Starting phenix.real_space_refine
on Mon May 12 22:43:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k20_36808/05_2025/8k20_36808.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k20_36808/05_2025/8k20_36808.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k20_36808/05_2025/8k20_36808.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k20_36808/05_2025/8k20_36808.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k20_36808/05_2025/8k20_36808.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k20_36808/05_2025/8k20_36808.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     S      55      5.16       5
     C    5899      2.51       5
     N    1618      2.21       5
     O    1783      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9356
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2596
          Classifications: {'peptide': 337}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 321}
    Chain: "B"
      Number of atoms: 1618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1618
          Classifications: {'peptide': 208}
          Link IDs: {'PTRANS': 3, 'TRANS': 204}
    Chain: "C"
      Number of atoms: 1312
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 1312
          Classifications: {'peptide': 171}
          Link IDs: {'PTRANS': 3, 'TRANS': 167}
    Chain: "D"
      Number of atoms: 624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 624
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "F"
      Number of atoms: 609
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 609
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 1, 'TRANS': 75}
    Chain: "E"
      Number of atoms: 2596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2596
          Classifications: {'peptide': 337}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 321}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' FE': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.72, per 1000 atoms: 0.83
  Number of scatterers: 9356
  At special positions: 0
  Unit cell: (85.14, 96.32, 159.1, 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)
     Fe      1     26.01
     S      55     16.00
     O    1783      8.00
     N    1618      7.00
     C    5899      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  19 " - pdb=" SG  CYS F  19 " 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: 2.43
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2260

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 14 sheets defined
      55.0% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 69
      removed outlier: 4.924A  pdb=" N   LEU A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
      Proline residue:  A  59  - end of helix
    Processing helix  chain 'A' and resid 71 through 75
    Processing helix  chain 'A' and resid 86 through 105
      removed outlier: 3.757A  pdb=" N   LEU A  90 " --> pdb=" O   MET A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 126
    Processing helix  chain 'A' and resid 160 through 173
    Processing helix  chain 'A' and resid 179 through 189
    Processing helix  chain 'A' and resid 208 through 225
      removed outlier: 4.060A  pdb=" N   LYS A 224 " --> pdb=" O   GLU A 220 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ASN A 225 " --> pdb=" O   GLU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 257
    Processing helix  chain 'A' and resid 265 through 270
    Processing helix  chain 'A' and resid 271 through 284
    Processing helix  chain 'A' and resid 299 through 314
      removed outlier: 4.443A  pdb=" N   ILE A 303 " --> pdb=" O   ASN A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 322
    Processing helix  chain 'A' and resid 335 through 340
      removed outlier: 3.924A  pdb=" N   GLU A 339 " --> pdb=" O   ALA A 335 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LYS A 340 " --> pdb=" O   VAL A 336 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 335 through 340'
    Processing helix  chain 'B' and resid 45 through 70
    Processing helix  chain 'B' and resid 97 through 108
    Processing helix  chain 'B' and resid 110 through 131
      removed outlier: 3.897A  pdb=" N   GLY B 131 " --> pdb=" O   LYS B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 183
      removed outlier: 3.809A  pdb=" N   LYS B 169 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 188
      removed outlier: 4.632A  pdb=" N   CYS B 187 " --> pdb=" O   HIS B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 202
    Processing helix  chain 'B' and resid 204 through 221
      removed outlier: 3.671A  pdb=" N   THR B 208 " --> pdb=" O   GLN B 204 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LYS B 221 " --> pdb=" O   GLN B 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 9
      No H-bonds generated for 'chain 'C' and resid 7 through 9'
    Processing helix  chain 'C' and resid 22 through 33
    Processing helix  chain 'C' and resid 45 through 47
      No H-bonds generated for 'chain 'C' and resid 45 through 47'
    Processing helix  chain 'C' and resid 49 through 66
      removed outlier: 4.198A  pdb=" N   LEU C  53 " --> pdb=" O   ASP C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 84
      removed outlier: 3.626A  pdb=" N   SER C  83 " --> pdb=" O   VAL C  79 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLY C  84 " --> pdb=" O   TYR C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 95
    Processing helix  chain 'C' and resid 112 through 123
    Processing helix  chain 'C' and resid 132 through 137
    Processing helix  chain 'C' and resid 138 through 147
    Processing helix  chain 'C' and resid 149 through 154
    Processing helix  chain 'C' and resid 157 through 169
    Processing helix  chain 'C' and resid 170 through 172
      No H-bonds generated for 'chain 'C' and resid 170 through 172'
    Processing helix  chain 'D' and resid 27 through 40
      removed outlier: 3.734A  pdb=" N   ALA D  31 " --> pdb=" O   SER D  27 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 93
    Processing helix  chain 'F' and resid 27 through 39
      removed outlier: 3.674A  pdb=" N   ALA F  31 " --> pdb=" O   SER F  27 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 68 through 91
    Processing helix  chain 'E' and resid 45 through 69
      removed outlier: 4.593A  pdb=" N   LEU E  58 " --> pdb=" O   LEU E  54 " (cutoff:3.500A)
      Proline residue:  E  59  - end of helix
    Processing helix  chain 'E' and resid 86 through 105
    Processing helix  chain 'E' and resid 113 through 126
    Processing helix  chain 'E' and resid 160 through 172
    Processing helix  chain 'E' and resid 179 through 190
    Processing helix  chain 'E' and resid 208 through 226
    Processing helix  chain 'E' and resid 229 through 257
      removed outlier: 3.611A  pdb=" N   LEU E 233 " --> pdb=" O   THR E 229 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 266 through 269
    Processing helix  chain 'E' and resid 270 through 284
      removed outlier: 4.122A  pdb=" N   GLN E 274 " --> pdb=" O   ASN E 270 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 292 through 297
      removed outlier: 3.516A  pdb=" N   ILE E 297 " --> pdb=" O   ASP E 293 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 299 through 314
      removed outlier: 3.862A  pdb=" N   ILE E 303 " --> pdb=" O   ASN E 299 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   TYR E 305 " --> pdb=" O   ALA E 301 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   THR E 306 " --> pdb=" O   MET E 302 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ASN E 313 " --> pdb=" O   LEU E 309 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLY E 314 " --> pdb=" O   ALA E 310 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 318 through 322
      removed outlier: 3.856A  pdb=" N   SER E 322 " --> pdb=" O   ILE E 319 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 329 through 333
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30
      removed outlier: 7.224A  pdb=" N   ILE A  21 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 30
      removed outlier: 7.224A  pdb=" N   ILE A  21 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   ILE A   8 " --> pdb=" O   CYS A  79 " (cutoff:3.500A)
      removed outlier: 7.867A  pdb=" N   THR A  81 " --> pdb=" O   ILE A   8 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   PHE A  10 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   GLY A  83 " --> pdb=" O   PHE A  10 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   ILE A  78 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL A 111 " --> pdb=" O   ILE A  78 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   TYR A  80 " --> pdb=" O   VAL A 111 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 155
      removed outlier: 6.464A  pdb=" N   VAL A 142 " --> pdb=" O   PHE A 153 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLU A 155 " --> pdb=" O   THR A 140 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   THR A 140 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   VAL A 131 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   VAL A 264 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   LEU A 133 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   VAL A 261 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 201 through 202
    Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 17
      removed outlier: 3.607A  pdb=" N   LYS B  16 " --> pdb=" O   VAL B  23 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   SER B  86 " --> pdb=" O   VAL B  80 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   VAL B  80 " --> pdb=" O   SER B  86 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   THR B  88 " --> pdb=" O   TYR B  78 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 94 through 96
    Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 5
      removed outlier: 3.605A  pdb=" N   ALA C 107 " --> pdb=" O   SER C  40 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   SER C  40 " --> pdb=" O   ALA C 107 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 5
      removed outlier: 4.077A  pdb=" N   LEU C  16 " --> pdb=" O   ILE C 128 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 17 through 21
    Processing sheet with id=AB1, first strand: chain 'F' and resid 17 through 21
    Processing sheet with id=AB2, first strand: chain 'E' and resid 28 through 30
      removed outlier: 7.199A  pdb=" N   ILE E  21 " --> pdb=" O   LEU E  29 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 28 through 30
      removed outlier: 7.199A  pdb=" N   ILE E  21 " --> pdb=" O   LEU E  29 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   VAL E  22 " --> pdb=" O   ALA E   7 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   ALA E   7 " --> pdb=" O   VAL E  22 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   ILE E   6 " --> pdb=" O   ASP E  76 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   ILE E  78 " --> pdb=" O   ILE E   6 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   ILE E   8 " --> pdb=" O   ILE E  78 " (cutoff:3.500A)
      removed outlier: 5.394A  pdb=" N   TYR E  80 " --> pdb=" O   ILE E   8 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   PHE E  10 " --> pdb=" O   TYR E  80 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   LYS E  82 " --> pdb=" O   PHE E  10 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 149 through 155
      removed outlier: 5.065A  pdb=" N   TYR E 150 " --> pdb=" O   SER E 146 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   SER E 146 " --> pdb=" O   TYR E 150 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   ILE E 152 " --> pdb=" O   ALA E 144 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ALA E 144 " --> pdb=" O   ILE E 152 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLY E 154 " --> pdb=" O   VAL E 142 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   VAL E 131 " --> pdb=" O   LEU E 262 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   VAL E 264 " --> pdb=" O   VAL E 131 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   LEU E 133 " --> pdb=" O   VAL E 264 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 201 through 202

    549 hydrogen bonds defined for protein.
    1569 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.74

  Time building geometry restraints manager: 2.84 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3131
        1.35 -     1.47: 2075
        1.47 -     1.59: 4219
        1.59 -     1.72: 0
        1.72 -     1.84: 83
  Bond restraints: 9508
  Sorted by residual:
  bond pdb=" CB  PRO D  46 "
       pdb=" CG  PRO D  46 "
    ideal  model  delta    sigma   weight residual
    1.492  1.567 -0.075 5.00e-02 4.00e+02 2.26e+00
  bond pdb=" CG  PRO D  46 "
       pdb=" CD  PRO D  46 "
    ideal  model  delta    sigma   weight residual
    1.503  1.455  0.048 3.40e-02 8.65e+02 1.97e+00
  bond pdb=" CB  ARG A 167 "
       pdb=" CG  ARG A 167 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.16e-01
  bond pdb=" CB  CYS F  19 "
       pdb=" SG  CYS F  19 "
    ideal  model  delta    sigma   weight residual
    1.808  1.837 -0.029 3.30e-02 9.18e+02 7.85e-01
  bond pdb=" CB  MET E 302 "
       pdb=" CG  MET E 302 "
    ideal  model  delta    sigma   weight residual
    1.520  1.495  0.025 3.00e-02 1.11e+03 7.09e-01
  ... (remaining 9503 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 12637
        1.83 -     3.66: 189
        3.66 -     5.49: 28
        5.49 -     7.32: 8
        7.32 -     9.15: 1
  Bond angle restraints: 12863
  Sorted by residual:
  angle pdb=" N   VAL E 336 "
        pdb=" CA  VAL E 336 "
        pdb=" C   VAL E 336 "
      ideal   model   delta    sigma   weight residual
     113.71  109.48    4.23 9.50e-01 1.11e+00 1.99e+01
  angle pdb=" CG  ARG A 167 "
        pdb=" CD  ARG A 167 "
        pdb=" NE  ARG A 167 "
      ideal   model   delta    sigma   weight residual
     112.00  121.15   -9.15 2.20e+00 2.07e-01 1.73e+01
  angle pdb=" CA  PRO D  46 "
        pdb=" N   PRO D  46 "
        pdb=" CD  PRO D  46 "
      ideal   model   delta    sigma   weight residual
     112.00  107.18    4.82 1.40e+00 5.10e-01 1.18e+01
  angle pdb=" C   CYS D  19 "
        pdb=" CA  CYS D  19 "
        pdb=" CB  CYS D  19 "
      ideal   model   delta    sigma   weight residual
     111.78  105.76    6.02 1.98e+00 2.55e-01 9.23e+00
  angle pdb=" C   ASP A 166 "
        pdb=" N   ARG A 167 "
        pdb=" CA  ARG A 167 "
      ideal   model   delta    sigma   weight residual
     121.14  115.92    5.22 1.75e+00 3.27e-01 8.91e+00
  ... (remaining 12858 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.38: 5037
       15.38 -    30.76: 574
       30.76 -    46.14: 124
       46.14 -    61.52: 29
       61.52 -    76.90: 11
  Dihedral angle restraints: 5775
    sinusoidal: 2279
      harmonic: 3496
  Sorted by residual:
  dihedral pdb=" CA  SER D  18 "
           pdb=" C   SER D  18 "
           pdb=" N   CYS D  19 "
           pdb=" CA  CYS D  19 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.66   27.34     0      5.00e+00 4.00e-02 2.99e+01
  dihedral pdb=" CA  TYR C 103 "
           pdb=" C   TYR C 103 "
           pdb=" N   ILE C 104 "
           pdb=" CA  ILE C 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.26  -19.74     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  ARG A 167 "
           pdb=" C   ARG A 167 "
           pdb=" N   PHE A 168 "
           pdb=" CA  PHE A 168 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.54   16.46     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 5772 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1090
       0.042 -    0.085: 323
       0.085 -    0.127: 82
       0.127 -    0.169: 9
       0.169 -    0.211: 4
  Chirality restraints: 1508
  Sorted by residual:
  chirality pdb=" CB  ILE A  37 "
            pdb=" CA  ILE A  37 "
            pdb=" CG1 ILE A  37 "
            pdb=" CG2 ILE A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CG  LEU F  21 "
            pdb=" CB  LEU F  21 "
            pdb=" CD1 LEU F  21 "
            pdb=" CD2 LEU F  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.18e-01
  chirality pdb=" CB  ILE A  17 "
            pdb=" CA  ILE A  17 "
            pdb=" CG1 ILE A  17 "
            pdb=" CG2 ILE A  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.36e-01
  ... (remaining 1505 not shown)

  Planarity restraints: 1651
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D  45 "   -0.072 5.00e-02 4.00e+02   1.06e-01 1.81e+01
        pdb=" N   PRO D  46 "    0.184 5.00e-02 4.00e+02
        pdb=" CA  PRO D  46 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO D  46 "   -0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN F  45 "    0.041 5.00e-02 4.00e+02   6.21e-02 6.17e+00
        pdb=" N   PRO F  46 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO F  46 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO F  46 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 273 "   -0.011 2.00e-02 2.50e+03   2.26e-02 5.12e+00
        pdb=" C   LEU E 273 "    0.039 2.00e-02 2.50e+03
        pdb=" O   LEU E 273 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLN E 274 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1648 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 183
        2.66 -     3.22: 9191
        3.22 -     3.78: 15442
        3.78 -     4.34: 19622
        4.34 -     4.90: 31867
  Nonbonded interactions: 76305
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 298 "
            pdb="FE    FE A 401 "
     model   vdw
     2.100 2.260
  nonbonded pdb=" OG  SER C  98 "
            pdb=" OD1 ASN C 100 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" O   LEU A  24 "
            pdb=" OH  TYR A 305 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" N   ASP F  16 "
            pdb=" OE2 GLU F  65 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" OG1 THR E  23 "
            pdb=" OD1 ASP E  25 "
     model   vdw
     2.240 3.040
  ... (remaining 76300 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 4 through 339)
  selection = (chain 'E' and resid 4 through 339)
}
ncs_group {
  reference = (chain 'D' and resid 16 through 92)
  selection = chain 'F'
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.880
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6422
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   9509  Z= 0.127
  Angle     :  0.600   9.152  12865  Z= 0.328
  Chirality :  0.043   0.211   1508
  Planarity :  0.005   0.106   1651
  Dihedral  : 14.078  76.901   3512
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.24), residues: 1197
  helix:  1.67 (0.21), residues: 594
  sheet: -0.45 (0.37), residues: 189
  loop : -0.40 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP E 104 
 HIS   0.004   0.001   HIS A  52 
 PHE   0.017   0.001   PHE F  76 
 TYR   0.018   0.001   TYR C 103 
 ARG   0.003   0.000   ARG A 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12196 (  545)
  hydrogen bonds       : angle       5.61877 ( 1569)
  SS BOND              : bond        0.00267 (    1)
  SS BOND              : angle       5.65363 (    2)
  covalent geometry    : bond        0.00268 ( 9508)
  covalent geometry    : angle       0.59585 (12863)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TRP cc_start: 0.4952 (m-10) cc_final: 0.4701 (m100)
REVERT: B  208 THR cc_start: 0.9039 (p) cc_final: 0.8563 (p)
REVERT: C   17 PHE cc_start: 0.8463 (m-80) cc_final: 0.7946 (m-80)
REVERT: C  105 LEU cc_start: 0.7598 (tp) cc_final: 0.7050 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1879
  time to fit residues: 27.3937
Evaluate side-chains
  75 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 88 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 59 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   chunk 35 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 106 optimal weight:    9.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 138 ASN
E 163 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.087886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.072096 restraints weight = 53101.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.073853 restraints weight = 31046.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.075090 restraints weight = 21665.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6543
moved from start:          0.1103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9509  Z= 0.139
  Angle     :  0.565   7.629  12865  Z= 0.298
  Chirality :  0.043   0.160   1508
  Planarity :  0.004   0.067   1651
  Dihedral  :  4.282  20.683   1301
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  6.80 %
    Favored  : 92.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.25), residues: 1197
  helix:  1.50 (0.21), residues: 612
  sheet: -0.73 (0.35), residues: 205
  loop : -0.39 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 104 
 HIS   0.005   0.001   HIS C  75 
 PHE   0.016   0.001   PHE F  76 
 TYR   0.018   0.002   TYR C 103 
 ARG   0.004   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04103 (  545)
  hydrogen bonds       : angle       4.91412 ( 1569)
  SS BOND              : bond        0.00561 (    1)
  SS BOND              : angle       2.82927 (    2)
  covalent geometry    : bond        0.00299 ( 9508)
  covalent geometry    : angle       0.56404 (12863)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   17 PHE cc_start: 0.8231 (m-80) cc_final: 0.7831 (m-80)
REVERT: C  105 LEU cc_start: 0.6971 (tp) cc_final: 0.6603 (mt)
REVERT: C  116 MET cc_start: 0.7094 (mmm) cc_final: 0.6767 (mmm)
REVERT: E  276 MET cc_start: 0.7162 (ppp) cc_final: 0.6871 (ppp)
  outliers start: 7
  outliers final: 5
  residues processed: 91
  average time/residue: 0.1928
  time to fit residues: 25.7030
Evaluate side-chains
  79 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain D residue   19 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0030
   chunk 90 optimal weight:    9.9990
   chunk 31 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 44 optimal weight:    6.9990
   chunk 87 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.7592

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.087746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.071871 restraints weight = 52937.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.073708 restraints weight = 31150.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.075000 restraints weight = 21635.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6549
moved from start:          0.1310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9509  Z= 0.128
  Angle     :  0.538   7.839  12865  Z= 0.282
  Chirality :  0.042   0.140   1508
  Planarity :  0.004   0.058   1651
  Dihedral  :  4.207  21.178   1301
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 10.68 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.25), residues: 1197
  helix:  1.53 (0.21), residues: 613
  sheet: -0.69 (0.36), residues: 195
  loop : -0.34 (0.33), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 104 
 HIS   0.004   0.001   HIS C  75 
 PHE   0.012   0.001   PHE F  76 
 TYR   0.015   0.002   TYR C 103 
 ARG   0.003   0.000   ARG B  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03861 (  545)
  hydrogen bonds       : angle       4.76312 ( 1569)
  SS BOND              : bond        0.00372 (    1)
  SS BOND              : angle       2.49286 (    2)
  covalent geometry    : bond        0.00274 ( 9508)
  covalent geometry    : angle       0.53668 (12863)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 MET cc_start: 0.7381 (pmm) cc_final: 0.7063 (pmm)
REVERT: B  152 LEU cc_start: 0.6188 (tp) cc_final: 0.5725 (pt)
REVERT: C   17 PHE cc_start: 0.8141 (m-80) cc_final: 0.7787 (m-80)
REVERT: C  116 MET cc_start: 0.7336 (mmm) cc_final: 0.7079 (mmm)
REVERT: E    5 MET cc_start: 0.2930 (ptm) cc_final: 0.1968 (ptm)
REVERT: E  276 MET cc_start: 0.7151 (ppp) cc_final: 0.6876 (ppp)
  outliers start: 14
  outliers final: 9
  residues processed: 90
  average time/residue: 0.1972
  time to fit residues: 26.1732
Evaluate side-chains
  77 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  209 PHE
Chi-restraints excluded: chain C residue    5 ASN
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   53 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 108 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 110 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 93 optimal weight:    0.5980
   chunk 84 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 114 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 135 HIS
** C  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  30 HIS
E 274 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.084905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.068666 restraints weight = 53872.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.070372 restraints weight = 32789.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 73)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.071573 restraints weight = 23212.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6723
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9509  Z= 0.238
  Angle     :  0.671   8.226  12865  Z= 0.358
  Chirality :  0.046   0.196   1508
  Planarity :  0.004   0.056   1651
  Dihedral  :  4.756  22.093   1301
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 16.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 14.17 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.25), residues: 1197
  helix:  1.01 (0.21), residues: 609
  sheet: -1.25 (0.38), residues: 182
  loop : -0.79 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E 104 
 HIS   0.009   0.002   HIS E 113 
 PHE   0.025   0.002   PHE A 208 
 TYR   0.021   0.002   TYR E 305 
 ARG   0.009   0.001   ARG A 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04762 (  545)
  hydrogen bonds       : angle       5.28328 ( 1569)
  SS BOND              : bond        0.00608 (    1)
  SS BOND              : angle       2.48741 (    2)
  covalent geometry    : bond        0.00509 ( 9508)
  covalent geometry    : angle       0.67000 (12863)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 ASP cc_start: 0.8105 (t70) cc_final: 0.7711 (t70)
REVERT: C   17 PHE cc_start: 0.8218 (m-80) cc_final: 0.7754 (m-80)
REVERT: C  116 MET cc_start: 0.7394 (mmm) cc_final: 0.7113 (mmm)
REVERT: E    5 MET cc_start: 0.3373 (ptm) cc_final: 0.2430 (ptm)
REVERT: E  276 MET cc_start: 0.7199 (ppp) cc_final: 0.6999 (ppp)
REVERT: E  299 ASN cc_start: 0.4579 (OUTLIER) cc_final: 0.3089 (t0)
REVERT: E  302 MET cc_start: 0.4333 (tpp) cc_final: 0.3845 (tpp)
  outliers start: 27
  outliers final: 16
  residues processed: 90
  average time/residue: 0.1731
  time to fit residues: 23.9216
Evaluate side-chains
  81 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  209 PHE
Chi-restraints excluded: chain C residue    5 ASN
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   33 ILE
Chi-restraints excluded: chain D residue   53 MET
Chi-restraints excluded: chain E residue   19 VAL
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  163 ASN
Chi-restraints excluded: chain E residue  299 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 35 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 98 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.086529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.070485 restraints weight = 54029.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.072186 restraints weight = 32448.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.073376 restraints weight = 22744.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6639
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9509  Z= 0.141
  Angle     :  0.570   6.744  12865  Z= 0.299
  Chirality :  0.043   0.173   1508
  Planarity :  0.004   0.051   1651
  Dihedral  :  4.475  20.056   1301
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.28 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.25), residues: 1197
  helix:  1.30 (0.21), residues: 606
  sheet: -1.17 (0.38), residues: 182
  loop : -0.67 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 205 
 HIS   0.004   0.001   HIS C  75 
 PHE   0.009   0.001   PHE B 209 
 TYR   0.015   0.002   TYR C 103 
 ARG   0.002   0.000   ARG F  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04009 (  545)
  hydrogen bonds       : angle       4.96757 ( 1569)
  SS BOND              : bond        0.00480 (    1)
  SS BOND              : angle       2.46169 (    2)
  covalent geometry    : bond        0.00302 ( 9508)
  covalent geometry    : angle       0.56943 (12863)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
REVERT: B  152 LEU cc_start: 0.6299 (tp) cc_final: 0.5857 (pt)
REVERT: C   17 PHE cc_start: 0.8224 (m-80) cc_final: 0.7792 (m-80)
REVERT: C  116 MET cc_start: 0.7351 (mmm) cc_final: 0.6991 (mmp)
REVERT: E    5 MET cc_start: 0.2884 (ptm) cc_final: 0.1992 (ptm)
REVERT: E  100 LEU cc_start: 0.4130 (OUTLIER) cc_final: 0.3731 (mm)
  outliers start: 19
  outliers final: 8
  residues processed: 85
  average time/residue: 0.1755
  time to fit residues: 22.7545
Evaluate side-chains
  73 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain C residue    5 ASN
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain E residue   19 VAL
Chi-restraints excluded: chain E residue  100 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 52 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   chunk 94 optimal weight:    0.0770
   chunk 45 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 27 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 313 ASN
** C  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 274 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.087102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.071119 restraints weight = 53511.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.072869 restraints weight = 32005.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.074110 restraints weight = 22575.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6595
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9509  Z= 0.122
  Angle     :  0.568   9.223  12865  Z= 0.296
  Chirality :  0.043   0.158   1508
  Planarity :  0.003   0.051   1651
  Dihedral  :  4.365  20.227   1301
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 19.13 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.25), residues: 1197
  helix:  1.36 (0.21), residues: 610
  sheet: -1.10 (0.38), residues: 181
  loop : -0.56 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 205 
 HIS   0.005   0.001   HIS F  63 
 PHE   0.016   0.001   PHE A 242 
 TYR   0.015   0.001   TYR C 103 
 ARG   0.002   0.000   ARG E 272 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03835 (  545)
  hydrogen bonds       : angle       4.82490 ( 1569)
  SS BOND              : bond        0.00759 (    1)
  SS BOND              : angle       2.88128 (    2)
  covalent geometry    : bond        0.00260 ( 9508)
  covalent geometry    : angle       0.56706 (12863)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  152 LEU cc_start: 0.6271 (tp) cc_final: 0.5839 (pt)
REVERT: C   17 PHE cc_start: 0.8202 (m-80) cc_final: 0.7759 (m-80)
REVERT: C  116 MET cc_start: 0.7407 (mmm) cc_final: 0.7056 (mmp)
REVERT: E    5 MET cc_start: 0.2891 (ptm) cc_final: 0.2055 (ptm)
REVERT: E  100 LEU cc_start: 0.4081 (OUTLIER) cc_final: 0.3668 (mm)
  outliers start: 20
  outliers final: 14
  residues processed: 93
  average time/residue: 0.1763
  time to fit residues: 24.9332
Evaluate side-chains
  82 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  217 GLN
Chi-restraints excluded: chain C residue    5 ASN
Chi-restraints excluded: chain C residue   14 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain F residue   19 CYS
Chi-restraints excluded: chain E residue   19 VAL
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain E residue  315 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 80 optimal weight:    0.0980
   chunk 45 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 114 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 210 ASN
** C  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.084893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.068579 restraints weight = 54793.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.070250 restraints weight = 33446.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.071429 restraints weight = 23843.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6733
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9509  Z= 0.222
  Angle     :  0.677   9.752  12865  Z= 0.357
  Chirality :  0.047   0.389   1508
  Planarity :  0.004   0.052   1651
  Dihedral  :  4.760  20.028   1301
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 16.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.81 %
    Favored  : 77.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.25), residues: 1197
  helix:  1.07 (0.21), residues: 602
  sheet: -1.32 (0.40), residues: 161
  loop : -0.93 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP E 104 
 HIS   0.007   0.002   HIS E 117 
 PHE   0.021   0.002   PHE A 208 
 TYR   0.020   0.002   TYR F  35 
 ARG   0.004   0.001   ARG E 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04667 (  545)
  hydrogen bonds       : angle       5.27799 ( 1569)
  SS BOND              : bond        0.00867 (    1)
  SS BOND              : angle       2.65796 (    2)
  covalent geometry    : bond        0.00479 ( 9508)
  covalent geometry    : angle       0.67663 (12863)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 67
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 ASP cc_start: 0.8188 (t70) cc_final: 0.7826 (t70)
REVERT: B  183 MET cc_start: 0.8876 (ppp) cc_final: 0.8596 (ppp)
REVERT: E    5 MET cc_start: 0.2898 (ptm) cc_final: 0.2038 (ptm)
REVERT: E  100 LEU cc_start: 0.4418 (OUTLIER) cc_final: 0.3952 (mm)
REVERT: E  253 MET cc_start: 0.2031 (tpt) cc_final: 0.1795 (tpt)
REVERT: E  276 MET cc_start: 0.7487 (ppp) cc_final: 0.6600 (ppp)
  outliers start: 25
  outliers final: 18
  residues processed: 85
  average time/residue: 0.1823
  time to fit residues: 23.9070
Evaluate side-chains
  81 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain C residue    5 ASN
Chi-restraints excluded: chain C residue   14 VAL
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   53 MET
Chi-restraints excluded: chain F residue   19 CYS
Chi-restraints excluded: chain E residue   19 VAL
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain E residue  163 ASN
Chi-restraints excluded: chain E residue  299 ASN
Chi-restraints excluded: chain E residue  315 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0040
   chunk 87 optimal weight:    0.3980
   chunk 21 optimal weight:   10.0000
   chunk 99 optimal weight:    7.9990
   chunk 89 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 90 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.8596

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 210 ASN
** C  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.086267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.070177 restraints weight = 54266.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.071939 restraints weight = 32211.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.073172 restraints weight = 22519.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6641
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9509  Z= 0.140
  Angle     :  0.599   7.926  12865  Z= 0.312
  Chirality :  0.045   0.375   1508
  Planarity :  0.004   0.050   1651
  Dihedral  :  4.544  19.742   1301
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 20.19 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.25), residues: 1197
  helix:  1.23 (0.21), residues: 604
  sheet: -1.33 (0.40), residues: 161
  loop : -0.86 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 205 
 HIS   0.005   0.001   HIS F  63 
 PHE   0.011   0.001   PHE A 242 
 TYR   0.015   0.002   TYR C 103 
 ARG   0.003   0.000   ARG D  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04117 (  545)
  hydrogen bonds       : angle       5.01219 ( 1569)
  SS BOND              : bond        0.00609 (    1)
  SS BOND              : angle       2.86637 (    2)
  covalent geometry    : bond        0.00302 ( 9508)
  covalent geometry    : angle       0.59841 (12863)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
REVERT: B  152 LEU cc_start: 0.6308 (tp) cc_final: 0.5848 (pt)
REVERT: C   17 PHE cc_start: 0.8411 (m-80) cc_final: 0.7896 (m-80)
REVERT: D   46 PRO cc_start: 0.8547 (Cg_exo) cc_final: 0.8299 (Cg_endo)
REVERT: E    5 MET cc_start: 0.2807 (ptm) cc_final: 0.2007 (ptm)
REVERT: E  100 LEU cc_start: 0.4292 (OUTLIER) cc_final: 0.3807 (mm)
REVERT: E  235 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.6137 (t80)
REVERT: E  253 MET cc_start: 0.1887 (tpt) cc_final: 0.1617 (tpt)
REVERT: E  276 MET cc_start: 0.7636 (ppp) cc_final: 0.6688 (ppp)
  outliers start: 23
  outliers final: 18
  residues processed: 85
  average time/residue: 0.1760
  time to fit residues: 22.8853
Evaluate side-chains
  86 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  217 GLN
Chi-restraints excluded: chain C residue    5 ASN
Chi-restraints excluded: chain C residue   14 VAL
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   33 ILE
Chi-restraints excluded: chain F residue   19 CYS
Chi-restraints excluded: chain E residue   19 VAL
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain E residue  299 ASN
Chi-restraints excluded: chain E residue  315 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0470
   chunk 88 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 32 optimal weight:    0.4980
   chunk 72 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.5680

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.087170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.071272 restraints weight = 53943.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.073014 restraints weight = 31877.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.074245 restraints weight = 22340.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6597
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9509  Z= 0.121
  Angle     :  0.579   8.022  12865  Z= 0.299
  Chirality :  0.044   0.276   1508
  Planarity :  0.003   0.047   1651
  Dihedral  :  4.350  20.195   1301
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 20.29 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.25), residues: 1197
  helix:  1.40 (0.21), residues: 606
  sheet: -1.29 (0.39), residues: 170
  loop : -0.73 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 205 
 HIS   0.005   0.001   HIS F  63 
 PHE   0.013   0.001   PHE A 242 
 TYR   0.016   0.001   TYR C 103 
 ARG   0.002   0.000   ARG E 272 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03849 (  545)
  hydrogen bonds       : angle       4.80841 ( 1569)
  SS BOND              : bond        0.00578 (    1)
  SS BOND              : angle       2.99858 (    2)
  covalent geometry    : bond        0.00259 ( 9508)
  covalent geometry    : angle       0.57771 (12863)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 ASP cc_start: 0.8133 (t70) cc_final: 0.7704 (t70)
REVERT: C   17 PHE cc_start: 0.8453 (m-80) cc_final: 0.7973 (m-80)
REVERT: D   46 PRO cc_start: 0.8608 (Cg_exo) cc_final: 0.8355 (Cg_endo)
REVERT: F   17 PHE cc_start: 0.7684 (m-80) cc_final: 0.7452 (m-80)
REVERT: E    5 MET cc_start: 0.2745 (ptm) cc_final: 0.1966 (ptm)
REVERT: E  100 LEU cc_start: 0.4091 (OUTLIER) cc_final: 0.3619 (mm)
REVERT: E  253 MET cc_start: 0.1817 (tpt) cc_final: 0.1575 (tpt)
REVERT: E  276 MET cc_start: 0.7561 (ppp) cc_final: 0.6467 (ppp)
REVERT: E  280 MET cc_start: 0.8602 (mpp) cc_final: 0.8310 (mpp)
REVERT: E  302 MET cc_start: 0.4751 (tpp) cc_final: 0.4472 (tpp)
  outliers start: 19
  outliers final: 15
  residues processed: 88
  average time/residue: 0.1723
  time to fit residues: 23.2775
Evaluate side-chains
  84 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  217 GLN
Chi-restraints excluded: chain C residue    5 ASN
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain F residue   19 CYS
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain E residue  248 ILE
Chi-restraints excluded: chain E residue  299 ASN
Chi-restraints excluded: chain E residue  315 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 100 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 102 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 94 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 106 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.086333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.070306 restraints weight = 54512.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.072076 restraints weight = 32527.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.073296 restraints weight = 22842.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6649
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9509  Z= 0.147
  Angle     :  0.599   8.282  12865  Z= 0.311
  Chirality :  0.044   0.278   1508
  Planarity :  0.003   0.043   1651
  Dihedral  :  4.414  20.568   1301
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 19.90 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.25), residues: 1197
  helix:  1.30 (0.21), residues: 605
  sheet: -1.21 (0.40), residues: 168
  loop : -0.79 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 205 
 HIS   0.005   0.001   HIS F  63 
 PHE   0.011   0.001   PHE E  10 
 TYR   0.015   0.001   TYR C 103 
 ARG   0.002   0.000   ARG D  51 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04050 (  545)
  hydrogen bonds       : angle       4.89621 ( 1569)
  SS BOND              : bond        0.00707 (    1)
  SS BOND              : angle       2.94236 (    2)
  covalent geometry    : bond        0.00317 ( 9508)
  covalent geometry    : angle       0.59764 (12863)

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

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

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2394 Ramachandran restraints generated.
    1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 ASP cc_start: 0.8126 (t70) cc_final: 0.7712 (t70)
REVERT: C   17 PHE cc_start: 0.8431 (m-80) cc_final: 0.7905 (m-80)
REVERT: D   46 PRO cc_start: 0.8596 (Cg_exo) cc_final: 0.8345 (Cg_endo)
REVERT: F   17 PHE cc_start: 0.7696 (m-80) cc_final: 0.7471 (m-80)
REVERT: E    5 MET cc_start: 0.2805 (ptm) cc_final: 0.2041 (ptm)
REVERT: E  100 LEU cc_start: 0.4287 (OUTLIER) cc_final: 0.3787 (mm)
REVERT: E  253 MET cc_start: 0.1977 (tpt) cc_final: 0.1714 (tpt)
REVERT: E  276 MET cc_start: 0.7559 (ppp) cc_final: 0.6401 (ppp)
REVERT: E  280 MET cc_start: 0.8586 (mpp) cc_final: 0.8308 (mpp)
REVERT: E  299 ASN cc_start: 0.4009 (OUTLIER) cc_final: 0.3275 (t0)
  outliers start: 21
  outliers final: 18
  residues processed: 84
  average time/residue: 0.1608
  time to fit residues: 21.2712
Evaluate side-chains
  87 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 67
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  261 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  217 GLN
Chi-restraints excluded: chain C residue    5 ASN
Chi-restraints excluded: chain D residue   19 CYS
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain F residue   19 CYS
Chi-restraints excluded: chain E residue   19 VAL
Chi-restraints excluded: chain E residue   54 LEU
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain E residue  248 ILE
Chi-restraints excluded: chain E residue  299 ASN
Chi-restraints excluded: chain E residue  315 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 115 optimal weight:    0.0980
   chunk 114 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 116 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   chunk 98 optimal weight:    0.5980
   chunk 97 optimal weight:    6.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.086989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.070880 restraints weight = 54509.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.072666 restraints weight = 32569.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.073895 restraints weight = 22863.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6622
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9509  Z= 0.126
  Angle     :  0.584   8.395  12865  Z= 0.301
  Chirality :  0.044   0.262   1508
  Planarity :  0.003   0.043   1651
  Dihedral  :  4.338  20.554   1301
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 20.39 %
    Favored  : 77.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.25), residues: 1197
  helix:  1.37 (0.21), residues: 606
  sheet: -1.22 (0.40), residues: 166
  loop : -0.77 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 205 
 HIS   0.005   0.001   HIS F  63 
 PHE   0.012   0.001   PHE A 242 
 TYR   0.015   0.001   TYR C 103 
 ARG   0.002   0.000   ARG D  51 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03874 (  545)
  hydrogen bonds       : angle       4.81563 ( 1569)
  SS BOND              : bond        0.00605 (    1)
  SS BOND              : angle       2.98589 (    2)
  covalent geometry    : bond        0.00270 ( 9508)
  covalent geometry    : angle       0.58271 (12863)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3722.05 seconds
wall clock time: 66 minutes 16.05 seconds (3976.05 seconds total)