Starting phenix.real_space_refine
on Sat Aug 23 05:46:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjs_39348/08_2025/8yjs_39348.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjs_39348/08_2025/8yjs_39348.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjs_39348/08_2025/8yjs_39348.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjs_39348/08_2025/8yjs_39348.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yjs_39348/08_2025/8yjs_39348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjs_39348/08_2025/8yjs_39348.map"
  }
  resolution = 3.55
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 331 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      61      5.49       5
     S      61      5.16       5
     C    6031      2.51       5
     N    1657      2.21       5
     O    2070      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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9880
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "C"
      Number of atoms: 1951
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1951
          Classifications: {'peptide': 254}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 246}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 2769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2769
          Classifications: {'peptide': 351}
          Link IDs: {'PTRANS': 15, 'TRANS': 335}
    Chain: "B"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1947
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 7, 'TRANS': 245}
    Chain: "A"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1947
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 7, 'TRANS': 245}
    Chain: "J"
      Number of atoms: 387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 387
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
    Chain: "E"
      Number of atoms: 590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 590
          Classifications: {'DNA': 29}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 28}
    Chain: "F"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 229
          Classifications: {'DNA': 11}
          Link IDs: {'rna3p': 10}
    Chain: "H"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 60
          Classifications: {'DNA': 3}
          Link IDs: {'rna3p': 2}
  Time building chain proxies: 2.29, per 1000 atoms: 0.23
  Number of scatterers: 9880
  At special positions: 0
  Unit cell: (107.07, 98.77, 106.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      61     16.00
     P      61     15.00
     O    2070      8.00
     N    1657      7.00
     C    6031      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 135 " - pdb=" SG  CYS C 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 135 " - pdb=" SG  CYS B 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 135 " - pdb=" SG  CYS A 162 " 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: 0.77
  Conformation dependent library (CDL) restraints added in 287.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2098

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 8 sheets defined
      30.7% alpha, 24.2% beta
      15 base pairs and 52 stacking pairs defined.
    Time for finding SS restraints: 1.23
  Creating SS restraints...
    Processing helix  chain 'C' and resid 9 through 20
      removed outlier: 3.554A  pdb=" N   LYS C  20 " --> pdb=" O   LEU C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 80
    Processing helix  chain 'C' and resid 140 through 155
      removed outlier: 4.066A  pdb=" N   HIS C 153 " --> pdb=" O   ARG C 149 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ILE C 154 " --> pdb=" O   ASP C 150 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLY C 155 " --> pdb=" O   LEU C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 216
    Processing helix  chain 'D' and resid 6 through 14
    Processing helix  chain 'D' and resid 22 through 26
      removed outlier: 3.504A  pdb=" N   SER D  25 " --> pdb=" O   ASP D  22 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   TYR D  26 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 22 through 26'
    Processing helix  chain 'D' and resid 35 through 45
    Processing helix  chain 'D' and resid 61 through 77
    Processing helix  chain 'D' and resid 90 through 92
      No H-bonds generated for 'chain 'D' and resid 90 through 92'
    Processing helix  chain 'D' and resid 93 through 118
      removed outlier: 4.032A  pdb=" N   ALA D 116 " --> pdb=" O   GLN D 112 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA D 117 " --> pdb=" O   GLN D 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 129
    Processing helix  chain 'D' and resid 134 through 149
      removed outlier: 3.524A  pdb=" N   ASN D 138 " --> pdb=" O   THR D 134 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 158 through 169
    Processing helix  chain 'D' and resid 181 through 186
    Processing helix  chain 'D' and resid 209 through 217
    Processing helix  chain 'D' and resid 219 through 231
    Processing helix  chain 'D' and resid 242 through 253
      removed outlier: 3.552A  pdb=" N   ALA D 246 " --> pdb=" O   GLY D 242 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 262
      removed outlier: 4.113A  pdb=" N   ARG D 262 " --> pdb=" O   GLU D 258 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 285
      removed outlier: 3.533A  pdb=" N   ALA D 279 " --> pdb=" O   LEU D 275 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 302 through 313
      removed outlier: 3.669A  pdb=" N   LEU D 306 " --> pdb=" O   ASN D 302 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 317 through 334
      removed outlier: 4.006A  pdb=" N   GLY D 334 " --> pdb=" O   LYS D 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 20
    Processing helix  chain 'B' and resid 72 through 82
    Processing helix  chain 'B' and resid 140 through 152
    Processing helix  chain 'B' and resid 208 through 216
    Processing helix  chain 'B' and resid 217 through 222
      Proline residue:  B 220  - end of helix
      No H-bonds generated for 'chain 'B' and resid 217 through 222'
    Processing helix  chain 'A' and resid 8 through 20
      removed outlier: 4.146A  pdb=" N   LEU A  12 " --> pdb=" O   GLN A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 80
    Processing helix  chain 'A' and resid 141 through 152
    Processing helix  chain 'A' and resid 208 through 216
    Processing helix  chain 'A' and resid 217 through 219
      No H-bonds generated for 'chain 'A' and resid 217 through 219'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 59 through 60
      removed outlier: 3.721A  pdb=" N   PHE C   2 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU B 205 " --> pdb=" O   ILE B 160 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 66 through 71
      removed outlier: 7.163A  pdb=" N   GLU C  25 " --> pdb=" O   MET C  40 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   MET C  40 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   CYS C  27 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   GLN C  38 " --> pdb=" O   CYS C  27 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLY C 245 " --> pdb=" O   ILE C 241 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   TYR C 239 " --> pdb=" O   LEU C 247 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLU C 238 " --> pdb=" O   THR C 226 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 123 through 127
      removed outlier: 6.621A  pdb=" N   VAL C 123 " --> pdb=" O   SER D 349 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   SER D 349 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   GLN C 125 " --> pdb=" O   THR D 347 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LYS D 345 " --> pdb=" O   GLY C 127 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 204 through 208
      removed outlier: 5.199A  pdb=" N   ALA C 157 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   SER C 172 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 19 through 21
      removed outlier: 3.680A  pdb=" N   GLU D 206 " --> pdb=" O   ARG D  19 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   ALA D 175 " --> pdb=" O   MET D 191 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ASP D  34 " --> pdb=" O   ALA D 176 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 61
    Processing sheet with id=AA7, first strand: chain 'B' and resid 67 through 71
      removed outlier: 3.633A  pdb=" N   MET B  68 " --> pdb=" O   TRP B  28 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 66 through 71
      removed outlier: 5.337A  pdb=" N   SER A 230 " --> pdb=" O   PRO A 234 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   MET A 229 " --> pdb=" O   CYS A 135 " (cutoff:3.500A)

    430 hydrogen bonds defined for protein.
    1209 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      30 hydrogen bonds
      60 hydrogen bond angles
      0 basepair planarities
      15 basepair parallelities
      52 stacking parallelities
  Total time for adding SS restraints: 1.61

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2513
        1.33 -     1.45: 1975
        1.45 -     1.57: 5443
        1.57 -     1.69: 125
        1.69 -     1.81: 98
  Bond restraints: 10154
  Sorted by residual:
  bond pdb=" C   THR C 219 "
       pdb=" N   PRO C 220 "
    ideal  model  delta    sigma   weight residual
    1.337  1.388 -0.052 9.80e-03 1.04e+04 2.79e+01
  bond pdb=" CB  ASN B  24 "
       pdb=" CG  ASN B  24 "
    ideal  model  delta    sigma   weight residual
    1.516  1.570 -0.054 2.50e-02 1.60e+03 4.75e+00
  bond pdb=" CB  GLN D 112 "
       pdb=" CG  GLN D 112 "
    ideal  model  delta    sigma   weight residual
    1.520  1.585 -0.065 3.00e-02 1.11e+03 4.72e+00
  bond pdb=" CA  ALA D 176 "
       pdb=" CB  ALA D 176 "
    ideal  model  delta    sigma   weight residual
    1.531  1.460  0.071 3.28e-02 9.30e+02 4.71e+00
  bond pdb=" CA  VAL D  52 "
       pdb=" CB  VAL D  52 "
    ideal  model  delta    sigma   weight residual
    1.540  1.570 -0.029 1.36e-02 5.41e+03 4.70e+00
  ... (remaining 10149 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.09: 13670
        3.09 -     6.18: 245
        6.18 -     9.26: 40
        9.26 -    12.35: 7
       12.35 -    15.44: 1
  Bond angle restraints: 13963
  Sorted by residual:
  angle pdb=" C   ASP D  51 "
        pdb=" N   VAL D  52 "
        pdb=" CA  VAL D  52 "
      ideal   model   delta    sigma   weight residual
     121.97  131.68   -9.71 1.80e+00 3.09e-01 2.91e+01
  angle pdb=" CA  ARG B  64 "
        pdb=" CB  ARG B  64 "
        pdb=" CG  ARG B  64 "
      ideal   model   delta    sigma   weight residual
     114.10  124.27  -10.17 2.00e+00 2.50e-01 2.59e+01
  angle pdb=" N   VAL B  45 "
        pdb=" CA  VAL B  45 "
        pdb=" C   VAL B  45 "
      ideal   model   delta    sigma   weight residual
     113.71  109.21    4.50 9.50e-01 1.11e+00 2.24e+01
  angle pdb=" CA  VAL D  52 "
        pdb=" CB  VAL D  52 "
        pdb=" CG1 VAL D  52 "
      ideal   model   delta    sigma   weight residual
     110.40  118.35   -7.95 1.70e+00 3.46e-01 2.19e+01
  angle pdb=" CB  GLN D 112 "
        pdb=" CG  GLN D 112 "
        pdb=" CD  GLN D 112 "
      ideal   model   delta    sigma   weight residual
     112.60  120.51   -7.91 1.70e+00 3.46e-01 2.16e+01
  ... (remaining 13958 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 5043
       17.89 -    35.79: 731
       35.79 -    53.68: 287
       53.68 -    71.57: 62
       71.57 -    89.46: 14
  Dihedral angle restraints: 6137
    sinusoidal: 2903
      harmonic: 3234
  Sorted by residual:
  dihedral pdb=" CA  GLU B 198 "
           pdb=" C   GLU B 198 "
           pdb=" N   MET B 199 "
           pdb=" CA  MET B 199 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.81  -27.19     0      5.00e+00 4.00e-02 2.96e+01
  dihedral pdb=" CA  PHE D 126 "
           pdb=" C   PHE D 126 "
           pdb=" N   THR D 127 "
           pdb=" CA  THR D 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.09   24.91     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" CA  ASN C  95 "
           pdb=" C   ASN C  95 "
           pdb=" N   ALA C  96 "
           pdb=" CA  ALA C  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.64  -22.36     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 6134 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 1504
       0.111 -    0.223: 93
       0.223 -    0.334: 9
       0.334 -    0.445: 0
       0.445 -    0.556: 1
  Chirality restraints: 1607
  Sorted by residual:
  chirality pdb=" CB  VAL D  52 "
            pdb=" CA  VAL D  52 "
            pdb=" CG1 VAL D  52 "
            pdb=" CG2 VAL D  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.07   -0.56 2.00e-01 2.50e+01 7.74e+00
  chirality pdb=" CB  ILE C  23 "
            pdb=" CA  ILE C  23 "
            pdb=" CG1 ILE C  23 "
            pdb=" CG2 ILE C  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CB  VAL A 123 "
            pdb=" CA  VAL A 123 "
            pdb=" CG1 VAL A 123 "
            pdb=" CG2 VAL A 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.70e+00
  ... (remaining 1604 not shown)

  Planarity restraints: 1587
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 201 "   -0.080 5.00e-02 4.00e+02   1.19e-01 2.28e+01
        pdb=" N   PRO B 202 "    0.207 5.00e-02 4.00e+02
        pdb=" CA  PRO B 202 "   -0.065 5.00e-02 4.00e+02
        pdb=" CD  PRO B 202 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 274 "    0.028 2.00e-02 2.50e+03   2.74e-02 1.88e+01
        pdb=" CG  TRP D 274 "   -0.073 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 274 "    0.036 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 274 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 274 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 274 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 274 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 274 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 274 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 274 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 136 "    0.018 2.00e-02 2.50e+03   3.59e-02 1.29e+01
        pdb=" C   VAL B 136 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   VAL B 136 "    0.024 2.00e-02 2.50e+03
        pdb=" N   VAL B 137 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1584 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 3071
        2.86 -     3.37: 8455
        3.37 -     3.88: 17488
        3.88 -     4.39: 19562
        4.39 -     4.90: 32794
  Nonbonded interactions: 81370
  Sorted by model distance:
  nonbonded pdb=" O   MET D  67 "
            pdb=" OG1 THR D  71 "
     model   vdw
     2.347 3.040
  nonbonded pdb=" O   THR B 216 "
            pdb=" OG1 THR B 219 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" O   THR A 216 "
            pdb=" OG1 THR A 219 "
     model   vdw
     2.373 3.040
  nonbonded pdb=" OE2 GLU D  76 "
            pdb=" NE  ARG D 327 "
     model   vdw
     2.383 3.120
  nonbonded pdb=" OG  SER B 222 "
            pdb=" O   THR B 224 "
     model   vdw
     2.392 3.040
  ... (remaining 81365 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 108 or (resid 109 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 110 through 254))
  selection = (chain 'B' and (resid 2 through 108 or (resid 109 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 110 through 254))
  selection = (chain 'C' and resid 2 through 254)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.840
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.360
  Find NCS groups from input model:        0.070
  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:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
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      :  0.006   0.071  10157  Z= 0.269
  Angle     :  1.026  15.440  13969  Z= 0.536
  Chirality :  0.059   0.556   1607
  Planarity :  0.008   0.119   1587
  Dihedral  : 19.677  89.464   4030
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.62 (0.20), residues: 1103
  helix: -2.73 (0.20), residues: 311
  sheet: -2.07 (0.26), residues: 312
  loop : -2.21 (0.23), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG D 129 
 TYR   0.028   0.003   TYR B 249 
 PHE   0.059   0.003   PHE B 214 
 TRP   0.073   0.005   TRP D 274 
 HIS   0.005   0.001   HIS D 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00617 (10154)
  covalent geometry    : angle       1.02662 (13963)
  SS BOND              : bond        0.00221 (    3)
  SS BOND              : angle       0.55622 (    6)
  hydrogen bonds       : bond        0.20336 (  460)
  hydrogen bonds       : angle      10.02207 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.369 
Fit side-chains
REVERT: D   10 ILE cc_start: 0.8766 (mm) cc_final: 0.8529 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0845
  time to fit residues: 17.3813
Evaluate side-chains
  108 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  21 ASN
B  38 GLN
B  84 ASN
B 108 GLN
A 131 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.135491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.103997 restraints weight = 15272.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.107280 restraints weight = 10708.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.108372 restraints weight = 6651.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.108671 restraints weight = 5790.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.109059 restraints weight = 5594.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10157  Z= 0.168
  Angle     :  0.609   7.080  13969  Z= 0.336
  Chirality :  0.043   0.238   1607
  Planarity :  0.005   0.069   1587
  Dihedral  : 20.803  88.477   1901
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.30 %
    Favored  : 90.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.53 (0.22), residues: 1103
  helix: -1.04 (0.26), residues: 327
  sheet: -1.93 (0.27), residues: 303
  loop : -1.80 (0.25), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 129 
 TYR   0.009   0.001   TYR C 211 
 PHE   0.025   0.002   PHE B 214 
 TRP   0.031   0.002   TRP D 274 
 HIS   0.004   0.001   HIS D 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (10154)
  covalent geometry    : angle       0.60897 (13963)
  SS BOND              : bond        0.00217 (    3)
  SS BOND              : angle       0.40250 (    6)
  hydrogen bonds       : bond        0.04635 (  460)
  hydrogen bonds       : angle       6.83458 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.355 
Fit side-chains
REVERT: D   10 ILE cc_start: 0.8836 (mm) cc_final: 0.8589 (mm)
REVERT: B  199 MET cc_start: 0.5496 (tpt) cc_final: 0.5211 (mmm)
REVERT: A  116 MET cc_start: 0.8602 (ttp) cc_final: 0.8381 (ttm)
REVERT: A  229 MET cc_start: 0.8093 (pmm) cc_final: 0.7686 (ptp)
  outliers start: 11
  outliers final: 8
  residues processed: 139
  average time/residue: 0.0738
  time to fit residues: 15.2584
Evaluate side-chains
  114 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain A residue   24 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 89 optimal weight:    0.0970
   chunk 20 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 99 optimal weight:    0.3980
   chunk 104 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0970
   overall best weight:    0.4576

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
C  49 GLN
D  21 ASN
B 108 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.135188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.103495 restraints weight = 15271.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.106689 restraints weight = 10627.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.107924 restraints weight = 6596.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.108212 restraints weight = 5714.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.108558 restraints weight = 5551.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10157  Z= 0.136
  Angle     :  0.544   6.126  13969  Z= 0.298
  Chirality :  0.042   0.242   1607
  Planarity :  0.004   0.056   1587
  Dihedral  : 20.441  87.244   1901
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 11.62 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.95 (0.23), residues: 1103
  helix: -0.03 (0.28), residues: 326
  sheet: -1.86 (0.27), residues: 284
  loop : -1.72 (0.24), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  53 
 TYR   0.015   0.001   TYR B 211 
 PHE   0.018   0.001   PHE B 214 
 TRP   0.023   0.002   TRP D 274 
 HIS   0.002   0.001   HIS D 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (10154)
  covalent geometry    : angle       0.54383 (13963)
  SS BOND              : bond        0.00112 (    3)
  SS BOND              : angle       0.51507 (    6)
  hydrogen bonds       : bond        0.04000 (  460)
  hydrogen bonds       : angle       6.09948 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.368 
Fit side-chains
REVERT: C   32 SER cc_start: 0.8845 (t) cc_final: 0.8633 (m)
REVERT: C  199 MET cc_start: 0.7112 (tpp) cc_final: 0.5747 (mtm)
REVERT: D   10 ILE cc_start: 0.8868 (mm) cc_final: 0.8615 (mm)
REVERT: D  126 PHE cc_start: 0.7524 (m-80) cc_final: 0.7238 (m-10)
REVERT: D  259 ILE cc_start: 0.7945 (mm) cc_final: 0.7486 (mt)
REVERT: B  199 MET cc_start: 0.5724 (tpt) cc_final: 0.3623 (mtm)
  outliers start: 13
  outliers final: 9
  residues processed: 132
  average time/residue: 0.0623
  time to fit residues: 12.8839
Evaluate side-chains
  117 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0040
   chunk 52 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0770
   chunk 45 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   overall best weight:    0.5752

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

Flipped N/Q/H residues before XYZ refinement:
D  21 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.135053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.101753 restraints weight = 15141.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.105137 restraints weight = 11020.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.106400 restraints weight = 6772.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.106826 restraints weight = 5860.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.107173 restraints weight = 5651.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10157  Z= 0.148
  Angle     :  0.539   5.572  13969  Z= 0.295
  Chirality :  0.042   0.269   1607
  Planarity :  0.003   0.052   1587
  Dihedral  : 20.339  89.747   1901
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.28 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.24), residues: 1103
  helix:  0.47 (0.28), residues: 328
  sheet: -1.89 (0.27), residues: 304
  loop : -1.43 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  53 
 TYR   0.012   0.001   TYR B 211 
 PHE   0.014   0.001   PHE B 215 
 TRP   0.018   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (10154)
  covalent geometry    : angle       0.53887 (13963)
  SS BOND              : bond        0.00108 (    3)
  SS BOND              : angle       0.35157 (    6)
  hydrogen bonds       : bond        0.03749 (  460)
  hydrogen bonds       : angle       5.77876 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.243 
Fit side-chains
REVERT: C   32 SER cc_start: 0.8837 (t) cc_final: 0.8625 (m)
REVERT: C   75 MET cc_start: 0.8714 (tpp) cc_final: 0.8407 (ttt)
REVERT: C   88 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8831 (mt)
REVERT: D   10 ILE cc_start: 0.8884 (mm) cc_final: 0.8634 (mm)
REVERT: D  126 PHE cc_start: 0.7531 (m-80) cc_final: 0.7270 (m-10)
REVERT: D  259 ILE cc_start: 0.8251 (mm) cc_final: 0.7633 (mt)
REVERT: D  274 TRP cc_start: 0.7999 (t60) cc_final: 0.7634 (t60)
REVERT: B   64 ARG cc_start: 0.8207 (tpt-90) cc_final: 0.7916 (tmt170)
REVERT: B   86 ASP cc_start: 0.7787 (m-30) cc_final: 0.7556 (m-30)
REVERT: B  199 MET cc_start: 0.5689 (tpt) cc_final: 0.3602 (mtm)
  outliers start: 20
  outliers final: 11
  residues processed: 137
  average time/residue: 0.0781
  time to fit residues: 15.6908
Evaluate side-chains
  121 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   88 ILE
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 20 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9990
   chunk 106 optimal weight:    0.8980
   chunk 111 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 85 optimal weight:    0.0070
   chunk 34 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 6 optimal weight:    0.2980
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
D  21 ASN
D  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.135007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.101602 restraints weight = 15157.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.104785 restraints weight = 11141.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.106413 restraints weight = 6955.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.106677 restraints weight = 5867.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.107050 restraints weight = 5688.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10157  Z= 0.138
  Angle     :  0.533   6.505  13969  Z= 0.288
  Chirality :  0.042   0.293   1607
  Planarity :  0.003   0.051   1587
  Dihedral  : 20.282  88.907   1901
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 14.52 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.34 (0.24), residues: 1103
  helix:  0.81 (0.29), residues: 327
  sheet: -1.83 (0.27), residues: 304
  loop : -1.34 (0.26), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   5 
 TYR   0.017   0.001   TYR B 211 
 PHE   0.012   0.001   PHE D  27 
 TRP   0.014   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10154)
  covalent geometry    : angle       0.53340 (13963)
  SS BOND              : bond        0.00050 (    3)
  SS BOND              : angle       0.33833 (    6)
  hydrogen bonds       : bond        0.03575 (  460)
  hydrogen bonds       : angle       5.60101 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.366 
Fit side-chains
REVERT: C   32 SER cc_start: 0.8809 (t) cc_final: 0.8603 (m)
REVERT: D   10 ILE cc_start: 0.8863 (mm) cc_final: 0.8607 (mm)
REVERT: D   74 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8637 (mtp)
REVERT: D  126 PHE cc_start: 0.7573 (m-80) cc_final: 0.7317 (m-10)
REVERT: D  259 ILE cc_start: 0.8206 (mm) cc_final: 0.7591 (mt)
REVERT: D  274 TRP cc_start: 0.7999 (t60) cc_final: 0.7677 (t60)
REVERT: B   86 ASP cc_start: 0.7779 (m-30) cc_final: 0.7578 (m-30)
REVERT: B  199 MET cc_start: 0.5697 (tpt) cc_final: 0.3645 (mtm)
REVERT: A   75 MET cc_start: 0.9060 (ttt) cc_final: 0.8698 (ttt)
  outliers start: 26
  outliers final: 14
  residues processed: 135
  average time/residue: 0.0732
  time to fit residues: 15.0074
Evaluate side-chains
  124 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain D residue   74 MET
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0020
   chunk 14 optimal weight:    0.7980
   chunk 107 optimal weight:    0.6980
   overall best weight:    0.6988

-------------------------------------------------------------------------------
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 = 0.3798 r_free = 0.3798 target = 0.133053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.099583 restraints weight = 15157.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.102755 restraints weight = 11208.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.104087 restraints weight = 7022.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.104449 restraints weight = 6029.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.104827 restraints weight = 5842.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10157  Z= 0.160
  Angle     :  0.555   5.866  13969  Z= 0.298
  Chirality :  0.043   0.313   1607
  Planarity :  0.003   0.051   1587
  Dihedral  : 20.282  89.949   1901
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.66 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.25 (0.24), residues: 1103
  helix:  0.84 (0.29), residues: 328
  sheet: -1.82 (0.26), residues: 322
  loop : -1.17 (0.27), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 261 
 TYR   0.019   0.002   TYR B 211 
 PHE   0.014   0.001   PHE B 215 
 TRP   0.016   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (10154)
  covalent geometry    : angle       0.55504 (13963)
  SS BOND              : bond        0.00041 (    3)
  SS BOND              : angle       0.41921 (    6)
  hydrogen bonds       : bond        0.03626 (  460)
  hydrogen bonds       : angle       5.63317 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.239 
Fit side-chains
REVERT: D  126 PHE cc_start: 0.7656 (m-80) cc_final: 0.7369 (m-10)
REVERT: D  259 ILE cc_start: 0.8152 (mm) cc_final: 0.7716 (mt)
REVERT: D  274 TRP cc_start: 0.8097 (t60) cc_final: 0.7805 (t60)
REVERT: B   75 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8137 (tmm)
REVERT: A   75 MET cc_start: 0.9010 (ttt) cc_final: 0.8648 (ttt)
  outliers start: 21
  outliers final: 15
  residues processed: 127
  average time/residue: 0.0793
  time to fit residues: 15.3174
Evaluate side-chains
  123 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   73 THR
Chi-restraints excluded: chain C residue  132 GLU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 84 optimal weight:    0.8980
   chunk 102 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.129387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.096800 restraints weight = 15358.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.099849 restraints weight = 10726.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.101228 restraints weight = 6703.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.101548 restraints weight = 5769.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.101887 restraints weight = 5537.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.3245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10157  Z= 0.186
  Angle     :  0.583   7.152  13969  Z= 0.308
  Chirality :  0.043   0.308   1607
  Planarity :  0.003   0.047   1587
  Dihedral  : 20.347  89.669   1901
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.08 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.30 (0.24), residues: 1103
  helix:  0.82 (0.29), residues: 328
  sheet: -1.93 (0.25), residues: 332
  loop : -1.12 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   5 
 TYR   0.022   0.002   TYR B 211 
 PHE   0.018   0.002   PHE B 215 
 TRP   0.015   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (10154)
  covalent geometry    : angle       0.58289 (13963)
  SS BOND              : bond        0.00083 (    3)
  SS BOND              : angle       0.55137 (    6)
  hydrogen bonds       : bond        0.03749 (  460)
  hydrogen bonds       : angle       5.72825 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.246 
Fit side-chains
REVERT: C  156 ASP cc_start: 0.6875 (p0) cc_final: 0.6612 (p0)
REVERT: D  126 PHE cc_start: 0.7665 (m-80) cc_final: 0.7377 (m-10)
REVERT: D  259 ILE cc_start: 0.8163 (mm) cc_final: 0.7758 (mt)
REVERT: D  274 TRP cc_start: 0.8107 (t60) cc_final: 0.7842 (t60)
REVERT: B   75 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8112 (tmm)
REVERT: A   75 MET cc_start: 0.9020 (ttt) cc_final: 0.8661 (ttt)
REVERT: A  199 MET cc_start: 0.5621 (tpt) cc_final: 0.5248 (tpt)
  outliers start: 22
  outliers final: 14
  residues processed: 118
  average time/residue: 0.0862
  time to fit residues: 14.8046
Evaluate side-chains
  112 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  299 SER
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 97 optimal weight:    9.9990
   chunk 82 optimal weight:    0.6980
   chunk 95 optimal weight:    0.8980
   chunk 21 optimal weight:    0.1980
   chunk 61 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   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 = 0.3761 r_free = 0.3761 target = 0.130144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.098570 restraints weight = 15250.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.101875 restraints weight = 10535.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.102574 restraints weight = 6500.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.103120 restraints weight = 5865.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.103361 restraints weight = 5635.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.3307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10157  Z= 0.157
  Angle     :  0.566   6.367  13969  Z= 0.301
  Chirality :  0.043   0.341   1607
  Planarity :  0.003   0.043   1587
  Dihedral  : 20.313  88.053   1901
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.39 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.27 (0.25), residues: 1103
  helix:  0.86 (0.29), residues: 328
  sheet: -1.90 (0.25), residues: 343
  loop : -1.08 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   5 
 TYR   0.023   0.002   TYR B 211 
 PHE   0.015   0.001   PHE B 215 
 TRP   0.015   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (10154)
  covalent geometry    : angle       0.56562 (13963)
  SS BOND              : bond        0.00070 (    3)
  SS BOND              : angle       0.46191 (    6)
  hydrogen bonds       : bond        0.03548 (  460)
  hydrogen bonds       : angle       5.67926 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: C  156 ASP cc_start: 0.6852 (p0) cc_final: 0.6571 (p0)
REVERT: C  244 MET cc_start: 0.8535 (mpp) cc_final: 0.8308 (mpp)
REVERT: D  126 PHE cc_start: 0.7661 (m-80) cc_final: 0.7334 (m-10)
REVERT: D  259 ILE cc_start: 0.8165 (mm) cc_final: 0.7749 (mt)
REVERT: B   75 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8102 (tmm)
REVERT: A   75 MET cc_start: 0.9021 (ttt) cc_final: 0.8668 (ttt)
  outliers start: 17
  outliers final: 15
  residues processed: 116
  average time/residue: 0.0926
  time to fit residues: 15.4056
Evaluate side-chains
  118 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 94 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 106 optimal weight:    0.5980
   chunk 83 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3779 r_free = 0.3779 target = 0.131821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.098547 restraints weight = 14967.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.101953 restraints weight = 10713.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.103160 restraints weight = 6580.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.103531 restraints weight = 5707.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.103887 restraints weight = 5510.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.3386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10157  Z= 0.167
  Angle     :  0.575   6.540  13969  Z= 0.306
  Chirality :  0.043   0.334   1607
  Planarity :  0.003   0.043   1587
  Dihedral  : 20.313  88.044   1901
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.60 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.30 (0.25), residues: 1103
  helix:  0.83 (0.29), residues: 328
  sheet: -1.93 (0.25), residues: 343
  loop : -1.07 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 332 
 TYR   0.022   0.002   TYR B 211 
 PHE   0.011   0.001   PHE C 169 
 TRP   0.017   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (10154)
  covalent geometry    : angle       0.57512 (13963)
  SS BOND              : bond        0.00071 (    3)
  SS BOND              : angle       0.47448 (    6)
  hydrogen bonds       : bond        0.03601 (  460)
  hydrogen bonds       : angle       5.68065 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.248 
Fit side-chains
REVERT: C  156 ASP cc_start: 0.6887 (p0) cc_final: 0.6586 (p0)
REVERT: D  126 PHE cc_start: 0.7709 (m-80) cc_final: 0.7367 (m-10)
REVERT: D  259 ILE cc_start: 0.8151 (mm) cc_final: 0.7730 (mt)
REVERT: B   75 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8088 (tmm)
REVERT: A   75 MET cc_start: 0.9026 (ttt) cc_final: 0.8674 (ttt)
  outliers start: 20
  outliers final: 16
  residues processed: 115
  average time/residue: 0.0915
  time to fit residues: 15.0384
Evaluate side-chains
  117 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  299 SER
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 15 optimal weight:    0.0270
   chunk 57 optimal weight:    0.6980
   chunk 39 optimal weight:    0.3980
   chunk 1 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0870
   chunk 70 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.3816

-------------------------------------------------------------------------------
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 = 0.3811 r_free = 0.3811 target = 0.134169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.101092 restraints weight = 14962.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.104278 restraints weight = 10967.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.105555 restraints weight = 6859.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.106061 restraints weight = 5936.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.106345 restraints weight = 5730.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10157  Z= 0.128
  Angle     :  0.552   7.435  13969  Z= 0.295
  Chirality :  0.042   0.343   1607
  Planarity :  0.003   0.042   1587
  Dihedral  : 20.222  86.073   1901
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 16.80 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.18 (0.24), residues: 1103
  helix:  0.91 (0.29), residues: 329
  sheet: -1.77 (0.25), residues: 337
  loop : -1.11 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   5 
 TYR   0.017   0.001   TYR B 211 
 PHE   0.011   0.001   PHE D 126 
 TRP   0.019   0.001   TRP D 274 
 HIS   0.004   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (10154)
  covalent geometry    : angle       0.55253 (13963)
  SS BOND              : bond        0.00057 (    3)
  SS BOND              : angle       0.37445 (    6)
  hydrogen bonds       : bond        0.03373 (  460)
  hydrogen bonds       : angle       5.56568 ( 1269)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.321 
Fit side-chains
REVERT: D  126 PHE cc_start: 0.7677 (m-80) cc_final: 0.7343 (m-10)
REVERT: D  259 ILE cc_start: 0.8190 (mm) cc_final: 0.7788 (mt)
REVERT: D  325 VAL cc_start: 0.9161 (t) cc_final: 0.8934 (t)
REVERT: B   75 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8122 (tmm)
REVERT: A  199 MET cc_start: 0.5528 (tpt) cc_final: 0.5059 (tpt)
  outliers start: 14
  outliers final: 11
  residues processed: 122
  average time/residue: 0.0872
  time to fit residues: 15.3724
Evaluate side-chains
  117 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain D residue  177 THR
Chi-restraints excluded: chain D residue  253 HIS
Chi-restraints excluded: chain D residue  294 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   75 MET
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   24 ASN
Chi-restraints excluded: chain A residue  203 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 104 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9990
   chunk 94 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 91 optimal weight:    0.5980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.131686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.098579 restraints weight = 15175.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.101808 restraints weight = 11042.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.102861 restraints weight = 6834.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.103303 restraints weight = 6001.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.103639 restraints weight = 5762.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  10157  Z= 0.176
  Angle     :  0.591   8.193  13969  Z= 0.312
  Chirality :  0.044   0.338   1607
  Planarity :  0.003   0.042   1587
  Dihedral  : 20.266  87.925   1901
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.12 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.20 (0.25), residues: 1103
  helix:  0.85 (0.29), residues: 327
  sheet: -1.78 (0.26), residues: 337
  loop : -1.07 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 332 
 TYR   0.022   0.002   TYR B 211 
 PHE   0.014   0.002   PHE D  27 
 TRP   0.019   0.002   TRP D 274 
 HIS   0.002   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (10154)
  covalent geometry    : angle       0.59069 (13963)
  SS BOND              : bond        0.00178 (    3)
  SS BOND              : angle       0.60405 (    6)
  hydrogen bonds       : bond        0.03559 (  460)
  hydrogen bonds       : angle       5.63662 ( 1269)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1366.07 seconds
wall clock time: 24 minutes 26.13 seconds (1466.13 seconds total)