Starting phenix.real_space_refine
on Sat May  2 23:28:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uk2_64230/05_2026/9uk2_64230.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uk2_64230/05_2026/9uk2_64230.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uk2_64230/05_2026/9uk2_64230.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uk2_64230/05_2026/9uk2_64230.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uk2_64230/05_2026/9uk2_64230.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uk2_64230/05_2026/9uk2_64230.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.069
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     C    5719      2.51       5
     N    1542      2.21       5
     O    1674      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8999
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2400
          Classifications: {'peptide': 300}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 289}
    Chain: "B"
      Number of atoms: 1847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1847
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 6, 'TRANS': 222}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "C"
      Number of atoms: 2575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2575
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 5, 'TRANS': 329}
    Chain: "D"
      Number of atoms: 394
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 394
          Classifications: {'peptide': 51}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
    Chain: "E"
      Number of atoms: 1780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1780
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.77, per 1000 atoms: 0.20
  Number of scatterers: 8999
  At special positions: 0
  Unit cell: (88.92, 123.975, 128.25, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      64     16.00
     O    1674      8.00
     N    1542      7.00
     C    5719      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 106 " - pdb=" SG  CYS A 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  60 " - pdb=" SG  CYS E 134 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 197 " - pdb=" SG  CYS E 267 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 250.6 milliseconds
  

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2150

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 14 sheets defined
      38.4% alpha, 23.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 35
    Processing helix  chain 'A' and resid 35 through 62
      Proline residue:  A  49  - end of helix
      removed outlier: 3.719A  pdb=" N   MET A  62 " --> pdb=" O   TYR A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 85
      removed outlier: 3.978A  pdb=" N   SER A  85 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 95
      removed outlier: 3.853A  pdb=" N   LEU A  89 " --> pdb=" O   SER A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 137
      removed outlier: 3.669A  pdb=" N   PHE A 111 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   PHE A 113 " --> pdb=" O   ILE A 109 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   HIS A 114 " --> pdb=" O   ARG A 110 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   SER A 120 " --> pdb=" O   ASN A 116 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ILE A 121 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LEU A 122 " --> pdb=" O   TYR A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 145
      removed outlier: 3.577A  pdb=" N   HIS A 145 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 142 through 145'
    Processing helix  chain 'A' and resid 146 through 166
      removed outlier: 4.049A  pdb=" N   ALA A 150 " --> pdb=" O   LYS A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 171
    Processing helix  chain 'A' and resid 192 through 207
    Processing helix  chain 'A' and resid 207 through 227
    Processing helix  chain 'A' and resid 235 through 268
      removed outlier: 3.812A  pdb=" N   ALA A 239 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
      Proline residue:  A 256  - end of helix
      removed outlier: 3.573A  pdb=" N   VAL A 262 " --> pdb=" O   HIS A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 288
    Processing helix  chain 'A' and resid 293 through 301
    Processing helix  chain 'A' and resid 306 through 323
    Processing helix  chain 'B' and resid 6 through 31
    Processing helix  chain 'B' and resid 45 through 57
    Processing helix  chain 'B' and resid 95 through 101
      removed outlier: 3.715A  pdb=" N   GLN B  98 " --> pdb=" O   LYS B  95 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASN B 101 " --> pdb=" O   GLN B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 130
    Processing helix  chain 'B' and resid 145 through 156
      removed outlier: 3.965A  pdb=" N   LEU B 149 " --> pdb=" O   LYS B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 169
      removed outlier: 3.618A  pdb=" N   PHE B 167 " --> pdb=" O   PHE B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 203
      removed outlier: 3.689A  pdb=" N   THR B 187 " --> pdb=" O   ASP B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 243
    Processing helix  chain 'C' and resid 7 through 25
      removed outlier: 3.795A  pdb=" N   CYS C  25 " --> pdb=" O   ALA C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 35
    Processing helix  chain 'D' and resid 12 through 25
      removed outlier: 4.209A  pdb=" N   ILE D  25 " --> pdb=" O   MET D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.539A  pdb=" N   ALA D  33 " --> pdb=" O   LYS D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 59
    Processing helix  chain 'E' and resid 66 through 70
    Processing helix  chain 'E' and resid 125 through 129
    Processing helix  chain 'E' and resid 258 through 262
      removed outlier: 3.572A  pdb=" N   VAL E 262 " --> pdb=" O   ALA E 259 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 175
    Processing sheet with id=AA2, first strand: chain 'B' and resid 70 through 75
      removed outlier: 3.759A  pdb=" N   ALA B 105 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   ILE B 106 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   PHE B 142 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   PHE B 108 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   ASN B 144 " --> pdb=" O   PHE B 108 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   VAL B 110 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   VAL B 139 " --> pdb=" O   TYR B 212 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   HIS B 214 " --> pdb=" O   VAL B 139 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   LEU B 141 " --> pdb=" O   HIS B 214 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51
      removed outlier: 6.638A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.579A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASN C  88 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105
      removed outlier: 7.065A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   GLY C 116 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 4.949A  pdb=" N   ILE C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 153
      removed outlier: 3.606A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   GLN C 156 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE C 157 " --> pdb=" O   TRP C 169 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   THR C 178 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192
      removed outlier: 7.074A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ALA C 208 " --> pdb=" O   THR C 221 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   THR C 221 " --> pdb=" O   ALA C 208 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   LEU C 210 " --> pdb=" O   ARG C 219 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.541A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLN C 259 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.836A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLY C 306 " --> pdb=" O   VAL C 296 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 41 through 45
    Processing sheet with id=AB2, first strand: chain 'E' and resid 48 through 50
      removed outlier: 6.148A  pdb=" N   ARG E  76 " --> pdb=" O   TRP E  85 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   TRP E  85 " --> pdb=" O   ARG E  76 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 48 through 50
      removed outlier: 4.006A  pdb=" N   PHE E 148 " --> pdb=" O   ARG E 136 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 178 through 179
    Processing sheet with id=AB5, first strand: chain 'E' and resid 184 through 185
      removed outlier: 6.434A  pdb=" N   LEU E 212 " --> pdb=" O   TYR E 228 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   TYR E 228 " --> pdb=" O   LEU E 212 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   TRP E 214 " --> pdb=" O   LEU E 226 " (cutoff:3.500A)

    457 hydrogen bonds defined for protein.
    1272 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: 1.42

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2909
        1.34 -     1.46: 2241
        1.46 -     1.58: 3947
        1.58 -     1.70: 0
        1.70 -     1.82: 89
  Bond restraints: 9186
  Sorted by residual:
  bond pdb=" C   ILE A  29 "
       pdb=" N   PRO A  30 "
    ideal  model  delta    sigma   weight residual
    1.335  1.370 -0.035 1.36e-02 5.41e+03 6.46e+00
  bond pdb=" CA  ILE A  29 "
       pdb=" CB  ILE A  29 "
    ideal  model  delta    sigma   weight residual
    1.534  1.545 -0.011 6.80e-03 2.16e+04 2.52e+00
  bond pdb=" CA  ASP C 291 "
       pdb=" C   ASP C 291 "
    ideal  model  delta    sigma   weight residual
    1.523  1.498  0.025 1.80e-02 3.09e+03 1.92e+00
  bond pdb=" CA  ILE A  29 "
       pdb=" C   ILE A  29 "
    ideal  model  delta    sigma   weight residual
    1.520  1.531 -0.012 8.80e-03 1.29e+04 1.73e+00
  bond pdb=" C   ILE A 166 "
       pdb=" N   PRO A 167 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.012 1.19e-02 7.06e+03 9.81e-01
  ... (remaining 9181 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 11946
        1.27 -     2.54: 403
        2.54 -     3.81: 75
        3.81 -     5.08: 19
        5.08 -     6.34: 8
  Bond angle restraints: 12451
  Sorted by residual:
  angle pdb=" N   GLN C 259 "
        pdb=" CA  GLN C 259 "
        pdb=" C   GLN C 259 "
      ideal   model   delta    sigma   weight residual
     108.34  112.55   -4.21 1.31e+00 5.83e-01 1.03e+01
  angle pdb=" C   VAL A 134 "
        pdb=" N   ILE A 135 "
        pdb=" CA  ILE A 135 "
      ideal   model   delta    sigma   weight residual
     122.66  119.84    2.82 9.70e-01 1.06e+00 8.48e+00
  angle pdb=" C   ASN A  28 "
        pdb=" N   ILE A  29 "
        pdb=" CA  ILE A  29 "
      ideal   model   delta    sigma   weight residual
     120.24  121.97   -1.73 6.30e-01 2.52e+00 7.51e+00
  angle pdb=" C   ARG E 229 "
        pdb=" N   MET E 230 "
        pdb=" CA  MET E 230 "
      ideal   model   delta    sigma   weight residual
     121.54  126.77   -5.23 1.91e+00 2.74e-01 7.50e+00
  angle pdb=" C   VAL E  86 "
        pdb=" N   ALA E  87 "
        pdb=" CA  ALA E  87 "
      ideal   model   delta    sigma   weight residual
     122.29  117.79    4.50 1.65e+00 3.67e-01 7.45e+00
  ... (remaining 12446 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.57: 5022
       16.57 -    33.13: 349
       33.13 -    49.70: 62
       49.70 -    66.26: 15
       66.26 -    82.83: 8
  Dihedral angle restraints: 5456
    sinusoidal: 2125
      harmonic: 3331
  Sorted by residual:
  dihedral pdb=" CA  TYR E 273 "
           pdb=" C   TYR E 273 "
           pdb=" N   PRO E 274 "
           pdb=" CA  PRO E 274 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  126.86   53.14     0      5.00e+00 4.00e-02 1.13e+02
  dihedral pdb=" CB  CYS E 197 "
           pdb=" SG  CYS E 197 "
           pdb=" SG  CYS E 267 "
           pdb=" CB  CYS E 267 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.73  -80.73     1      1.00e+01 1.00e-02 8.05e+01
  dihedral pdb=" CA  GLY E  92 "
           pdb=" C   GLY E  92 "
           pdb=" N   SER E  93 "
           pdb=" CA  SER E  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.99  -19.01     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 5453 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 983
       0.040 -    0.079: 331
       0.079 -    0.119: 92
       0.119 -    0.158: 13
       0.158 -    0.198: 2
  Chirality restraints: 1421
  Sorted by residual:
  chirality pdb=" CB  ILE A  29 "
            pdb=" CA  ILE A  29 "
            pdb=" CG1 ILE A  29 "
            pdb=" CG2 ILE A  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.77e-01
  chirality pdb=" CA  TYR B 191 "
            pdb=" N   TYR B 191 "
            pdb=" C   TYR B 191 "
            pdb=" CB  TYR B 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.48e-01
  chirality pdb=" CA  ILE B 140 "
            pdb=" N   ILE B 140 "
            pdb=" C   ILE B 140 "
            pdb=" CB  ILE B 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.25e-01
  ... (remaining 1418 not shown)

  Planarity restraints: 1574
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E 273 "   -0.044 5.00e-02 4.00e+02   6.67e-02 7.12e+00
        pdb=" N   PRO E 274 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO E 274 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO E 274 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 166 "    0.028 5.00e-02 4.00e+02   4.23e-02 2.86e+00
        pdb=" N   PRO A 167 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 167 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 167 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D  52 "   -0.027 5.00e-02 4.00e+02   4.15e-02 2.75e+00
        pdb=" N   PRO D  53 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO D  53 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO D  53 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1571 not shown)

  Histogram of nonbonded interaction distances:
        2.59 -     3.05: 5481
        3.05 -     3.51: 8604
        3.51 -     3.98: 13688
        3.98 -     4.44: 16299
        4.44 -     4.90: 27106
  Nonbonded interactions: 71178
  Sorted by model distance:
  nonbonded pdb=" N   TYR E 140 "
            pdb=" O   TYR E 140 "
     model   vdw
     2.588 2.496
  nonbonded pdb=" N   GLY E  94 "
            pdb=" N   THR E  95 "
     model   vdw
     2.591 2.560
  nonbonded pdb=" N   GLU E 272 "
            pdb=" O   GLU E 272 "
     model   vdw
     2.605 2.496
  nonbonded pdb=" O   GLN C  17 "
            pdb=" OD1 ASP C  20 "
     model   vdw
     2.611 3.040
  nonbonded pdb=" N   ASP C  76 "
            pdb=" OD1 ASP C  76 "
     model   vdw
     2.613 3.120
  ... (remaining 71173 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.770
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.650
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
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   0.046   9189  Z= 0.135
  Angle     :  0.583   6.344  12457  Z= 0.319
  Chirality :  0.043   0.198   1421
  Planarity :  0.004   0.067   1574
  Dihedral  : 12.083  82.831   3297
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.25), residues: 1131
  helix:  2.16 (0.26), residues: 399
  sheet:  0.46 (0.31), residues: 272
  loop : -1.13 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 314 
 TYR   0.012   0.001   TYR E 228 
 PHE   0.028   0.001   PHE A 127 
 TRP   0.012   0.001   TRP C  82 
 HIS   0.005   0.001   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9186)
  covalent geometry    : angle       0.58199 (12451)
  SS BOND              : bond        0.00418 (    3)
  SS BOND              : angle       1.32840 (    6)
  hydrogen bonds       : bond        0.14151 (  450)
  hydrogen bonds       : angle       5.44332 ( 1272)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ASP cc_start: 0.8094 (m-30) cc_final: 0.7780 (m-30)
REVERT: C  134 ARG cc_start: 0.8374 (ptt90) cc_final: 0.8109 (ptt90)
REVERT: C  161 SER cc_start: 0.8735 (t) cc_final: 0.8508 (t)
REVERT: C  214 ARG cc_start: 0.7812 (mmt180) cc_final: 0.7602 (mmt180)
REVERT: D   21 MET cc_start: 0.6375 (mmm) cc_final: 0.5798 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.6701
  time to fit residues: 83.5250
Evaluate side-chains
  91 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0270
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    0.7640

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

Flipped N/Q/H residues before XYZ refinement:
B  82 HIS
** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 GLN
C 239 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.173910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.137029 restraints weight = 9854.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 1.91
r_work: 0.3307 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.0930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9189  Z= 0.116
  Angle     :  0.534   6.565  12457  Z= 0.282
  Chirality :  0.042   0.213   1421
  Planarity :  0.004   0.066   1574
  Dihedral  :  4.481  49.557   1246
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  7.46 %
    Favored  : 90.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.25), residues: 1131
  helix:  2.26 (0.26), residues: 401
  sheet:  0.76 (0.31), residues: 263
  loop : -1.12 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 132 
 TYR   0.014   0.001   TYR E 228 
 PHE   0.019   0.001   PHE A 127 
 TRP   0.012   0.001   TRP C  82 
 HIS   0.003   0.001   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9186)
  covalent geometry    : angle       0.53347 (12451)
  SS BOND              : bond        0.00511 (    3)
  SS BOND              : angle       1.10565 (    6)
  hydrogen bonds       : bond        0.04285 (  450)
  hydrogen bonds       : angle       4.32221 ( 1272)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.250 
Fit side-chains
REVERT: B   20 ASP cc_start: 0.8276 (m-30) cc_final: 0.7984 (m-30)
REVERT: B  117 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.5942 (mtm180)
REVERT: B  132 ARG cc_start: 0.7368 (ttp-110) cc_final: 0.7054 (mtm180)
REVERT: B  208 ARG cc_start: 0.7623 (mmm160) cc_final: 0.6186 (mtm-85)
REVERT: C  161 SER cc_start: 0.8795 (t) cc_final: 0.8559 (t)
REVERT: C  175 GLN cc_start: 0.7398 (mm-40) cc_final: 0.7188 (mp10)
REVERT: C  214 ARG cc_start: 0.7855 (mmt180) cc_final: 0.7564 (mmt180)
REVERT: C  217 MET cc_start: 0.7118 (ppp) cc_final: 0.6774 (ppp)
REVERT: C  228 ASP cc_start: 0.7485 (m-30) cc_final: 0.6787 (p0)
REVERT: D   21 MET cc_start: 0.6410 (mmm) cc_final: 0.5820 (mtm)
  outliers start: 18
  outliers final: 10
  residues processed: 111
  average time/residue: 0.6461
  time to fit residues: 75.7295
Evaluate side-chains
  107 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  116 ASN
Chi-restraints excluded: chain B residue  117 ARG
Chi-restraints excluded: chain B residue  127 SER
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  237 ASN
Chi-restraints excluded: chain E residue   45 SER
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain E residue  242 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0050
   chunk 98 optimal weight:    0.0070
   chunk 10 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0570
   chunk 59 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0980
   chunk 55 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.1730

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

Flipped N/Q/H residues before XYZ refinement:
** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 GLN
C 237 ASN
C 239 ASN
E 232 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.179385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.141519 restraints weight = 9812.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.90
r_work: 0.3357 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9189  Z= 0.085
  Angle     :  0.463   6.612  12457  Z= 0.245
  Chirality :  0.040   0.223   1421
  Planarity :  0.004   0.063   1574
  Dihedral  :  4.047  46.716   1246
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  8.97 %
    Favored  : 89.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.26), residues: 1131
  helix:  2.57 (0.26), residues: 401
  sheet:  0.94 (0.31), residues: 268
  loop : -0.95 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  32 
 TYR   0.012   0.001   TYR E 228 
 PHE   0.008   0.001   PHE C 241 
 TRP   0.010   0.001   TRP C  82 
 HIS   0.002   0.000   HIS E  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00170 ( 9186)
  covalent geometry    : angle       0.46229 (12451)
  SS BOND              : bond        0.00379 (    3)
  SS BOND              : angle       0.80987 (    6)
  hydrogen bonds       : bond        0.03177 (  450)
  hydrogen bonds       : angle       3.95648 ( 1272)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A  246 LEU cc_start: 0.8014 (mt) cc_final: 0.7745 (mp)
REVERT: B   29 LYS cc_start: 0.6995 (tppt) cc_final: 0.6618 (tmmt)
REVERT: B  191 TYR cc_start: 0.7771 (m-80) cc_final: 0.7426 (m-80)
REVERT: B  208 ARG cc_start: 0.7681 (mmm160) cc_final: 0.6127 (mtm-85)
REVERT: C  214 ARG cc_start: 0.7792 (mmt180) cc_final: 0.7493 (mmt180)
REVERT: C  217 MET cc_start: 0.7065 (ppp) cc_final: 0.6830 (ppp)
REVERT: C  228 ASP cc_start: 0.7389 (m-30) cc_final: 0.6833 (p0)
REVERT: D   21 MET cc_start: 0.6429 (mmm) cc_final: 0.5809 (mtm)
  outliers start: 17
  outliers final: 3
  residues processed: 117
  average time/residue: 0.6037
  time to fit residues: 75.0365
Evaluate side-chains
  103 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain E residue  107 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 86 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0980
   chunk 54 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 101 optimal weight:    7.9990
   chunk 105 optimal weight:    0.9990
   overall best weight:    0.7986

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

Flipped N/Q/H residues before XYZ refinement:
C 220 GLN
C 230 ASN
C 239 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.173660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.136605 restraints weight = 10013.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.97
r_work: 0.3298 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.1345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9189  Z= 0.114
  Angle     :  0.512   7.267  12457  Z= 0.269
  Chirality :  0.041   0.201   1421
  Planarity :  0.004   0.065   1574
  Dihedral  :  4.219  48.359   1246
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 10.89 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.25), residues: 1131
  helix:  2.67 (0.26), residues: 395
  sheet:  1.00 (0.31), residues: 264
  loop : -1.03 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 132 
 TYR   0.011   0.001   TYR E 228 
 PHE   0.012   0.001   PHE A 127 
 TRP   0.009   0.001   TRP C  82 
 HIS   0.006   0.001   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9186)
  covalent geometry    : angle       0.51211 (12451)
  SS BOND              : bond        0.00470 (    3)
  SS BOND              : angle       0.88718 (    6)
  hydrogen bonds       : bond        0.04060 (  450)
  hydrogen bonds       : angle       4.02907 ( 1272)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.321 
Fit side-chains
REVERT: B   20 ASP cc_start: 0.8298 (m-30) cc_final: 0.7984 (m-30)
REVERT: B   29 LYS cc_start: 0.7274 (tppt) cc_final: 0.6879 (tmmt)
REVERT: B  191 TYR cc_start: 0.7795 (m-80) cc_final: 0.7492 (m-80)
REVERT: B  208 ARG cc_start: 0.7618 (mmm160) cc_final: 0.6080 (mtm-85)
REVERT: C  161 SER cc_start: 0.8796 (t) cc_final: 0.8541 (t)
REVERT: C  214 ARG cc_start: 0.7794 (mmt180) cc_final: 0.7477 (mmt180)
REVERT: C  217 MET cc_start: 0.7120 (ppp) cc_final: 0.6840 (ppp)
REVERT: C  228 ASP cc_start: 0.7479 (m-30) cc_final: 0.6815 (p0)
REVERT: D   21 MET cc_start: 0.6492 (mmm) cc_final: 0.5781 (mtm)
REVERT: E  273 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.6326 (t80)
  outliers start: 16
  outliers final: 9
  residues processed: 109
  average time/residue: 0.5769
  time to fit residues: 67.0429
Evaluate side-chains
  112 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  116 ASN
Chi-restraints excluded: chain E residue   45 SER
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain E residue  121 MET
Chi-restraints excluded: chain E residue  273 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 23 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 81 optimal weight:    0.6980
   chunk 108 optimal weight:    0.0670
   chunk 67 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 GLN
C 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.174339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.137909 restraints weight = 9923.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 1.93
r_work: 0.3318 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.1421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9189  Z= 0.103
  Angle     :  0.499   7.278  12457  Z= 0.262
  Chirality :  0.041   0.137   1421
  Planarity :  0.004   0.063   1574
  Dihedral  :  4.184  48.286   1246
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 11.69 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.25), residues: 1131
  helix:  2.58 (0.26), residues: 401
  sheet:  0.99 (0.32), residues: 260
  loop : -0.98 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 132 
 TYR   0.011   0.001   TYR E 228 
 PHE   0.010   0.001   PHE C 241 
 TRP   0.010   0.001   TRP C  82 
 HIS   0.006   0.001   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 9186)
  covalent geometry    : angle       0.49855 (12451)
  SS BOND              : bond        0.00500 (    3)
  SS BOND              : angle       0.84145 (    6)
  hydrogen bonds       : bond        0.03779 (  450)
  hydrogen bonds       : angle       3.97390 ( 1272)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.270 
Fit side-chains
REVERT: B    9 ASP cc_start: 0.7311 (m-30) cc_final: 0.7098 (m-30)
REVERT: B   29 LYS cc_start: 0.7260 (tppt) cc_final: 0.6894 (tmmt)
REVERT: B  208 ARG cc_start: 0.7672 (mmm160) cc_final: 0.6100 (mtm-85)
REVERT: C  161 SER cc_start: 0.8774 (t) cc_final: 0.8527 (t)
REVERT: C  217 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6809 (ppp)
REVERT: C  228 ASP cc_start: 0.7482 (m-30) cc_final: 0.6850 (p0)
REVERT: C  262 MET cc_start: 0.8471 (tpp) cc_final: 0.8264 (mmt)
REVERT: D   21 MET cc_start: 0.6551 (mmm) cc_final: 0.5875 (mtm)
REVERT: E  114 LYS cc_start: 0.7586 (mtmt) cc_final: 0.7334 (mtmm)
REVERT: E  273 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.6434 (t80)
  outliers start: 18
  outliers final: 9
  residues processed: 113
  average time/residue: 0.6125
  time to fit residues: 73.5536
Evaluate side-chains
  107 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  116 ASN
Chi-restraints excluded: chain B residue  127 SER
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain E residue  121 MET
Chi-restraints excluded: chain E residue  273 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 32 optimal weight:    0.0980
   chunk 39 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 104 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0770
   chunk 42 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    1.0142

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 GLN
C 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.172457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.134953 restraints weight = 9882.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 1.99
r_work: 0.3266 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9189  Z= 0.127
  Angle     :  0.535   7.475  12457  Z= 0.279
  Chirality :  0.042   0.140   1421
  Planarity :  0.004   0.065   1574
  Dihedral  :  4.344  49.714   1246
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.50 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.25), residues: 1131
  helix:  2.63 (0.26), residues: 395
  sheet:  0.89 (0.32), residues: 261
  loop : -1.01 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 132 
 TYR   0.011   0.001   TYR E 228 
 PHE   0.010   0.001   PHE C 241 
 TRP   0.010   0.001   TRP C  82 
 HIS   0.006   0.001   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9186)
  covalent geometry    : angle       0.53431 (12451)
  SS BOND              : bond        0.00555 (    3)
  SS BOND              : angle       0.90954 (    6)
  hydrogen bonds       : bond        0.04360 (  450)
  hydrogen bonds       : angle       4.09234 ( 1272)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.311 
Fit side-chains
REVERT: B   20 ASP cc_start: 0.8279 (m-30) cc_final: 0.7994 (m-30)
REVERT: B   29 LYS cc_start: 0.7375 (tppt) cc_final: 0.6883 (tptt)
REVERT: B  144 ASN cc_start: 0.8296 (t0) cc_final: 0.8089 (t0)
REVERT: B  191 TYR cc_start: 0.7913 (m-80) cc_final: 0.7373 (m-80)
REVERT: B  208 ARG cc_start: 0.7605 (mmm160) cc_final: 0.6048 (mtm-85)
REVERT: C  161 SER cc_start: 0.8885 (t) cc_final: 0.8609 (t)
REVERT: C  217 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6931 (ppp)
REVERT: C  228 ASP cc_start: 0.7514 (m-30) cc_final: 0.6871 (p0)
REVERT: D   21 MET cc_start: 0.6564 (mmm) cc_final: 0.5841 (mtm)
REVERT: E  114 LYS cc_start: 0.7698 (mtmt) cc_final: 0.7411 (mtmm)
REVERT: E  273 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.6476 (t80)
  outliers start: 21
  outliers final: 11
  residues processed: 112
  average time/residue: 0.5921
  time to fit residues: 70.6581
Evaluate side-chains
  110 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  116 ASN
Chi-restraints excluded: chain B residue  127 SER
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain E residue  121 MET
Chi-restraints excluded: chain E residue  273 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 67 optimal weight:    0.4980
   chunk 79 optimal weight:    0.9990
   chunk 104 optimal weight:    7.9990
   chunk 78 optimal weight:    0.0000
   chunk 53 optimal weight:   10.0000
   chunk 16 optimal weight:    7.9990
   chunk 108 optimal weight:    4.9990
   chunk 102 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 43 optimal weight:    9.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    1.2990

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 GLN
C 220 GLN
C 239 ASN
E 270 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.170699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.133461 restraints weight = 9921.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 1.94
r_work: 0.3244 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9189  Z= 0.149
  Angle     :  0.567   7.664  12457  Z= 0.296
  Chirality :  0.043   0.142   1421
  Planarity :  0.004   0.065   1574
  Dihedral  :  4.527  50.539   1246
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 12.40 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.25), residues: 1131
  helix:  2.52 (0.26), residues: 395
  sheet:  0.73 (0.31), residues: 266
  loop : -1.10 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 132 
 TYR   0.012   0.002   TYR B 191 
 PHE   0.010   0.002   PHE C 151 
 TRP   0.011   0.001   TRP E  85 
 HIS   0.007   0.001   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9186)
  covalent geometry    : angle       0.56675 (12451)
  SS BOND              : bond        0.00576 (    3)
  SS BOND              : angle       0.94676 (    6)
  hydrogen bonds       : bond        0.04745 (  450)
  hydrogen bonds       : angle       4.20940 ( 1272)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   98 ASN cc_start: 0.8561 (m110) cc_final: 0.8088 (m110)
REVERT: B   20 ASP cc_start: 0.8334 (m-30) cc_final: 0.8063 (m-30)
REVERT: B   29 LYS cc_start: 0.7425 (tppt) cc_final: 0.6922 (tptt)
REVERT: B  144 ASN cc_start: 0.8315 (t0) cc_final: 0.7934 (t0)
REVERT: B  191 TYR cc_start: 0.7946 (m-80) cc_final: 0.7527 (m-80)
REVERT: C   22 ARG cc_start: 0.6408 (OUTLIER) cc_final: 0.6135 (mtt180)
REVERT: C  161 SER cc_start: 0.8930 (t) cc_final: 0.8633 (t)
REVERT: C  175 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6713 (mt0)
REVERT: C  214 ARG cc_start: 0.7908 (mmt-90) cc_final: 0.7522 (mmt-90)
REVERT: C  217 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6933 (ppp)
REVERT: C  228 ASP cc_start: 0.7494 (m-30) cc_final: 0.6839 (p0)
REVERT: C  262 MET cc_start: 0.8443 (tpp) cc_final: 0.8235 (mmt)
REVERT: D   21 MET cc_start: 0.6567 (mmm) cc_final: 0.5776 (mtm)
REVERT: E  178 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8210 (mmm)
REVERT: E  240 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7183 (ttm110)
REVERT: E  273 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.6521 (t80)
  outliers start: 25
  outliers final: 13
  residues processed: 110
  average time/residue: 0.5486
  time to fit residues: 64.3917
Evaluate side-chains
  117 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  116 ASN
Chi-restraints excluded: chain B residue  127 SER
Chi-restraints excluded: chain C residue   22 ARG
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain E residue  121 MET
Chi-restraints excluded: chain E residue  178 MET
Chi-restraints excluded: chain E residue  240 ARG
Chi-restraints excluded: chain E residue  242 SER
Chi-restraints excluded: chain E residue  273 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 111 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 104 optimal weight:    7.9990
   chunk 77 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   chunk 98 optimal weight:    6.9990
   chunk 99 optimal weight:    3.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 GLN
C 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.168582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.130858 restraints weight = 9851.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 1.97
r_work: 0.3238 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9189  Z= 0.156
  Angle     :  0.578   7.625  12457  Z= 0.302
  Chirality :  0.043   0.145   1421
  Planarity :  0.004   0.065   1574
  Dihedral  :  4.588  50.717   1246
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 12.60 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.25), residues: 1131
  helix:  2.44 (0.26), residues: 395
  sheet:  0.69 (0.30), residues: 271
  loop : -1.13 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 132 
 TYR   0.013   0.002   TYR E  97 
 PHE   0.011   0.002   PHE A 111 
 TRP   0.012   0.001   TRP E  85 
 HIS   0.007   0.001   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 9186)
  covalent geometry    : angle       0.57803 (12451)
  SS BOND              : bond        0.00595 (    3)
  SS BOND              : angle       0.96968 (    6)
  hydrogen bonds       : bond        0.04841 (  450)
  hydrogen bonds       : angle       4.25569 ( 1272)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ASP cc_start: 0.8343 (m-30) cc_final: 0.8071 (m-30)
REVERT: B   29 LYS cc_start: 0.7410 (tppt) cc_final: 0.6901 (tptt)
REVERT: B  144 ASN cc_start: 0.8326 (t0) cc_final: 0.7921 (t0)
REVERT: B  208 ARG cc_start: 0.7772 (mmm160) cc_final: 0.6127 (mtm-85)
REVERT: C   22 ARG cc_start: 0.6371 (OUTLIER) cc_final: 0.5999 (mtt180)
REVERT: C  161 SER cc_start: 0.8925 (t) cc_final: 0.8629 (t)
REVERT: C  175 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.6735 (mt0)
REVERT: C  217 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6896 (ppp)
REVERT: C  228 ASP cc_start: 0.7457 (m-30) cc_final: 0.6778 (p0)
REVERT: C  262 MET cc_start: 0.8480 (tpp) cc_final: 0.8270 (mmt)
REVERT: D   21 MET cc_start: 0.6590 (mmm) cc_final: 0.5825 (mtm)
REVERT: E  114 LYS cc_start: 0.7732 (mtmt) cc_final: 0.7462 (mtmm)
REVERT: E  123 SER cc_start: 0.8325 (t) cc_final: 0.7946 (m)
REVERT: E  178 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8211 (mmm)
REVERT: E  240 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7168 (ttm110)
REVERT: E  273 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.6579 (t80)
  outliers start: 27
  outliers final: 17
  residues processed: 115
  average time/residue: 0.5968
  time to fit residues: 73.5280
Evaluate side-chains
  122 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  116 ASN
Chi-restraints excluded: chain B residue  127 SER
Chi-restraints excluded: chain C residue   22 ARG
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain E residue  121 MET
Chi-restraints excluded: chain E residue  178 MET
Chi-restraints excluded: chain E residue  193 VAL
Chi-restraints excluded: chain E residue  240 ARG
Chi-restraints excluded: chain E residue  242 SER
Chi-restraints excluded: chain E residue  273 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 107 optimal weight:    0.0470
   chunk 59 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 43 optimal weight:   10.0000
   chunk 111 optimal weight:    3.9990
   chunk 112 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 99 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.6680

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 GLN
C 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.172421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.135774 restraints weight = 9783.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 1.93
r_work: 0.3282 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9189  Z= 0.106
  Angle     :  0.518   7.393  12457  Z= 0.271
  Chirality :  0.041   0.140   1421
  Planarity :  0.004   0.062   1574
  Dihedral  :  4.348  49.215   1246
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.41 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.25), residues: 1131
  helix:  2.50 (0.26), residues: 401
  sheet:  0.80 (0.31), residues: 266
  loop : -1.02 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 132 
 TYR   0.012   0.001   TYR E 228 
 PHE   0.010   0.001   PHE C 241 
 TRP   0.010   0.001   TRP C  82 
 HIS   0.005   0.001   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 9186)
  covalent geometry    : angle       0.51812 (12451)
  SS BOND              : bond        0.00432 (    3)
  SS BOND              : angle       0.83691 (    6)
  hydrogen bonds       : bond        0.03925 (  450)
  hydrogen bonds       : angle       4.07881 ( 1272)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.353 
Fit side-chains
REVERT: B   20 ASP cc_start: 0.8309 (m-30) cc_final: 0.8019 (m-30)
REVERT: B   29 LYS cc_start: 0.7207 (tppt) cc_final: 0.6746 (tptt)
REVERT: B  144 ASN cc_start: 0.8155 (t0) cc_final: 0.7909 (t0)
REVERT: B  208 ARG cc_start: 0.7727 (mmm160) cc_final: 0.6090 (mtm-85)
REVERT: C   22 ARG cc_start: 0.6401 (OUTLIER) cc_final: 0.6022 (mtt180)
REVERT: C  161 SER cc_start: 0.8877 (t) cc_final: 0.8598 (t)
REVERT: C  214 ARG cc_start: 0.7935 (mmt-90) cc_final: 0.7629 (mmt-90)
REVERT: C  217 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6956 (ppp)
REVERT: C  228 ASP cc_start: 0.7455 (m-30) cc_final: 0.6832 (p0)
REVERT: D   21 MET cc_start: 0.6515 (mmm) cc_final: 0.5766 (mtm)
REVERT: E  114 LYS cc_start: 0.7672 (mtmt) cc_final: 0.7413 (mtmm)
REVERT: E  123 SER cc_start: 0.8334 (t) cc_final: 0.7950 (m)
REVERT: E  240 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7213 (ttm110)
REVERT: E  273 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.6631 (t80)
  outliers start: 21
  outliers final: 14
  residues processed: 112
  average time/residue: 0.6178
  time to fit residues: 74.0325
Evaluate side-chains
  117 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  116 ASN
Chi-restraints excluded: chain B residue  127 SER
Chi-restraints excluded: chain C residue   22 ARG
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain E residue  121 MET
Chi-restraints excluded: chain E residue  240 ARG
Chi-restraints excluded: chain E residue  242 SER
Chi-restraints excluded: chain E residue  273 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 78 optimal weight:    0.2980
   chunk 86 optimal weight:    6.9990
   chunk 112 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 GLN
C 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.171939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.135391 restraints weight = 9907.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 1.91
r_work: 0.3284 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9189  Z= 0.115
  Angle     :  0.527   7.849  12457  Z= 0.275
  Chirality :  0.041   0.139   1421
  Planarity :  0.004   0.064   1574
  Dihedral  :  4.350  49.467   1246
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.71 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.25), residues: 1131
  helix:  2.50 (0.26), residues: 401
  sheet:  0.82 (0.31), residues: 261
  loop : -1.05 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG B 132 
 TYR   0.012   0.001   TYR E 228 
 PHE   0.010   0.001   PHE C 241 
 TRP   0.011   0.001   TRP C  82 
 HIS   0.005   0.001   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9186)
  covalent geometry    : angle       0.52680 (12451)
  SS BOND              : bond        0.00450 (    3)
  SS BOND              : angle       0.83591 (    6)
  hydrogen bonds       : bond        0.04081 (  450)
  hydrogen bonds       : angle       4.07351 ( 1272)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.362 
Fit side-chains
REVERT: B   20 ASP cc_start: 0.8311 (m-30) cc_final: 0.8016 (m-30)
REVERT: B   29 LYS cc_start: 0.7256 (tppt) cc_final: 0.6781 (tptt)
REVERT: B  144 ASN cc_start: 0.8182 (t0) cc_final: 0.7894 (t0)
REVERT: B  208 ARG cc_start: 0.7727 (mmm160) cc_final: 0.6070 (mtm-85)
REVERT: C   22 ARG cc_start: 0.6352 (OUTLIER) cc_final: 0.5975 (mtt180)
REVERT: C  161 SER cc_start: 0.8912 (t) cc_final: 0.8614 (t)
REVERT: C  214 ARG cc_start: 0.7925 (mmt-90) cc_final: 0.7588 (mmt-90)
REVERT: C  217 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6947 (ppp)
REVERT: C  228 ASP cc_start: 0.7443 (m-30) cc_final: 0.6840 (p0)
REVERT: D   21 MET cc_start: 0.6555 (mmm) cc_final: 0.5795 (mtm)
REVERT: E  114 LYS cc_start: 0.7715 (mtmt) cc_final: 0.7450 (mtmm)
REVERT: E  123 SER cc_start: 0.8323 (t) cc_final: 0.7947 (m)
REVERT: E  240 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7203 (ttm110)
REVERT: E  273 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.6624 (t80)
  outliers start: 21
  outliers final: 13
  residues processed: 111
  average time/residue: 0.6234
  time to fit residues: 73.9535
Evaluate side-chains
  118 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  116 ASN
Chi-restraints excluded: chain B residue  127 SER
Chi-restraints excluded: chain C residue   22 ARG
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain E residue  121 MET
Chi-restraints excluded: chain E residue  240 ARG
Chi-restraints excluded: chain E residue  242 SER
Chi-restraints excluded: chain E residue  273 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0770
   chunk 82 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 85 optimal weight:   20.0000
   chunk 92 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 GLN
C 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.172707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.136256 restraints weight = 9750.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 1.91
r_work: 0.3295 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9189  Z= 0.108
  Angle     :  0.518   7.827  12457  Z= 0.271
  Chirality :  0.041   0.139   1421
  Planarity :  0.004   0.064   1574
  Dihedral  :  4.286  49.038   1246
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 13.71 %
    Favored  : 84.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.25), residues: 1131
  helix:  2.55 (0.26), residues: 401
  sheet:  0.82 (0.31), residues: 266
  loop : -1.01 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG B 132 
 TYR   0.012   0.001   TYR E 228 
 PHE   0.010   0.001   PHE C 241 
 TRP   0.010   0.001   TRP C  82 
 HIS   0.005   0.001   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 9186)
  covalent geometry    : angle       0.51810 (12451)
  SS BOND              : bond        0.00415 (    3)
  SS BOND              : angle       0.80612 (    6)
  hydrogen bonds       : bond        0.03878 (  450)
  hydrogen bonds       : angle       4.03563 ( 1272)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3226.41 seconds
wall clock time: 55 minutes 39.58 seconds (3339.58 seconds total)