3010.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.139148 restraints weight = 2337.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.140301 restraints weight = 1975.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.3445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5724  Z= 0.177
  Angle     :  0.679   7.742   7764  Z= 0.341
  Chirality :  0.041   0.143    910
  Planarity :  0.005   0.050    959
  Dihedral  :  6.010  54.950    796
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  8.34 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 29.27 %
    Favored  : 65.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.32), residues: 731
  helix:  1.19 (0.26), residues: 406
  sheet: -1.65 (0.55), residues: 89
  loop : -2.66 (0.41), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 109 
 TYR   0.017   0.002   TYR A 410 
 PHE   0.013   0.002   PHE A 288 
 TRP   0.015   0.001   TRP A  81 
 HIS   0.002   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 5720)
  covalent geometry    : angle       0.67552 ( 7756)
  SS BOND              : bond        0.00145 (    4)
  SS BOND              : angle       2.36785 (    8)
  hydrogen bonds       : bond        0.05124 (  325)
  hydrogen bonds       : angle       4.29657 (  957)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 111
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.7777 (mptt) cc_final: 0.7251 (mtmm)
REVERT: A   81 TRP cc_start: 0.7861 (t-100) cc_final: 0.7365 (t60)
REVERT: A   99 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6739 (tt)
REVERT: A  183 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.6123 (t80)
REVERT: A  233 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7665 (tp30)
REVERT: A  288 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.6902 (t80)
REVERT: A  380 MET cc_start: 0.7372 (tpp) cc_final: 0.7010 (tpp)
REVERT: A  409 MET cc_start: 0.7802 (mmp) cc_final: 0.7332 (mmm)
REVERT: A  434 ASP cc_start: 0.7892 (t0) cc_final: 0.7681 (t0)
REVERT: B   29 ARG cc_start: 0.8477 (mtp85) cc_final: 0.8201 (mtm180)
REVERT: C   73 SER cc_start: 0.8462 (t) cc_final: 0.8247 (p)
REVERT: C   95 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6332 (ttp)
REVERT: C   97 TYR cc_start: 0.7521 (m-80) cc_final: 0.6835 (m-80)
  outliers start: 33
  outliers final: 23
  residues processed: 131
  average time/residue: 0.0664
  time to fit residues: 11.7462
Evaluate side-chains
  138 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  382 SER
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   41 ILE
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   95 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 63 optimal weight:    9.9990
   chunk 46 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0270
   overall best weight:    0.6038

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.167794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.133636 restraints weight = 7821.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.138011 restraints weight = 4244.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.140998 restraints weight = 2827.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.142905 restraints weight = 2145.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.144205 restraints weight = 1789.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.3540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5724  Z= 0.139
  Angle     :  0.649   7.406   7764  Z= 0.323
  Chirality :  0.040   0.140    910
  Planarity :  0.004   0.048    959
  Dihedral  :  5.857  53.821    796
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  7.66 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 30.96 %
    Favored  : 64.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.32), residues: 731
  helix:  1.34 (0.26), residues: 400
  sheet: -1.40 (0.57), residues: 84
  loop : -2.53 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 109 
 TYR   0.015   0.001   TYR A 429 
 PHE   0.014   0.001   PHE A 284 
 TRP   0.012   0.001   TRP A  81 
 HIS   0.002   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 5720)
  covalent geometry    : angle       0.64642 ( 7756)
  SS BOND              : bond        0.00194 (    4)
  SS BOND              : angle       1.99826 (    8)
  hydrogen bonds       : bond        0.04768 (  325)
  hydrogen bonds       : angle       4.21711 (  957)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.7758 (mptt) cc_final: 0.7235 (mtmm)
REVERT: A   81 TRP cc_start: 0.7796 (t-100) cc_final: 0.7329 (t60)
REVERT: A   99 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6771 (tt)
REVERT: A  183 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.6007 (t80)
REVERT: A  233 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7567 (tm-30)
REVERT: A  288 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6834 (t80)
REVERT: A  321 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8148 (mm)
REVERT: A  380 MET cc_start: 0.7285 (tpp) cc_final: 0.6749 (tpp)
REVERT: A  409 MET cc_start: 0.7744 (mmp) cc_final: 0.7288 (mmm)
REVERT: C   73 SER cc_start: 0.8494 (t) cc_final: 0.8249 (p)
REVERT: C   95 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6416 (ttp)
  outliers start: 25
  outliers final: 17
  residues processed: 129
  average time/residue: 0.0664
  time to fit residues: 11.6407
Evaluate side-chains
  136 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  208 TRP
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  288 PHE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  382 SER
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain B residue   34 CYS
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   60 ILE
Chi-restraints excluded: chain C residue   95 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 120 GLN

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 = 0.162874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.128372 restraints weight = 7773.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.132651 restraints weight = 4344.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.135494 restraints weight = 2939.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.137413 restraints weight = 2264.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.138614 restraints weight = 1904.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5724  Z= 0.160
  Angle     :  0.671   7.897   7764  Z= 0.336
  Chirality :  0.041   0.144    910
  Planarity :  0.005   0.049    959
  Dihedral  :  5.561  53.636    792
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  8.62 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 30.96 %
    Favored  : 64.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.41 (0.32), residues: 731
  helix:  1.28 (0.26), residues: 400
  sheet: -1.40 (0.57), residues: 85
  loop : -2.51 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 109 
 TYR   0.016   0.001   TYR A 410 
 PHE   0.013   0.001   PHE A 284 
 TRP   0.013   0.001   TRP A  81 
 HIS   0.002   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 5720)
  covalent geometry    : angle       0.66901 ( 7756)
  SS BOND              : bond        0.00176 (    4)
  SS BOND              : angle       1.60871 (    8)
  hydrogen bonds       : bond        0.04958 (  325)
  hydrogen bonds       : angle       4.26552 (  957)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1047.49 seconds
wall clock time: 18 minutes 43.63 seconds (1123.63 seconds total)