Starting phenix.real_space_refine
on Sat May  2 13:20:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/11oq_75891/05_2026/11oq_75891.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/11oq_75891/05_2026/11oq_75891.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/11oq_75891/05_2026/11oq_75891.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/11oq_75891/05_2026/11oq_75891.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/11oq_75891/05_2026/11oq_75891.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/11oq_75891/05_2026/11oq_75891.map"
  }
  resolution = 3.2
  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=   0.009
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      22      5.16       5
     C    3579      2.51       5
     N     965      2.21       5
     O    1107      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5673
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1476
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1476
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 10, 'TRANS': 171}
    Chain: "H"
      Number of atoms: 1620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1620
          Classifications: {'peptide': 217}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 203}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
    Chain: "K"
      Number of atoms: 928
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 120, 925
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
      Conformer: "B"
        Number of residues, atoms: 120, 925
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          bond proxies already assigned to first conformer: 940
    Chain: "L"
      Number of atoms: 1649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1649
          Classifications: {'peptide': 216}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203}
  Time building chain proxies: 1.52, per 1000 atoms: 0.27
  Number of scatterers: 5673
  At special positions: 0
  Unit cell: (81.969, 84.732, 115.125, 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      22     16.00
     O    1107      8.00
     N     965      7.00
     C    3579      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 143 " - pdb=" SG  CYS H 199 " distance=2.04
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " 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: 0.41
  Conformation dependent library (CDL) restraints added in 205.7 milliseconds
  

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1352

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 16 sheets defined
      10.1% alpha, 34.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 3.725A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 370
      removed outlier: 4.038A  pdb=" N   TYR A 369 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASN A 370 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 366 through 370'
    Processing helix  chain 'A' and resid 386 through 390
      removed outlier: 3.771A  pdb=" N   ASP A 389 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 386 through 390'
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.238A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.723A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 188 through 195
      removed outlier: 4.034A  pdb=" N   GLY H 193 " --> pdb=" O   SER H 189 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   THR H 194 " --> pdb=" O   SER H 190 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 62 through 65
      removed outlier: 3.760A  pdb=" N   GLN K  65 " --> pdb=" O   ASP K  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 62 through 65'
    Processing helix  chain 'K' and resid 87 through 91
      removed outlier: 3.601A  pdb=" N   THR K  91 " --> pdb=" O   PRO K  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.997A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 123 through 130
      removed outlier: 3.512A  pdb=" N   SER L 129 " --> pdb=" O   GLU L 125 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   GLY L 130 " --> pdb=" O   GLN L 126 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 185 through 189
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
      removed outlier: 3.831A  pdb=" N   TYR A 489 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 5
    Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.414A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 125 through 127
      removed outlier: 3.871A  pdb=" N   GLY H 142 " --> pdb=" O   LEU H 127 " (cutoff:3.500A)
      removed outlier: 5.056A  pdb=" N   ALA H 140 " --> pdb=" O   VAL H 187 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL H 187 " --> pdb=" O   ALA H 140 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   GLY H 142 " --> pdb=" O   VAL H 185 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   VAL H 185 " --> pdb=" O   GLY H 142 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   LEU H 144 " --> pdb=" O   SER H 183 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   SER H 183 " --> pdb=" O   LEU H 144 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   LYS H 146 " --> pdb=" O   LEU H 181 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   LEU H 181 " --> pdb=" O   LYS H 146 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 125 through 127
      removed outlier: 3.871A  pdb=" N   GLY H 142 " --> pdb=" O   LEU H 127 " (cutoff:3.500A)
      removed outlier: 5.056A  pdb=" N   ALA H 140 " --> pdb=" O   VAL H 187 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL H 187 " --> pdb=" O   ALA H 140 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   GLY H 142 " --> pdb=" O   VAL H 185 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   VAL H 185 " --> pdb=" O   GLY H 142 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   LEU H 144 " --> pdb=" O   SER H 183 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   SER H 183 " --> pdb=" O   LEU H 144 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   LYS H 146 " --> pdb=" O   LEU H 181 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   LEU H 181 " --> pdb=" O   LYS H 146 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 154 through 157
      removed outlier: 4.202A  pdb=" N   TYR H 197 " --> pdb=" O   VAL H 214 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'K' and resid 19 through 23
      removed outlier: 4.293A  pdb=" N   LEU K  20 " --> pdb=" O   LEU K  81 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER K  71 " --> pdb=" O   TYR K  80 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'K' and resid 58 through 60
      removed outlier: 5.264A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ALA K  49 " --> pdb=" O   TRP K  36 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.490A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 107 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.490A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 107 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR L  99 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 19 through 20
    Processing sheet with id=AB6, first strand: chain 'L' and resid 116 through 120
      removed outlier: 3.554A  pdb=" N   VAL L 135 " --> pdb=" O   PHE L 120 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 146 through 152

    171 hydrogen bonds defined for protein.
    402 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: 0.85

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1826
        1.34 -     1.46: 1164
        1.46 -     1.57: 2798
        1.57 -     1.69: 0
        1.69 -     1.81: 26
  Bond restraints: 5814
  Sorted by residual:
  bond pdb=" CA  ASN A 448 "
       pdb=" C   ASN A 448 "
    ideal  model  delta    sigma   weight residual
    1.523  1.554 -0.030 1.80e-02 3.09e+03 2.85e+00
  bond pdb=" CB  GLN H   1 "
       pdb=" CG  GLN H   1 "
    ideal  model  delta    sigma   weight residual
    1.520  1.556 -0.036 3.00e-02 1.11e+03 1.46e+00
  bond pdb=" CB  ASN A 448 "
       pdb=" CG  ASN A 448 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 2.50e-02 1.60e+03 1.39e+00
  bond pdb=" CA  ASN A 448 "
       pdb=" CB  ASN A 448 "
    ideal  model  delta    sigma   weight residual
    1.531  1.549 -0.019 1.62e-02 3.81e+03 1.31e+00
  bond pdb=" CB  GLU H  89 "
       pdb=" CG  GLU H  89 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.23e+00
  ... (remaining 5809 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 7645
        1.58 -     3.16: 207
        3.16 -     4.74: 37
        4.74 -     6.32: 13
        6.32 -     7.90: 3
  Bond angle restraints: 7905
  Sorted by residual:
  angle pdb=" C   GLY A 502 "
        pdb=" N   VAL A 503 "
        pdb=" CA  VAL A 503 "
      ideal   model   delta    sigma   weight residual
     121.97  129.87   -7.90 1.80e+00 3.09e-01 1.93e+01
  angle pdb=" CA  ASN A 448 "
        pdb=" CB  ASN A 448 "
        pdb=" CG  ASN A 448 "
      ideal   model   delta    sigma   weight residual
     112.60  115.93   -3.33 1.00e+00 1.00e+00 1.11e+01
  angle pdb=" CB  GLN H   1 "
        pdb=" CG  GLN H   1 "
        pdb=" CD  GLN H   1 "
      ideal   model   delta    sigma   weight residual
     112.60  117.60   -5.00 1.70e+00 3.46e-01 8.63e+00
  angle pdb=" CB  GLU H  89 "
        pdb=" CG  GLU H  89 "
        pdb=" CD  GLU H  89 "
      ideal   model   delta    sigma   weight residual
     112.60  117.45   -4.85 1.70e+00 3.46e-01 8.14e+00
  angle pdb=" CA  GLU L 125 "
        pdb=" CB  GLU L 125 "
        pdb=" CG  GLU L 125 "
      ideal   model   delta    sigma   weight residual
     114.10  119.62   -5.52 2.00e+00 2.50e-01 7.61e+00
  ... (remaining 7900 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 3143
       17.96 -    35.91: 251
       35.91 -    53.87: 47
       53.87 -    71.82: 8
       71.82 -    89.78: 4
  Dihedral angle restraints: 3453
    sinusoidal: 1324
      harmonic: 2129
  Sorted by residual:
  dihedral pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -33.63  -52.37     1      1.00e+01 1.00e-02 3.74e+01
  dihedral pdb=" CB  CYS K  22 "
           pdb=" SG  CYS K  22 "
           pdb=" SG  CYS K  96 "
           pdb=" CB  CYS K  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   45.97   47.03     1      1.00e+01 1.00e-02 3.06e+01
  dihedral pdb=" CB  CYS H 143 "
           pdb=" SG  CYS H 143 "
           pdb=" SG  CYS H 199 "
           pdb=" CB  CYS H 199 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  131.00  -38.00     1      1.00e+01 1.00e-02 2.04e+01
  ... (remaining 3450 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 558
       0.036 -    0.071: 206
       0.071 -    0.107: 74
       0.107 -    0.142: 17
       0.142 -    0.178: 2
  Chirality restraints: 857
  Sorted by residual:
  chirality pdb=" CB  THR H 100 "
            pdb=" CA  THR H 100 "
            pdb=" OG1 THR H 100 "
            pdb=" CG2 THR H 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 7.88e-01
  chirality pdb=" CA  ILE A 434 "
            pdb=" N   ILE A 434 "
            pdb=" C   ILE A 434 "
            pdb=" CB  ILE A 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.10e-01
  chirality pdb=" CA  VAL H  37 "
            pdb=" N   VAL H  37 "
            pdb=" C   VAL H  37 "
            pdb=" CB  VAL H  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.67e-01
  ... (remaining 854 not shown)

  Planarity restraints: 1027
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 448 "    0.012 2.00e-02 2.50e+03   2.54e-02 6.43e+00
        pdb=" C   ASN A 448 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ASN A 448 "    0.017 2.00e-02 2.50e+03
        pdb=" N   TYR A 449 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 462 "    0.031 5.00e-02 4.00e+02   4.63e-02 3.43e+00
        pdb=" N   PRO A 463 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 463 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 463 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L  97 "   -0.133 9.50e-02 1.11e+02   6.02e-02 2.92e+00
        pdb=" NE  ARG L  97 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG L  97 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG L  97 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG L  97 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1024 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 1864
        2.85 -     3.36: 4936
        3.36 -     3.87: 9329
        3.87 -     4.39: 11034
        4.39 -     4.90: 19018
  Nonbonded interactions: 46181
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 448 "
            pdb=" OD1 ASN A 448 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" O   TYR K  94 "
            pdb=" CA  GLY K 114 "
     model   vdw
     2.452 2.752
  nonbonded pdb=" O   ASP H  99 "
            pdb=" OD1 ASP H  99 "
     model   vdw
     2.487 3.040
  nonbonded pdb=" N   GLU H  89 "
            pdb=" OE1 GLU H  89 "
     model   vdw
     2.529 3.120
  nonbonded pdb=" N   GLU L 125 "
            pdb=" OE1 GLU L 125 "
     model   vdw
     2.536 3.120
  ... (remaining 46176 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=0.30 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.740
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
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      :  0.003   0.036   5822  Z= 0.135
  Angle     :  0.657   7.901   7921  Z= 0.359
  Chirality :  0.043   0.178    857
  Planarity :  0.005   0.060   1027
  Dihedral  : 13.185  89.776   2077
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.99 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.16 %
    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: -0.54 (0.32), residues: 728
  helix: -3.26 (0.58), residues: 48
  sheet:  0.06 (0.32), residues: 275
  loop : -0.17 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG L  97 
 TYR   0.014   0.001   TYR A 351 
 PHE   0.011   0.001   PHE A 374 
 TRP   0.014   0.002   TRP L 150 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 5814)
  covalent geometry    : angle       0.65606 ( 7905)
  SS BOND              : bond        0.00309 (    8)
  SS BOND              : angle       0.86367 (   16)
  hydrogen bonds       : bond        0.11854 (  164)
  hydrogen bonds       : angle       8.00118 (  402)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 LYS cc_start: 0.8167 (mttt) cc_final: 0.6917 (ptmt)
REVERT: H   16 ARG cc_start: 0.7960 (mtt90) cc_final: 0.7421 (mtp85)
REVERT: H  120 LYS cc_start: 0.8368 (tptt) cc_final: 0.8124 (tttt)
REVERT: H  207 ASN cc_start: 0.8228 (t0) cc_final: 0.8013 (t0)
REVERT: K   72 ARG cc_start: 0.8037 (mmm160) cc_final: 0.7575 (ttt-90)
REVERT: K  110 TYR cc_start: 0.5937 (m-80) cc_final: 0.5576 (m-80)
REVERT: L   31 SER cc_start: 0.7752 (t) cc_final: 0.7346 (m)
REVERT: L   97 ARG cc_start: 0.8500 (ttm110) cc_final: 0.8218 (mtp-110)
REVERT: L  145 GLU cc_start: 0.8695 (mp0) cc_final: 0.8396 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1064
  time to fit residues: 16.6474
Evaluate side-chains
  113 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0870
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0970
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.3980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
A 505 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.152186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.121515 restraints weight = 17752.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 4.24
r_work: 0.3130 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3167
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3167
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.0805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5822  Z= 0.113
  Angle     :  0.523   5.598   7921  Z= 0.270
  Chirality :  0.041   0.160    857
  Planarity :  0.004   0.041   1027
  Dihedral  :  4.192  18.307    814
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  6.27 %
    Favored  : 92.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.16 %
    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: -0.47 (0.31), residues: 728
  helix: -3.13 (0.58), residues: 48
  sheet:  0.14 (0.32), residues: 277
  loop : -0.17 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 403 
 TYR   0.008   0.001   TYR A 495 
 PHE   0.012   0.001   PHE A 456 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.007   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 5814)
  covalent geometry    : angle       0.52036 ( 7905)
  SS BOND              : bond        0.00364 (    8)
  SS BOND              : angle       1.30798 (   16)
  hydrogen bonds       : bond        0.03020 (  164)
  hydrogen bonds       : angle       6.65361 (  402)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: A  386 LYS cc_start: 0.8088 (mttt) cc_final: 0.7646 (mtmt)
REVERT: H   16 ARG cc_start: 0.7944 (mtt90) cc_final: 0.7588 (mtp85)
REVERT: H   87 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6335 (mtp85)
REVERT: H  207 ASN cc_start: 0.8235 (t0) cc_final: 0.8031 (t0)
REVERT: K   34 MET cc_start: 0.7946 (mmt) cc_final: 0.7728 (mmt)
REVERT: K   83 MET cc_start: 0.7258 (mtt) cc_final: 0.7054 (mtt)
REVERT: K  110 TYR cc_start: 0.6315 (m-80) cc_final: 0.5896 (m-80)
REVERT: L   31 SER cc_start: 0.8111 (t) cc_final: 0.7627 (m)
  outliers start: 9
  outliers final: 7
  residues processed: 115
  average time/residue: 0.0914
  time to fit residues: 13.3067
Evaluate side-chains
  115 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  192 LEU
Chi-restraints excluded: chain K residue   81 LEU
Chi-restraints excluded: chain K residue   89 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 33 optimal weight:    0.3980
   chunk 44 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 70 optimal weight:    8.9990
   chunk 59 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 450 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.151236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.121520 restraints weight = 11825.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 2.98
r_work: 0.3169 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3200
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.1299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5822  Z= 0.126
  Angle     :  0.506   5.339   7921  Z= 0.262
  Chirality :  0.041   0.164    857
  Planarity :  0.004   0.041   1027
  Dihedral  :  4.165  17.401    814
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  :  9.00 %
    Favored  : 88.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.16 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.31), residues: 728
  helix: -3.37 (0.52), residues: 48
  sheet:  0.35 (0.32), residues: 272
  loop : -0.19 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 403 
 TYR   0.010   0.001   TYR K 108 
 PHE   0.017   0.001   PHE A 456 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.008   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5814)
  covalent geometry    : angle       0.50472 ( 7905)
  SS BOND              : bond        0.00287 (    8)
  SS BOND              : angle       1.01409 (   16)
  hydrogen bonds       : bond        0.02721 (  164)
  hydrogen bonds       : angle       6.38646 (  402)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 LYS cc_start: 0.8155 (mttt) cc_final: 0.7684 (mtmt)
REVERT: H   16 ARG cc_start: 0.7939 (mtt90) cc_final: 0.7494 (mtp85)
REVERT: H   87 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6695 (mtt90)
REVERT: H  207 ASN cc_start: 0.8210 (t0) cc_final: 0.7991 (t0)
REVERT: L   31 SER cc_start: 0.8050 (t) cc_final: 0.7584 (m)
REVERT: L  139 ASN cc_start: 0.8691 (t0) cc_final: 0.8364 (t0)
  outliers start: 15
  outliers final: 11
  residues processed: 108
  average time/residue: 0.0916
  time to fit residues: 12.3790
Evaluate side-chains
  112 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  144 LEU
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  192 LEU
Chi-restraints excluded: chain K residue   81 LEU
Chi-restraints excluded: chain K residue   89 GLU
Chi-restraints excluded: chain L residue   73 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 37 optimal weight:   20.0000
   chunk 20 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0050
   chunk 35 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   overall best weight:    0.8798

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.151371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.122674 restraints weight = 13589.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 3.30
r_work: 0.3187 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3138
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3138
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5822  Z= 0.149
  Angle     :  0.511   5.226   7921  Z= 0.266
  Chirality :  0.041   0.161    857
  Planarity :  0.004   0.044   1027
  Dihedral  :  4.277  17.779    814
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  :  9.16 %
    Favored  : 88.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.16 %
    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: -0.45 (0.31), residues: 728
  helix: -3.50 (0.50), residues: 48
  sheet:  0.19 (0.31), residues: 282
  loop : -0.13 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  97 
 TYR   0.010   0.001   TYR A 365 
 PHE   0.019   0.002   PHE A 456 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 5814)
  covalent geometry    : angle       0.50974 ( 7905)
  SS BOND              : bond        0.00323 (    8)
  SS BOND              : angle       1.02564 (   16)
  hydrogen bonds       : bond        0.02763 (  164)
  hydrogen bonds       : angle       6.33097 (  402)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: A  386 LYS cc_start: 0.8233 (mttt) cc_final: 0.7806 (mtmt)
REVERT: H   87 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.6101 (mtp85)
REVERT: H  207 ASN cc_start: 0.8219 (t0) cc_final: 0.8006 (t0)
REVERT: L   31 SER cc_start: 0.8144 (t) cc_final: 0.7702 (m)
  outliers start: 16
  outliers final: 12
  residues processed: 107
  average time/residue: 0.0967
  time to fit residues: 12.9506
Evaluate side-chains
  108 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  192 LEU
Chi-restraints excluded: chain K residue   69 THR
Chi-restraints excluded: chain K residue   89 GLU
Chi-restraints excluded: chain L residue   73 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 57 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 64 optimal weight:    5.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.141445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.108752 restraints weight = 8002.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.14
r_work: 0.3097 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2977
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2977 r_free = 0.2977    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2977 r_free = 0.2977    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2977
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   5822  Z= 0.255
  Angle     :  0.614   9.545   7921  Z= 0.317
  Chirality :  0.044   0.158    857
  Planarity :  0.004   0.041   1027
  Dihedral  :  4.799  19.199    814
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 10.61 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.16 %
    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: -0.72 (0.31), residues: 728
  helix: -3.67 (0.54), residues: 41
  sheet: -0.15 (0.30), residues: 296
  loop : -0.24 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L  97 
 TYR   0.016   0.002   TYR A 365 
 PHE   0.012   0.002   PHE H  27 
 TRP   0.017   0.002   TRP L 150 
 HIS   0.009   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00596 ( 5814)
  covalent geometry    : angle       0.61148 ( 7905)
  SS BOND              : bond        0.00451 (    8)
  SS BOND              : angle       1.31442 (   16)
  hydrogen bonds       : bond        0.03210 (  164)
  hydrogen bonds       : angle       6.78249 (  402)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.8492 (mttt) cc_final: 0.7966 (mtmt)
REVERT: A  409 GLN cc_start: 0.8938 (mt0) cc_final: 0.8467 (mt0)
REVERT: A  440 LYS cc_start: 0.8601 (mtpt) cc_final: 0.8133 (ttpp)
REVERT: A  448 ASN cc_start: 0.8516 (t0) cc_final: 0.7562 (t0)
REVERT: H   87 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6809 (mtt90)
REVERT: H  207 ASN cc_start: 0.8358 (t0) cc_final: 0.8076 (t0)
REVERT: L   31 SER cc_start: 0.8194 (t) cc_final: 0.7765 (m)
  outliers start: 18
  outliers final: 14
  residues processed: 114
  average time/residue: 0.1003
  time to fit residues: 14.0738
Evaluate side-chains
  117 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  192 LEU
Chi-restraints excluded: chain H residue  198 ILE
Chi-restraints excluded: chain K residue   69 THR
Chi-restraints excluded: chain K residue   89 GLU
Chi-restraints excluded: chain K residue  118 THR
Chi-restraints excluded: chain L residue   73 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:   20.0000
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
L   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.144369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.111670 restraints weight = 7879.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.16
r_work: 0.3148 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3023
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3023 r_free = 0.3023    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3023 r_free = 0.3023    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3023
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5822  Z= 0.151
  Angle     :  0.537   8.149   7921  Z= 0.278
  Chirality :  0.042   0.156    857
  Planarity :  0.004   0.051   1027
  Dihedral  :  4.564  18.593    814
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 11.58 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.16 %
    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 (0.31), residues: 728
  helix: -3.63 (0.53), residues: 41
  sheet: -0.13 (0.30), residues: 293
  loop : -0.22 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  97 
 TYR   0.014   0.001   TYR A 501 
 PHE   0.016   0.001   PHE L 211 
 TRP   0.015   0.001   TRP L 150 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 5814)
  covalent geometry    : angle       0.53611 ( 7905)
  SS BOND              : bond        0.00426 (    8)
  SS BOND              : angle       0.95575 (   16)
  hydrogen bonds       : bond        0.02849 (  164)
  hydrogen bonds       : angle       6.52532 (  402)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.8475 (mttt) cc_final: 0.7974 (mtmt)
REVERT: A  468 ILE cc_start: 0.9001 (pt) cc_final: 0.8453 (mt)
REVERT: H   87 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.6772 (mtt90)
REVERT: H  127 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8126 (pp)
REVERT: H  207 ASN cc_start: 0.8293 (t0) cc_final: 0.8054 (t0)
REVERT: L   31 SER cc_start: 0.8112 (t) cc_final: 0.7707 (m)
  outliers start: 14
  outliers final: 12
  residues processed: 107
  average time/residue: 0.0992
  time to fit residues: 13.3436
Evaluate side-chains
  110 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  127 LEU
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  192 LEU
Chi-restraints excluded: chain K residue   69 THR
Chi-restraints excluded: chain K residue   89 GLU
Chi-restraints excluded: chain K residue  118 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0040
   chunk 65 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
H 174 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.146759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.116871 restraints weight = 15128.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 3.90
r_work: 0.3076 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5822  Z= 0.115
  Angle     :  0.514   8.176   7921  Z= 0.265
  Chirality :  0.041   0.151    857
  Planarity :  0.004   0.046   1027
  Dihedral  :  4.341  17.800    814
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 11.58 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.16 %
    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: -0.65 (0.32), residues: 728
  helix: -3.45 (0.58), residues: 41
  sheet: -0.07 (0.31), residues: 288
  loop : -0.25 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG L  97 
 TYR   0.015   0.001   TYR A 501 
 PHE   0.016   0.001   PHE L 211 
 TRP   0.015   0.001   TRP L 150 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 5814)
  covalent geometry    : angle       0.51261 ( 7905)
  SS BOND              : bond        0.00333 (    8)
  SS BOND              : angle       0.97021 (   16)
  hydrogen bonds       : bond        0.02668 (  164)
  hydrogen bonds       : angle       6.33367 (  402)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.8349 (mttt) cc_final: 0.7890 (mtmt)
REVERT: A  468 ILE cc_start: 0.8959 (pt) cc_final: 0.8406 (mt)
REVERT: H   87 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6819 (mtt90)
REVERT: H  100 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.8058 (p)
REVERT: H  127 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7898 (pp)
REVERT: H  207 ASN cc_start: 0.8323 (t0) cc_final: 0.8096 (t0)
REVERT: L  160 ASN cc_start: 0.8580 (p0) cc_final: 0.8350 (p0)
  outliers start: 15
  outliers final: 11
  residues processed: 106
  average time/residue: 0.0913
  time to fit residues: 12.3039
Evaluate side-chains
  109 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  127 LEU
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  192 LEU
Chi-restraints excluded: chain K residue   69 THR
Chi-restraints excluded: chain K residue   89 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 63 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9980
   chunk 59 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.145649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.111035 restraints weight = 13555.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.89
r_work: 0.3120 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5822  Z= 0.127
  Angle     :  0.515   8.182   7921  Z= 0.266
  Chirality :  0.041   0.150    857
  Planarity :  0.004   0.044   1027
  Dihedral  :  4.308  17.516    814
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.38 %
    Favored  : 85.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.16 %
    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: 728
  helix: -3.43 (0.58), residues: 41
  sheet: -0.09 (0.30), residues: 298
  loop : -0.19 (0.33), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG L  97 
 TYR   0.012   0.001   TYR A 451 
 PHE   0.016   0.001   PHE L 211 
 TRP   0.015   0.001   TRP L 150 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5814)
  covalent geometry    : angle       0.51357 ( 7905)
  SS BOND              : bond        0.00340 (    8)
  SS BOND              : angle       1.05824 (   16)
  hydrogen bonds       : bond        0.02677 (  164)
  hydrogen bonds       : angle       6.29125 (  402)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.8378 (mttt) cc_final: 0.8015 (mtmt)
REVERT: A  468 ILE cc_start: 0.8972 (pt) cc_final: 0.8401 (mt)
REVERT: A  501 TYR cc_start: 0.6655 (m-80) cc_final: 0.6425 (m-80)
REVERT: H  100 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7935 (p)
REVERT: H  127 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7947 (pp)
REVERT: H  207 ASN cc_start: 0.8257 (t0) cc_final: 0.8042 (t0)
REVERT: L  160 ASN cc_start: 0.8549 (p0) cc_final: 0.8288 (p0)
  outliers start: 13
  outliers final: 11
  residues processed: 105
  average time/residue: 0.0840
  time to fit residues: 11.4524
Evaluate side-chains
  103 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  127 LEU
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  192 LEU
Chi-restraints excluded: chain K residue   69 THR
Chi-restraints excluded: chain K residue   89 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.146657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.117069 restraints weight = 16652.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 4.44
r_work: 0.3039 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3029
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3029
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5822  Z= 0.142
  Angle     :  0.535   8.220   7921  Z= 0.278
  Chirality :  0.042   0.156    857
  Planarity :  0.004   0.048   1027
  Dihedral  :  4.384  17.945    814
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 12.38 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.16 %
    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: 728
  helix: -3.39 (0.59), residues: 41
  sheet: -0.10 (0.30), residues: 298
  loop : -0.18 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG L  97 
 TYR   0.016   0.001   TYR H 179 
 PHE   0.016   0.001   PHE L 211 
 TRP   0.016   0.001   TRP L 150 
 HIS   0.007   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 5814)
  covalent geometry    : angle       0.53299 ( 7905)
  SS BOND              : bond        0.00342 (    8)
  SS BOND              : angle       1.11570 (   16)
  hydrogen bonds       : bond        0.02736 (  164)
  hydrogen bonds       : angle       6.39976 (  402)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.8357 (mttt) cc_final: 0.8020 (mtmt)
REVERT: A  468 ILE cc_start: 0.9021 (pt) cc_final: 0.8441 (mt)
REVERT: A  501 TYR cc_start: 0.6736 (m-80) cc_final: 0.6471 (m-80)
REVERT: H  127 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7974 (pp)
REVERT: H  207 ASN cc_start: 0.8345 (t0) cc_final: 0.8127 (t0)
REVERT: L  160 ASN cc_start: 0.8605 (p0) cc_final: 0.8335 (p0)
  outliers start: 14
  outliers final: 13
  residues processed: 101
  average time/residue: 0.0842
  time to fit residues: 11.0768
Evaluate side-chains
  106 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  127 LEU
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  192 LEU
Chi-restraints excluded: chain K residue   69 THR
Chi-restraints excluded: chain K residue   89 GLU
Chi-restraints excluded: chain K residue  118 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 45 optimal weight:    0.4980
   chunk 41 optimal weight:    0.0570
   chunk 67 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.146436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.112566 restraints weight = 16385.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 3.17
r_work: 0.3110 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3121
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3121
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5822  Z= 0.121
  Angle     :  0.521   8.098   7921  Z= 0.270
  Chirality :  0.041   0.149    857
  Planarity :  0.004   0.050   1027
  Dihedral  :  4.314  17.374    814
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 12.70 %
    Favored  : 85.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.16 %
    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: -0.54 (0.32), residues: 728
  helix: -3.34 (0.60), residues: 41
  sheet: -0.00 (0.31), residues: 295
  loop : -0.18 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG L  97 
 TYR   0.019   0.001   TYR H 179 
 PHE   0.016   0.001   PHE L 211 
 TRP   0.016   0.001   TRP L 150 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 5814)
  covalent geometry    : angle       0.51911 ( 7905)
  SS BOND              : bond        0.00309 (    8)
  SS BOND              : angle       1.07838 (   16)
  hydrogen bonds       : bond        0.02655 (  164)
  hydrogen bonds       : angle       6.30313 (  402)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.8324 (mttt) cc_final: 0.8001 (mtmt)
REVERT: A  448 ASN cc_start: 0.7908 (t0) cc_final: 0.7643 (t0)
REVERT: A  468 ILE cc_start: 0.8984 (pt) cc_final: 0.8406 (mt)
REVERT: A  501 TYR cc_start: 0.6629 (m-80) cc_final: 0.6420 (m-80)
REVERT: H  127 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7864 (pp)
REVERT: H  207 ASN cc_start: 0.8269 (t0) cc_final: 0.8062 (t0)
REVERT: L  160 ASN cc_start: 0.8534 (p0) cc_final: 0.8274 (p0)
  outliers start: 14
  outliers final: 13
  residues processed: 101
  average time/residue: 0.0913
  time to fit residues: 11.7827
Evaluate side-chains
  107 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  127 LEU
Chi-restraints excluded: chain H residue  156 SER
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  192 LEU
Chi-restraints excluded: chain K residue   69 THR
Chi-restraints excluded: chain K residue   89 GLU
Chi-restraints excluded: chain K residue  118 THR
Chi-restraints excluded: chain L residue   73 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 3 optimal weight:    0.4980
   chunk 53 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3700 r_free = 0.3700 target = 0.147100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.112690 restraints weight = 12410.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.77
r_work: 0.3129 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3127
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3127
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5822  Z= 0.126
  Angle     :  0.525   8.152   7921  Z= 0.272
  Chirality :  0.041   0.149    857
  Planarity :  0.004   0.050   1027
  Dihedral  :  4.317  17.388    814
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 12.86 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.16 %
    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: -0.54 (0.32), residues: 728
  helix: -3.32 (0.61), residues: 41
  sheet: -0.05 (0.30), residues: 305
  loop : -0.14 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG L  97 
 TYR   0.018   0.001   TYR H 179 
 PHE   0.015   0.001   PHE L 211 
 TRP   0.021   0.001   TRP L 150 
 HIS   0.007   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5814)
  covalent geometry    : angle       0.52341 ( 7905)
  SS BOND              : bond        0.00321 (    8)
  SS BOND              : angle       1.09998 (   16)
  hydrogen bonds       : bond        0.02676 (  164)
  hydrogen bonds       : angle       6.32852 (  402)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1723.83 seconds
wall clock time: 30 minutes 15.48 seconds (1815.48 seconds total)