Starting phenix.real_space_refine
on Mon May 12 12:41:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bue_44907/05_2025/9bue_44907.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bue_44907/05_2025/9bue_44907.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bue_44907/05_2025/9bue_44907.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bue_44907/05_2025/9bue_44907.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bue_44907/05_2025/9bue_44907.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bue_44907/05_2025/9bue_44907.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    5717      2.51       5
     N    1575      2.21       5
     O    1647      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9002
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1890
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2606
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "P"
      Number of atoms: 233
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 233
          Classifications: {'peptide': 32}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 28}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 2875
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2875
          Classifications: {'peptide': 366}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 16, 'TRANS': 349}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 197
          Unresolved non-hydrogen angles: 250
          Unresolved non-hydrogen dihedrals: 172
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 119
  Time building chain proxies: 5.49, per 1000 atoms: 0.61
  Number of scatterers: 9002
  At special positions: 0
  Unit cell: (79.12, 98.9, 151.36, 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      63     16.00
     O    1647      8.00
     N    1575      7.00
     C    5717      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P   2 " - pdb=" SG  CYS P   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  55 " - pdb=" SG  CYS R  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  72 " - pdb=" SG  CYS R 112 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  95 " - pdb=" SG  CYS R 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 219 " - pdb=" SG  CYS R 289 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.28
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2168

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 12 sheets defined
      41.6% alpha, 17.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 38
    Processing helix  chain 'A' and resid 52 through 60
      removed outlier: 3.785A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   MET A  60 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.613A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.585A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 3 through 26
      removed outlier: 3.535A  pdb=" N   LEU B   7 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.693A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 3.804A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 53 through 56
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'P' and resid 4 through 6
      No H-bonds generated for 'chain 'P' and resid 4 through 6'
    Processing helix  chain 'P' and resid 7 through 21
    Processing helix  chain 'R' and resid 39 through 62
    Processing helix  chain 'R' and resid 131 through 135
      removed outlier: 3.800A  pdb=" N   ASN R 135 " --> pdb=" O   THR R 132 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 138 through 173
      removed outlier: 3.879A  pdb=" N   ILE R 165 " --> pdb=" O   PHE R 161 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 205
      removed outlier: 3.882A  pdb=" N   LEU R 183 " --> pdb=" O   GLN R 179 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL R 203 " --> pdb=" O   ILE R 199 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   VAL R 205 " --> pdb=" O   HIS R 201 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 214
      removed outlier: 3.659A  pdb=" N   ARG R 214 " --> pdb=" O   GLU R 210 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 216 through 249
      removed outlier: 3.755A  pdb=" N   LYS R 220 " --> pdb=" O   PRO R 216 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   MET R 237 " --> pdb=" O   ASN R 233 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LEU R 238 " --> pdb=" O   TYR R 234 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   VAL R 249 " --> pdb=" O   HIS R 245 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 259 through 267
    Processing helix  chain 'R' and resid 267 through 285
      removed outlier: 3.935A  pdb=" N   LEU R 271 " --> pdb=" O   TRP R 267 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   VAL R 272 " --> pdb=" O   GLY R 268 " (cutoff:3.500A)
      Proline residue:  R 273  - end of helix
    Processing helix  chain 'R' and resid 287 through 291
      removed outlier: 3.947A  pdb=" N   LEU R 291 " --> pdb=" O   ASN R 288 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 295 through 297
      No H-bonds generated for 'chain 'R' and resid 295 through 297'
    Processing helix  chain 'R' and resid 298 through 331
      Proline residue:  R 304  - end of helix
      removed outlier: 3.526A  pdb=" N   MET R 327 " --> pdb=" O   LEU R 323 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ARG R 328 " --> pdb=" O   VAL R 324 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLU R 329 " --> pdb=" O   THR R 325 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR R 330 " --> pdb=" O   LYS R 326 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 333 through 353
      removed outlier: 4.076A  pdb=" N   TYR R 338 " --> pdb=" O   GLU R 334 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   LEU R 339 " --> pdb=" O   SER R 335 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   LYS R 340 " --> pdb=" O   HIS R 336 " (cutoff:3.500A)
      Proline residue:  R 350  - end of helix
    Processing helix  chain 'R' and resid 354 through 359
    Processing helix  chain 'R' and resid 365 through 382
    Processing helix  chain 'R' and resid 382 through 392
    Processing helix  chain 'R' and resid 395 through 413
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 4.043A  pdb=" N   LEU A  45 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.716A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.057A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL B  71 " --> pdb=" O   HIS B  62 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.600A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.649A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.816A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.761A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.612A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 11 through 12
      removed outlier: 8.718A  pdb=" N   VAL N  12 " --> pdb=" O   GLN N 123 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   THR N 125 " --> pdb=" O   VAL N  12 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   TYR N  94 " --> pdb=" O   THR N 122 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL N 124 " --> pdb=" O   ALA N  92 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 19 through 23
      removed outlier: 3.897A  pdb=" N   LEU N  20 " --> pdb=" O   LEU N  81 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   THR N  78 " --> pdb=" O   ASP N  73 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ASP N  73 " --> pdb=" O   THR N  78 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 91 through 94
    Processing sheet with id=AB3, first strand: chain 'R' and resid 120 through 121
      removed outlier: 3.738A  pdb=" N   ARG R 126 " --> pdb=" O   HIS R 121 " (cutoff:3.500A)

    437 hydrogen bonds defined for protein.
    1266 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.36

  Time building geometry restraints manager: 2.67 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2901
        1.34 -     1.46: 1510
        1.46 -     1.58: 4703
        1.58 -     1.70: 0
        1.70 -     1.82: 88
  Bond restraints: 9202
  Sorted by residual:
  bond pdb=" N   VAL A 224 "
       pdb=" CA  VAL A 224 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.25e-02 6.40e+03 1.02e+01
  bond pdb=" N   ARG A 228 "
       pdb=" CA  ARG A 228 "
    ideal  model  delta    sigma   weight residual
    1.453  1.491 -0.038 1.37e-02 5.33e+03 7.69e+00
  bond pdb=" N   ASP A 223 "
       pdb=" CA  ASP A 223 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.23e-02 6.61e+03 7.66e+00
  bond pdb=" N   THR P  30 "
       pdb=" CA  THR P  30 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.23e-02 6.61e+03 6.99e+00
  bond pdb=" N   VAL P  32 "
       pdb=" CA  VAL P  32 "
    ideal  model  delta    sigma   weight residual
    1.460  1.491 -0.032 1.21e-02 6.83e+03 6.91e+00
  ... (remaining 9197 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 12325
        2.33 -     4.66: 136
        4.66 -     6.99: 14
        6.99 -     9.32: 1
        9.32 -    11.65: 2
  Bond angle restraints: 12478
  Sorted by residual:
  angle pdb=" CA  PRO P  37 "
        pdb=" N   PRO P  37 "
        pdb=" CD  PRO P  37 "
      ideal   model   delta    sigma   weight residual
     112.00  103.88    8.12 1.40e+00 5.10e-01 3.36e+01
  angle pdb=" C   PHE A 222 "
        pdb=" CA  PHE A 222 "
        pdb=" CB  PHE A 222 "
      ideal   model   delta    sigma   weight residual
     112.09  105.43    6.66 1.43e+00 4.89e-01 2.17e+01
  angle pdb=" CA  PRO R  86 "
        pdb=" N   PRO R  86 "
        pdb=" CD  PRO R  86 "
      ideal   model   delta    sigma   weight residual
     112.00  106.50    5.50 1.40e+00 5.10e-01 1.55e+01
  angle pdb=" C   SER P  34 "
        pdb=" CA  SER P  34 "
        pdb=" CB  SER P  34 "
      ideal   model   delta    sigma   weight residual
     116.63  112.43    4.20 1.16e+00 7.43e-01 1.31e+01
  angle pdb=" O   THR P  36 "
        pdb=" C   THR P  36 "
        pdb=" N   PRO P  37 "
      ideal   model   delta    sigma   weight residual
     121.30  124.83   -3.53 1.03e+00 9.43e-01 1.17e+01
  ... (remaining 12473 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 4748
       17.89 -    35.77: 577
       35.77 -    53.66: 113
       53.66 -    71.55: 17
       71.55 -    89.44: 7
  Dihedral angle restraints: 5462
    sinusoidal: 2116
      harmonic: 3346
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -177.56  -89.44     1      1.00e+01 1.00e-02 9.51e+01
  dihedral pdb=" CB  CYS R  95 "
           pdb=" SG  CYS R  95 "
           pdb=" SG  CYS R 134 "
           pdb=" CB  CYS R 134 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.89  -63.89     1      1.00e+01 1.00e-02 5.38e+01
  dihedral pdb=" CB  CYS R  55 "
           pdb=" SG  CYS R  55 "
           pdb=" SG  CYS R  81 "
           pdb=" CB  CYS R  81 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.59  -45.59     1      1.00e+01 1.00e-02 2.88e+01
  ... (remaining 5459 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1196
       0.057 -    0.114: 174
       0.114 -    0.171: 17
       0.171 -    0.228: 1
       0.228 -    0.285: 3
  Chirality restraints: 1391
  Sorted by residual:
  chirality pdb=" CA  PRO P  37 "
            pdb=" N   PRO P  37 "
            pdb=" C   PRO P  37 "
            pdb=" CB  PRO P  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.43    0.29 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CA  PHE A 222 "
            pdb=" N   PHE A 222 "
            pdb=" C   PHE A 222 "
            pdb=" CB  PHE A 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" CA  ARG A 232 "
            pdb=" N   ARG A 232 "
            pdb=" C   ARG A 232 "
            pdb=" CB  ARG A 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 1388 not shown)

  Planarity restraints: 1595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R  85 "   -0.074 5.00e-02 4.00e+02   1.10e-01 1.92e+01
        pdb=" N   PRO R  86 "    0.189 5.00e-02 4.00e+02
        pdb=" CA  PRO R  86 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO R  86 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 331 "    0.035 5.00e-02 4.00e+02   5.32e-02 4.53e+00
        pdb=" N   PRO A 332 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 332 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 332 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 327 "   -0.033 5.00e-02 4.00e+02   5.07e-02 4.11e+00
        pdb=" N   PRO A 328 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 328 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 328 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1592 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 637
        2.74 -     3.28: 9082
        3.28 -     3.82: 14933
        3.82 -     4.36: 17001
        4.36 -     4.90: 29991
  Nonbonded interactions: 71644
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OG1 THR B 128 "
            pdb=" OE1 GLU B 130 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" N   GLU R 397 "
            pdb=" OE1 GLU R 397 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" OD1 ASP B 247 "
            pdb=" OG1 THR B 249 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.263 3.040
  ... (remaining 71639 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.520
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
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   0.107   9210  Z= 0.198
  Angle     :  0.574  11.650  12492  Z= 0.334
  Chirality :  0.042   0.285   1391
  Planarity :  0.005   0.110   1595
  Dihedral  : 15.562  86.620   3273
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 17.98 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.25), residues: 1126
  helix:  1.21 (0.25), residues: 433
  sheet:  0.32 (0.35), residues: 231
  loop : -0.37 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP R  79 
 HIS   0.003   0.000   HIS A 357 
 PHE   0.015   0.001   PHE R 119 
 TYR   0.024   0.001   TYR R  98 
 ARG   0.004   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25458 (  437)
  hydrogen bonds       : angle       7.34970 ( 1266)
  SS BOND              : bond        0.00145 (    7)
  SS BOND              : angle       0.77992 (   14)
  covalent geometry    : bond        0.00289 ( 9202)
  covalent geometry    : angle       0.57339 (12478)
  Misc. bond           : bond        0.10728 (    1)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 192
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 ARG cc_start: 0.7487 (ptp-110) cc_final: 0.7282 (ttp-110)
REVERT: B   42 ARG cc_start: 0.6199 (ttt180) cc_final: 0.5566 (ptm160)
REVERT: B  333 ASP cc_start: 0.8272 (p0) cc_final: 0.7787 (p0)
REVERT: R  187 MET cc_start: 0.7266 (tpp) cc_final: 0.6945 (tpt)
REVERT: R  213 ARG cc_start: 0.6404 (tpt-90) cc_final: 0.5767 (ptm160)
REVERT: R  229 MET cc_start: 0.7401 (tpp) cc_final: 0.7195 (tpp)
REVERT: R  332 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7625 (tm-30)
REVERT: R  410 LYS cc_start: 0.6817 (ptmt) cc_final: 0.6533 (pttm)
  outliers start: 4
  outliers final: 4
  residues processed: 194
  average time/residue: 0.2770
  time to fit residues: 68.4467
Evaluate side-chains
  175 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 171
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain B residue   10 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   chunk 87 optimal weight:    0.0010
   chunk 33 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0970
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.4784

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

Flipped N/Q/H residues before XYZ refinement:
B   6 GLN
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 194 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.183780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.145528 restraints weight = 11365.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.149027 restraints weight = 8041.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.151427 restraints weight = 5922.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.1388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9210  Z= 0.122
  Angle     :  0.527   5.919  12492  Z= 0.291
  Chirality :  0.041   0.185   1391
  Planarity :  0.004   0.063   1595
  Dihedral  :  4.563  67.277   1253
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 16.93 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.25), residues: 1126
  helix:  1.80 (0.25), residues: 440
  sheet:  0.35 (0.34), residues: 231
  loop : -0.49 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 223 
 PHE   0.022   0.001   PHE R 161 
 TYR   0.021   0.001   TYR R  98 
 ARG   0.003   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04932 (  437)
  hydrogen bonds       : angle       4.91291 ( 1266)
  SS BOND              : bond        0.00231 (    7)
  SS BOND              : angle       0.61693 (   14)
  covalent geometry    : bond        0.00248 ( 9202)
  covalent geometry    : angle       0.52648 (12478)
  Misc. bond           : bond        0.00078 (    1)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 195
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6614 (mp0)
REVERT: A   17 LYS cc_start: 0.8584 (mtmm) cc_final: 0.8377 (mttm)
REVERT: A  333 ARG cc_start: 0.7833 (tpt170) cc_final: 0.7382 (tpt170)
REVERT: B    6 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6532 (pp30)
REVERT: B   30 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7780 (tt)
REVERT: B   42 ARG cc_start: 0.6164 (ttt180) cc_final: 0.5489 (ptm160)
REVERT: B  210 LEU cc_start: 0.8449 (tp) cc_final: 0.8204 (tp)
REVERT: G   50 LEU cc_start: 0.8648 (mt) cc_final: 0.8446 (mp)
REVERT: R  137 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.6803 (m-10)
REVERT: R  157 SER cc_start: 0.8855 (p) cc_final: 0.8496 (m)
REVERT: R  187 MET cc_start: 0.7202 (tpp) cc_final: 0.6676 (tpt)
REVERT: R  213 ARG cc_start: 0.6511 (tpt-90) cc_final: 0.5812 (ptm160)
REVERT: R  276 ILE cc_start: 0.7742 (mm) cc_final: 0.7525 (mt)
REVERT: R  397 GLU cc_start: 0.8402 (pm20) cc_final: 0.8129 (pm20)
REVERT: R  410 LYS cc_start: 0.7311 (ptmt) cc_final: 0.6980 (pttm)
  outliers start: 27
  outliers final: 15
  residues processed: 212
  average time/residue: 0.2672
  time to fit residues: 73.3042
Evaluate side-chains
  196 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 177
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   60 TYR
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain P residue    1 LYS
Chi-restraints excluded: chain R residue  137 PHE
Chi-restraints excluded: chain R residue  199 ILE
Chi-restraints excluded: chain R residue  324 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 19 optimal weight:    6.9990
   chunk 100 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 84 optimal weight:    0.1980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.181798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.141947 restraints weight = 11601.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.145889 restraints weight = 8303.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.148086 restraints weight = 6314.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9210  Z= 0.113
  Angle     :  0.504   6.107  12492  Z= 0.276
  Chirality :  0.041   0.155   1391
  Planarity :  0.004   0.041   1595
  Dihedral  :  4.243  74.201   1246
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 16.51 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.26), residues: 1126
  helix:  2.05 (0.25), residues: 445
  sheet:  0.24 (0.34), residues: 235
  loop : -0.47 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.025   0.001   TYR R  98 
 ARG   0.006   0.000   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04113 (  437)
  hydrogen bonds       : angle       4.47089 ( 1266)
  SS BOND              : bond        0.00203 (    7)
  SS BOND              : angle       0.62897 (   14)
  covalent geometry    : bond        0.00242 ( 9202)
  covalent geometry    : angle       0.50409 (12478)
  Misc. bond           : bond        0.00007 (    1)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 187
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6661 (mp0)
REVERT: A  314 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6761 (tm-30)
REVERT: B   42 ARG cc_start: 0.6204 (ttt180) cc_final: 0.5486 (ptm160)
REVERT: B  234 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8578 (m-80)
REVERT: G    9 ILE cc_start: 0.7353 (pt) cc_final: 0.7052 (tt)
REVERT: R  137 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6743 (m-10)
REVERT: R  157 SER cc_start: 0.8805 (p) cc_final: 0.8562 (m)
REVERT: R  187 MET cc_start: 0.7161 (tpp) cc_final: 0.6659 (tpt)
REVERT: R  196 MET cc_start: 0.7773 (mtt) cc_final: 0.7523 (mtp)
REVERT: R  213 ARG cc_start: 0.6568 (tpt-90) cc_final: 0.5829 (ptm160)
REVERT: R  276 ILE cc_start: 0.7811 (mm) cc_final: 0.7576 (mt)
REVERT: R  410 LYS cc_start: 0.7431 (ptmt) cc_final: 0.7073 (pttm)
  outliers start: 39
  outliers final: 27
  residues processed: 210
  average time/residue: 0.2554
  time to fit residues: 69.7537
Evaluate side-chains
  206 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 176
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   60 TYR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain P residue    1 LYS
Chi-restraints excluded: chain R residue  137 PHE
Chi-restraints excluded: chain R residue  199 ILE
Chi-restraints excluded: chain R residue  247 LEU
Chi-restraints excluded: chain R residue  324 VAL
Chi-restraints excluded: chain R residue  361 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 31 optimal weight:    0.4980
   chunk 54 optimal weight:    0.0670
   chunk 85 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 68 optimal weight:    7.9990
   chunk 105 optimal weight:    0.9980
   chunk 92 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 82 optimal weight:    8.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8920

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.178731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.139120 restraints weight = 11486.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.142690 restraints weight = 8360.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.145072 restraints weight = 6200.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9210  Z= 0.124
  Angle     :  0.521   8.336  12492  Z= 0.278
  Chirality :  0.041   0.159   1391
  Planarity :  0.003   0.038   1595
  Dihedral  :  4.307  74.281   1246
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 16.93 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.26), residues: 1126
  helix:  2.13 (0.25), residues: 446
  sheet:  0.10 (0.34), residues: 235
  loop : -0.59 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.026   0.001   TYR R  98 
 ARG   0.004   0.000   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03819 (  437)
  hydrogen bonds       : angle       4.29734 ( 1266)
  SS BOND              : bond        0.00169 (    7)
  SS BOND              : angle       0.75107 (   14)
  covalent geometry    : bond        0.00281 ( 9202)
  covalent geometry    : angle       0.52095 (12478)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 180
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6762 (mp0)
REVERT: A  314 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6770 (tm-30)
REVERT: A  347 ARG cc_start: 0.7613 (ptp-110) cc_final: 0.7270 (ttp-170)
REVERT: B   42 ARG cc_start: 0.6296 (ttt180) cc_final: 0.5523 (ptm160)
REVERT: B   59 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7511 (m-10)
REVERT: B  172 GLU cc_start: 0.7389 (pt0) cc_final: 0.7163 (pt0)
REVERT: B  234 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8641 (m-80)
REVERT: R  137 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.6923 (m-80)
REVERT: R  157 SER cc_start: 0.8740 (p) cc_final: 0.8498 (m)
REVERT: R  187 MET cc_start: 0.7073 (tpp) cc_final: 0.6738 (tpt)
REVERT: R  213 ARG cc_start: 0.6539 (tpt-90) cc_final: 0.5895 (ptm160)
REVERT: R  410 LYS cc_start: 0.7478 (ptmt) cc_final: 0.7124 (pttm)
  outliers start: 41
  outliers final: 32
  residues processed: 204
  average time/residue: 0.2595
  time to fit residues: 68.5675
Evaluate side-chains
  210 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 174
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   60 TYR
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain P residue    1 LYS
Chi-restraints excluded: chain R residue  137 PHE
Chi-restraints excluded: chain R residue  199 ILE
Chi-restraints excluded: chain R residue  247 LEU
Chi-restraints excluded: chain R residue  324 VAL
Chi-restraints excluded: chain R residue  357 VAL
Chi-restraints excluded: chain R residue  361 TRP
Chi-restraints excluded: chain R residue  367 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 108 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0030
   chunk 100 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
A 390 GLN
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.177028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.138424 restraints weight = 11428.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.142476 restraints weight = 7947.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.144495 restraints weight = 5855.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9210  Z= 0.115
  Angle     :  0.515   7.596  12492  Z= 0.276
  Chirality :  0.041   0.146   1391
  Planarity :  0.003   0.037   1595
  Dihedral  :  4.348  75.276   1246
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 17.14 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.26), residues: 1126
  helix:  2.16 (0.25), residues: 446
  sheet:  0.08 (0.34), residues: 235
  loop : -0.63 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.025   0.001   TYR R  98 
 ARG   0.004   0.000   ARG A 389 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03564 (  437)
  hydrogen bonds       : angle       4.17268 ( 1266)
  SS BOND              : bond        0.00145 (    7)
  SS BOND              : angle       0.79821 (   14)
  covalent geometry    : bond        0.00259 ( 9202)
  covalent geometry    : angle       0.51483 (12478)
  Misc. bond           : bond        0.00009 (    1)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 179
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6867 (mp0)
REVERT: A  314 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6867 (tm-30)
REVERT: A  347 ARG cc_start: 0.7579 (ptp-110) cc_final: 0.7237 (ttp-170)
REVERT: B   59 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7532 (m-10)
REVERT: B  172 GLU cc_start: 0.7462 (pt0) cc_final: 0.7158 (pt0)
REVERT: B  190 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8563 (pt)
REVERT: B  234 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8595 (m-80)
REVERT: B  266 HIS cc_start: 0.7294 (OUTLIER) cc_final: 0.6908 (t70)
REVERT: R  137 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.6793 (m-10)
REVERT: R  157 SER cc_start: 0.8748 (p) cc_final: 0.8508 (m)
REVERT: R  187 MET cc_start: 0.7031 (tpp) cc_final: 0.6722 (tpt)
REVERT: R  213 ARG cc_start: 0.6573 (tpt-90) cc_final: 0.5947 (ptm160)
REVERT: R  346 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.6532 (mtp)
REVERT: R  397 GLU cc_start: 0.8364 (pm20) cc_final: 0.8141 (pm20)
REVERT: R  410 LYS cc_start: 0.7517 (ptmt) cc_final: 0.7185 (pttm)
  outliers start: 40
  outliers final: 27
  residues processed: 202
  average time/residue: 0.2591
  time to fit residues: 67.9951
Evaluate side-chains
  204 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 170
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   60 TYR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue  137 PHE
Chi-restraints excluded: chain R residue  199 ILE
Chi-restraints excluded: chain R residue  247 LEU
Chi-restraints excluded: chain R residue  324 VAL
Chi-restraints excluded: chain R residue  346 MET
Chi-restraints excluded: chain R residue  357 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 95 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
A 390 GLN
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.176598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.137249 restraints weight = 11528.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.140207 restraints weight = 8180.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.142615 restraints weight = 6289.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.2564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9210  Z= 0.122
  Angle     :  0.523   7.163  12492  Z= 0.278
  Chirality :  0.041   0.146   1391
  Planarity :  0.003   0.036   1595
  Dihedral  :  4.376  76.004   1246
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 17.46 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.26), residues: 1126
  helix:  2.20 (0.25), residues: 446
  sheet:  0.01 (0.34), residues: 235
  loop : -0.68 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.014   0.001   PHE R 161 
 TYR   0.022   0.001   TYR R  98 
 ARG   0.004   0.000   ARG A 389 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03542 (  437)
  hydrogen bonds       : angle       4.12513 ( 1266)
  SS BOND              : bond        0.00145 (    7)
  SS BOND              : angle       0.85219 (   14)
  covalent geometry    : bond        0.00278 ( 9202)
  covalent geometry    : angle       0.52236 (12478)
  Misc. bond           : bond        0.00016 (    1)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 174
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6907 (mp0)
REVERT: A  308 ILE cc_start: 0.6305 (OUTLIER) cc_final: 0.6085 (mm)
REVERT: A  347 ARG cc_start: 0.7576 (ptp-110) cc_final: 0.7231 (ttp-170)
REVERT: B   59 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7470 (m-10)
REVERT: B  172 GLU cc_start: 0.7574 (pt0) cc_final: 0.7202 (pt0)
REVERT: B  190 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8563 (pt)
REVERT: B  234 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8588 (m-80)
REVERT: B  266 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.6930 (t70)
REVERT: R  137 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.6850 (m-10)
REVERT: R  157 SER cc_start: 0.8764 (p) cc_final: 0.8533 (m)
REVERT: R  187 MET cc_start: 0.7043 (tpp) cc_final: 0.6756 (tpt)
REVERT: R  213 ARG cc_start: 0.6683 (tpt-90) cc_final: 0.5838 (ptm160)
REVERT: R  346 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6629 (mtp)
REVERT: R  410 LYS cc_start: 0.7603 (ptmt) cc_final: 0.7246 (pttm)
  outliers start: 44
  outliers final: 31
  residues processed: 202
  average time/residue: 0.2536
  time to fit residues: 67.4403
Evaluate side-chains
  202 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 163
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   60 TYR
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue  137 PHE
Chi-restraints excluded: chain R residue  160 ILE
Chi-restraints excluded: chain R residue  165 ILE
Chi-restraints excluded: chain R residue  199 ILE
Chi-restraints excluded: chain R residue  247 LEU
Chi-restraints excluded: chain R residue  324 VAL
Chi-restraints excluded: chain R residue  346 MET
Chi-restraints excluded: chain R residue  357 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 31 optimal weight:    0.2980
   chunk 46 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 103 optimal weight:    6.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 GLN
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.176340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.136944 restraints weight = 11638.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.140375 restraints weight = 8289.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.142619 restraints weight = 6225.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9210  Z= 0.117
  Angle     :  0.529   6.780  12492  Z= 0.281
  Chirality :  0.041   0.168   1391
  Planarity :  0.003   0.036   1595
  Dihedral  :  4.395  76.526   1246
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 18.40 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.26), residues: 1126
  helix:  2.23 (0.25), residues: 446
  sheet: -0.02 (0.34), residues: 235
  loop : -0.68 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.014   0.001   PHE N  68 
 TYR   0.021   0.001   TYR R  98 
 ARG   0.005   0.000   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03445 (  437)
  hydrogen bonds       : angle       4.11989 ( 1266)
  SS BOND              : bond        0.00150 (    7)
  SS BOND              : angle       0.85004 (   14)
  covalent geometry    : bond        0.00266 ( 9202)
  covalent geometry    : angle       0.52832 (12478)
  Misc. bond           : bond        0.00013 (    1)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 171
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 ILE cc_start: 0.6318 (OUTLIER) cc_final: 0.6085 (mm)
REVERT: B   59 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7466 (m-10)
REVERT: B  172 GLU cc_start: 0.7699 (pt0) cc_final: 0.7246 (pt0)
REVERT: B  190 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8575 (pt)
REVERT: B  234 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8660 (m-80)
REVERT: R  137 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.6842 (m-10)
REVERT: R  157 SER cc_start: 0.8768 (p) cc_final: 0.8542 (m)
REVERT: R  187 MET cc_start: 0.7145 (tpp) cc_final: 0.6880 (tpt)
REVERT: R  213 ARG cc_start: 0.6727 (tpt-90) cc_final: 0.5871 (ptm160)
REVERT: R  346 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6631 (mtp)
REVERT: R  410 LYS cc_start: 0.7627 (ptmt) cc_final: 0.7247 (pttm)
  outliers start: 45
  outliers final: 34
  residues processed: 200
  average time/residue: 0.2442
  time to fit residues: 64.3676
Evaluate side-chains
  206 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 166
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   60 TYR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue  137 PHE
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  160 ILE
Chi-restraints excluded: chain R residue  165 ILE
Chi-restraints excluded: chain R residue  199 ILE
Chi-restraints excluded: chain R residue  247 LEU
Chi-restraints excluded: chain R residue  324 VAL
Chi-restraints excluded: chain R residue  346 MET
Chi-restraints excluded: chain R residue  357 VAL
Chi-restraints excluded: chain R residue  367 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 23 optimal weight:   10.0000
   chunk 85 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 2 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0370
   chunk 16 optimal weight:    0.8980
   chunk 104 optimal weight:    0.9980
   chunk 7 optimal weight:    6.9990
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 GLN
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.173508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.134371 restraints weight = 11788.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.137412 restraints weight = 8064.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.139866 restraints weight = 6209.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9210  Z= 0.112
  Angle     :  0.522   6.542  12492  Z= 0.277
  Chirality :  0.041   0.159   1391
  Planarity :  0.003   0.036   1595
  Dihedral  :  4.388  77.399   1246
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 18.51 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.26), residues: 1126
  helix:  2.24 (0.25), residues: 446
  sheet: -0.04 (0.34), residues: 235
  loop : -0.63 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R  79 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.020   0.001   PHE A 222 
 TYR   0.020   0.001   TYR R  98 
 ARG   0.004   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03329 (  437)
  hydrogen bonds       : angle       4.03571 ( 1266)
  SS BOND              : bond        0.00151 (    7)
  SS BOND              : angle       0.85675 (   14)
  covalent geometry    : bond        0.00252 ( 9202)
  covalent geometry    : angle       0.52125 (12478)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 170
  time to evaluate  : 1.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8236 (mtm-85) cc_final: 0.7897 (mtm110)
REVERT: A  308 ILE cc_start: 0.6288 (OUTLIER) cc_final: 0.6067 (mm)
REVERT: B   59 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7489 (m-10)
REVERT: B  172 GLU cc_start: 0.7772 (pt0) cc_final: 0.7333 (pt0)
REVERT: B  190 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8587 (pt)
REVERT: B  234 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8612 (m-80)
REVERT: R  137 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.6873 (m-10)
REVERT: R  157 SER cc_start: 0.8767 (p) cc_final: 0.8551 (m)
REVERT: R  187 MET cc_start: 0.7081 (tpp) cc_final: 0.6843 (tpt)
REVERT: R  213 ARG cc_start: 0.6625 (tpt-90) cc_final: 0.6017 (mmm160)
REVERT: R  346 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6575 (mtp)
REVERT: R  359 PHE cc_start: 0.7879 (m-10) cc_final: 0.7522 (m-10)
REVERT: R  410 LYS cc_start: 0.7660 (ptmt) cc_final: 0.7274 (pttm)
  outliers start: 44
  outliers final: 34
  residues processed: 198
  average time/residue: 0.2572
  time to fit residues: 66.9611
Evaluate side-chains
  206 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 166
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   60 TYR
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue  137 PHE
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  160 ILE
Chi-restraints excluded: chain R residue  165 ILE
Chi-restraints excluded: chain R residue  199 ILE
Chi-restraints excluded: chain R residue  247 LEU
Chi-restraints excluded: chain R residue  324 VAL
Chi-restraints excluded: chain R residue  346 MET
Chi-restraints excluded: chain R residue  357 VAL
Chi-restraints excluded: chain R residue  361 TRP
Chi-restraints excluded: chain R residue  367 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 86 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 58 optimal weight:    0.1980
   chunk 107 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 40 optimal weight:    0.3980
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.177025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.139266 restraints weight = 11559.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.141418 restraints weight = 7669.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.143664 restraints weight = 5862.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9210  Z= 0.110
  Angle     :  0.528   7.409  12492  Z= 0.280
  Chirality :  0.041   0.156   1391
  Planarity :  0.003   0.035   1595
  Dihedral  :  3.771  17.971   1243
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 19.56 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.26), residues: 1126
  helix:  2.26 (0.25), residues: 446
  sheet: -0.08 (0.34), residues: 235
  loop : -0.66 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R  79 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.012   0.001   PHE A 222 
 TYR   0.020   0.001   TYR R  98 
 ARG   0.004   0.000   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03265 (  437)
  hydrogen bonds       : angle       3.99138 ( 1266)
  SS BOND              : bond        0.00155 (    7)
  SS BOND              : angle       0.85730 (   14)
  covalent geometry    : bond        0.00245 ( 9202)
  covalent geometry    : angle       0.52704 (12478)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 167
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 ILE cc_start: 0.6310 (OUTLIER) cc_final: 0.6071 (mm)
REVERT: B   59 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7505 (m-10)
REVERT: B  172 GLU cc_start: 0.7710 (pt0) cc_final: 0.7261 (pt0)
REVERT: B  190 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8584 (pt)
REVERT: B  234 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8613 (m-80)
REVERT: R  137 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.6951 (m-10)
REVERT: R  157 SER cc_start: 0.8802 (p) cc_final: 0.8558 (m)
REVERT: R  187 MET cc_start: 0.7067 (tpp) cc_final: 0.6866 (tpt)
REVERT: R  213 ARG cc_start: 0.6688 (tpt-90) cc_final: 0.6033 (mmm160)
REVERT: R  334 GLU cc_start: 0.8489 (tp30) cc_final: 0.8279 (tp30)
REVERT: R  346 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6554 (mtp)
REVERT: R  359 PHE cc_start: 0.7839 (m-10) cc_final: 0.7505 (m-10)
REVERT: R  410 LYS cc_start: 0.7702 (ptmt) cc_final: 0.7297 (pttm)
  outliers start: 45
  outliers final: 34
  residues processed: 195
  average time/residue: 0.2385
  time to fit residues: 61.6585
Evaluate side-chains
  205 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 165
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   60 TYR
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  137 PHE
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  160 ILE
Chi-restraints excluded: chain R residue  165 ILE
Chi-restraints excluded: chain R residue  199 ILE
Chi-restraints excluded: chain R residue  324 VAL
Chi-restraints excluded: chain R residue  346 MET
Chi-restraints excluded: chain R residue  357 VAL
Chi-restraints excluded: chain R residue  361 TRP
Chi-restraints excluded: chain R residue  367 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 88 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 80 optimal weight:    0.0070
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
A 390 GLN
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.176509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.137518 restraints weight = 11677.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.139781 restraints weight = 8248.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.142255 restraints weight = 6644.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9210  Z= 0.116
  Angle     :  0.537   8.687  12492  Z= 0.285
  Chirality :  0.041   0.151   1391
  Planarity :  0.003   0.036   1595
  Dihedral  :  3.825  18.019   1243
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 19.14 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.26), residues: 1126
  helix:  2.21 (0.25), residues: 448
  sheet: -0.12 (0.34), residues: 235
  loop : -0.68 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R  79 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.019   0.001   PHE R 161 
 TYR   0.020   0.001   TYR R  98 
 ARG   0.004   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03323 (  437)
  hydrogen bonds       : angle       4.01324 ( 1266)
  SS BOND              : bond        0.00148 (    7)
  SS BOND              : angle       0.89660 (   14)
  covalent geometry    : bond        0.00265 ( 9202)
  covalent geometry    : angle       0.53637 (12478)
  Misc. bond           : bond        0.00015 (    1)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 171
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8254 (mtm-85) cc_final: 0.7975 (mtm110)
REVERT: A  308 ILE cc_start: 0.6343 (OUTLIER) cc_final: 0.6099 (mm)
REVERT: B  172 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7343 (pt0)
REVERT: B  190 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8589 (pt)
REVERT: B  234 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8615 (m-80)
REVERT: R  137 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7010 (m-10)
REVERT: R  157 SER cc_start: 0.8792 (p) cc_final: 0.8548 (m)
REVERT: R  187 MET cc_start: 0.7060 (tpp) cc_final: 0.6833 (tpt)
REVERT: R  213 ARG cc_start: 0.6685 (tpt-90) cc_final: 0.6040 (mmm160)
REVERT: R  337 MET cc_start: 0.7815 (ptm) cc_final: 0.7503 (ptp)
REVERT: R  346 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6582 (mtp)
REVERT: R  359 PHE cc_start: 0.7844 (m-10) cc_final: 0.7568 (m-10)
REVERT: R  410 LYS cc_start: 0.7710 (ptmt) cc_final: 0.7313 (pttm)
  outliers start: 45
  outliers final: 35
  residues processed: 197
  average time/residue: 0.2417
  time to fit residues: 63.5897
Evaluate side-chains
  213 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 172
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   60 TYR
Chi-restraints excluded: chain N residue   80 TYR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  137 PHE
Chi-restraints excluded: chain R residue  142 LEU
Chi-restraints excluded: chain R residue  160 ILE
Chi-restraints excluded: chain R residue  165 ILE
Chi-restraints excluded: chain R residue  199 ILE
Chi-restraints excluded: chain R residue  324 VAL
Chi-restraints excluded: chain R residue  346 MET
Chi-restraints excluded: chain R residue  357 VAL
Chi-restraints excluded: chain R residue  361 TRP
Chi-restraints excluded: chain R residue  367 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 99 optimal weight:    7.9990
   chunk 57 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0270
   chunk 92 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0570
   chunk 93 optimal weight:    0.5980
   chunk 80 optimal weight:    6.9990
   chunk 104 optimal weight:    0.7980
   chunk 95 optimal weight:    4.9990
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.179707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.140792 restraints weight = 11715.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.144207 restraints weight = 8169.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.146529 restraints weight = 6197.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9210  Z= 0.107
  Angle     :  0.532   7.950  12492  Z= 0.284
  Chirality :  0.041   0.151   1391
  Planarity :  0.003   0.037   1595
  Dihedral  :  3.766  17.965   1243
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 19.87 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.26), residues: 1126
  helix:  2.26 (0.25), residues: 446
  sheet: -0.10 (0.34), residues: 235
  loop : -0.66 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R  79 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.014   0.001   PHE A 222 
 TYR   0.019   0.001   TYR R  98 
 ARG   0.006   0.000   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03189 (  437)
  hydrogen bonds       : angle       3.98445 ( 1266)
  SS BOND              : bond        0.00170 (    7)
  SS BOND              : angle       0.86478 (   14)
  covalent geometry    : bond        0.00239 ( 9202)
  covalent geometry    : angle       0.53174 (12478)
  Misc. bond           : bond        0.00005 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2980.35 seconds
wall clock time: 52 minutes 58.64 seconds (3178.64 seconds total)