Starting phenix.real_space_refine
on Wed Sep 17 07:24:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bkj_44642/09_2025/9bkj_44642.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bkj_44642/09_2025/9bkj_44642.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bkj_44642/09_2025/9bkj_44642.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bkj_44642/09_2025/9bkj_44642.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bkj_44642/09_2025/9bkj_44642.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bkj_44642/09_2025/9bkj_44642.map"
  }
  resolution = 2.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.103
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      57      5.16       5
     C    4357      2.51       5
     N    1150      2.21       5
     O    1231      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6795
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2483
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2483
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 124
          Unresolved non-hydrogen angles: 150
          Unresolved non-hydrogen dihedrals: 98
          Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 5, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 3, 'ASN%COO:plan1': 1}
          Unresolved non-hydrogen planarities: 106
    Chain: "G"
      Number of atoms: 396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 396
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "P"
      Number of atoms: 77
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 77
          Classifications: {'peptide': 8}
          Link IDs: {'TRANS': 7}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TYS:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 2234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2234
          Classifications: {'peptide': 283}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 13, 'TRANS': 269}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 24
    Chain: "A"
      Number of atoms: 1604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1604
          Classifications: {'peptide': 204}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 3, 'TRANS': 200}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 110
          Unresolved non-hydrogen dihedrals: 68
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 5, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 63
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.59, per 1000 atoms: 0.23
  Number of scatterers: 6795
  At special positions: 0
  Unit cell: (88.4, 88.4, 127.5, 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      57     16.00
     O    1231      8.00
     N    1150      7.00
     C    4357      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 114 " - pdb=" SG  CYS R 196 " distance=2.07

  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: 0.64
  Conformation dependent library (CDL) restraints added in 369.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1698

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 10 sheets defined
      47.8% alpha, 19.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 39 through 69
    Processing helix  chain 'R' and resid 74 through 104
      removed outlier: 3.528A  pdb=" N   PHE R  79 " --> pdb=" O   VAL R  75 " (cutoff:3.500A)
      Proline residue:  R  96  - end of helix
      removed outlier: 3.975A  pdb=" N   ILE R 100 " --> pdb=" O   PRO R  96 " (cutoff:3.500A)
      Proline residue:  R 101  - end of helix
    Processing helix  chain 'R' and resid 110 through 145
    Processing helix  chain 'R' and resid 147 through 151
    Processing helix  chain 'R' and resid 154 through 173
    Processing helix  chain 'R' and resid 174 through 179
      removed outlier: 3.940A  pdb=" N   ILE R 178 " --> pdb=" O   THR R 174 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 202 through 238
      removed outlier: 3.578A  pdb=" N   PHE R 218 " --> pdb=" O   LEU R 214 " (cutoff:3.500A)
      removed outlier: 5.416A  pdb=" N   ILE R 220 " --> pdb=" O   ILE R 216 " (cutoff:3.500A)
      Proline residue:  R 221  - end of helix
    Processing helix  chain 'R' and resid 306 through 339
      Proline residue:  R 328  - end of helix
    Processing helix  chain 'R' and resid 339 through 348
    Processing helix  chain 'R' and resid 349 through 371
      removed outlier: 4.214A  pdb=" N   SER R 362 " --> pdb=" O   LEU R 358 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   SER R 363 " --> pdb=" O   SER R 359 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   CYS R 364 " --> pdb=" O   TYR R 360 " (cutoff:3.500A)
      Proline residue:  R 367  - end of helix
    Processing helix  chain 'R' and resid 374 through 385
    Processing helix  chain 'A' and resid 19 through 38
    Processing helix  chain 'A' and resid 52 through 56
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.652A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 4.172A  pdb=" N   ARG A 283 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.540A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.818A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.533A  pdb=" N   ARG A 389 " --> pdb=" O   GLN A 385 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.406A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.746A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.915A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.670A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.720A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.457A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.726A  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: 6.361A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.419A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'R' and resid 180 through 181
    Processing sheet with id=AA9, first strand: chain 'R' and resid 185 through 186
    Processing sheet with id=AB1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 4.047A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)

    382 hydrogen bonds defined for protein.
    1101 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.06

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1442
        1.33 -     1.45: 1594
        1.45 -     1.58: 3809
        1.58 -     1.70: 1
        1.70 -     1.82: 84
  Bond restraints: 6930
  Sorted by residual:
  bond pdb=" OH  TYS P   2 "
       pdb=" S   TYS P   2 "
    ideal  model  delta    sigma   weight residual
    1.679  1.583  0.096 2.00e-02 2.50e+03 2.29e+01
  bond pdb=" CA  SER B 316 "
       pdb=" CB  SER B 316 "
    ideal  model  delta    sigma   weight residual
    1.531  1.477  0.054 1.56e-02 4.11e+03 1.20e+01
  bond pdb=" CA  ALA B  56 "
       pdb=" CB  ALA B  56 "
    ideal  model  delta    sigma   weight residual
    1.533  1.488  0.045 1.35e-02 5.49e+03 1.10e+01
  bond pdb=" N   HIS B 225 "
       pdb=" CA  HIS B 225 "
    ideal  model  delta    sigma   weight residual
    1.454  1.496 -0.042 1.34e-02 5.57e+03 9.88e+00
  bond pdb=" N   ASN R  98 "
       pdb=" CA  ASN R  98 "
    ideal  model  delta    sigma   weight residual
    1.455  1.495 -0.040 1.29e-02 6.01e+03 9.49e+00
  ... (remaining 6925 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 8961
        1.56 -     3.12: 355
        3.12 -     4.68: 82
        4.68 -     6.24: 16
        6.24 -     7.80: 6
  Bond angle restraints: 9420
  Sorted by residual:
  angle pdb=" N   CYS R 196 "
        pdb=" CA  CYS R 196 "
        pdb=" C   CYS R 196 "
      ideal   model   delta    sigma   weight residual
     110.42  103.21    7.21 1.46e+00 4.69e-01 2.44e+01
  angle pdb=" N   TRP B 332 "
        pdb=" CA  TRP B 332 "
        pdb=" C   TRP B 332 "
      ideal   model   delta    sigma   weight residual
     113.18  107.51    5.67 1.21e+00 6.83e-01 2.20e+01
  angle pdb=" C   MET P   6 "
        pdb=" N   ASP P   7 "
        pdb=" CA  ASP P   7 "
      ideal   model   delta    sigma   weight residual
     120.38  126.24   -5.86 1.37e+00 5.33e-01 1.83e+01
  angle pdb=" CA  PHE R 185 "
        pdb=" C   PHE R 185 "
        pdb=" O   PHE R 185 "
      ideal   model   delta    sigma   weight residual
     121.33  116.84    4.49 1.08e+00 8.57e-01 1.73e+01
  angle pdb=" C   MET R 173 "
        pdb=" N   THR R 174 "
        pdb=" CA  THR R 174 "
      ideal   model   delta    sigma   weight residual
     120.09  125.21   -5.12 1.25e+00 6.40e-01 1.68e+01
  ... (remaining 9415 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 3766
       17.92 -    35.84: 281
       35.84 -    53.75: 44
       53.75 -    71.67: 6
       71.67 -    89.59: 2
  Dihedral angle restraints: 4099
    sinusoidal: 1496
      harmonic: 2603
  Sorted by residual:
  dihedral pdb=" CA  CYS R  94 "
           pdb=" C   CYS R  94 "
           pdb=" N   MET R  95 "
           pdb=" CA  MET R  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.29  -17.71     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  PHE R 218 "
           pdb=" C   PHE R 218 "
           pdb=" N   LEU R 219 "
           pdb=" CA  LEU R 219 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.89  -17.11     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  LEU R 215 "
           pdb=" C   LEU R 215 "
           pdb=" N   ILE R 216 "
           pdb=" CA  ILE R 216 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.55  -16.45     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 4096 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 787
       0.042 -    0.084: 225
       0.084 -    0.126: 88
       0.126 -    0.168: 12
       0.168 -    0.210: 2
  Chirality restraints: 1114
  Sorted by residual:
  chirality pdb=" CA  TRP P   5 "
            pdb=" N   TRP P   5 "
            pdb=" C   TRP P   5 "
            pdb=" CB  TRP P   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CA  LEU R  99 "
            pdb=" N   LEU R  99 "
            pdb=" C   LEU R  99 "
            pdb=" CB  LEU R  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  MET R  72 "
            pdb=" N   MET R  72 "
            pdb=" C   MET R  72 "
            pdb=" CB  MET R  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.28e-01
  ... (remaining 1111 not shown)

  Planarity restraints: 1178
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 329 "    0.010 2.00e-02 2.50e+03   2.00e-02 4.00e+00
        pdb=" C   THR B 329 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   THR B 329 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLY B 330 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO R 184 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.85e+00
        pdb=" C   PRO R 184 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   PRO R 184 "    0.013 2.00e-02 2.50e+03
        pdb=" N   PHE R 185 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS R 196 "    0.009 2.00e-02 2.50e+03   1.91e-02 3.66e+00
        pdb=" C   CYS R 196 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   CYS R 196 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ARG R 197 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1175 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1556
        2.79 -     3.32: 6533
        3.32 -     3.84: 11364
        3.84 -     4.37: 13717
        4.37 -     4.90: 23585
  Nonbonded interactions: 56755
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   ASP B 163 "
            pdb=" OG1 THR B 164 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" NZ  LYS B 280 "
            pdb=" O   ASP B 322 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" OG1 THR B 128 "
            pdb=" O   ASN B 132 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OH  TYR B 289 "
            pdb=" NE1 TRP B 297 "
     model   vdw
     2.343 3.120
  ... (remaining 56750 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.020
  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:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.800
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6514
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      :  0.005   0.112   6932  Z= 0.319
  Angle     :  0.763   8.690   9422  Z= 0.479
  Chirality :  0.046   0.210   1114
  Planarity :  0.004   0.032   1178
  Dihedral  : 12.935  89.589   2398
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  1.96 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  1.13 %
    Favored  : 98.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.29), residues: 869
  helix:  2.14 (0.26), residues: 383
  sheet:  0.40 (0.39), residues: 171
  loop : -1.03 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 251 
 TYR   0.007   0.001   TYR B 289 
 PHE   0.020   0.001   PHE R 185 
 TRP   0.010   0.001   TRP A 234 
 HIS   0.006   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 6930)
  covalent geometry    : angle       0.75376 ( 9420)
  SS BOND              : bond        0.04192 (    1)
  SS BOND              : angle       8.21603 (    2)
  hydrogen bonds       : bond        0.15193 (  382)
  hydrogen bonds       : angle       5.37369 ( 1101)
  Misc. bond           : bond        0.11231 (    1)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 113
  time to evaluate  : 0.269 
Fit side-chains
REVERT: B  195 ASP cc_start: 0.6424 (p0) cc_final: 0.6090 (p0)
  outliers start: 5
  outliers final: 1
  residues processed: 117
  average time/residue: 0.7179
  time to fit residues: 87.4788
Evaluate side-chains
  98 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  317 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    5.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
B 266 HIS
B 268 ASN
R 131 ASN
** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.180148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.128774 restraints weight = 7216.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 2.07
r_work: 0.3507 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057   6932  Z= 0.285
  Angle     :  0.723   9.752   9422  Z= 0.378
  Chirality :  0.049   0.160   1114
  Planarity :  0.005   0.043   1178
  Dihedral  :  5.707  50.661    950
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 11.74 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.28), residues: 869
  helix:  1.96 (0.26), residues: 383
  sheet:  0.02 (0.37), residues: 183
  loop : -1.21 (0.33), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 373 
 TYR   0.018   0.003   TYR A 391 
 PHE   0.018   0.003   PHE B 199 
 TRP   0.018   0.003   TRP B 211 
 HIS   0.008   0.003   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00663 ( 6930)
  covalent geometry    : angle       0.72083 ( 9420)
  SS BOND              : bond        0.00974 (    1)
  SS BOND              : angle       3.84779 (    2)
  hydrogen bonds       : bond        0.05639 (  382)
  hydrogen bonds       : angle       4.63684 ( 1101)
  Misc. bond           : bond        0.00232 (    1)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.8146 (m-80) cc_final: 0.7718 (m-80)
REVERT: B  101 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8722 (mtp)
REVERT: B  195 ASP cc_start: 0.7293 (p0) cc_final: 0.7048 (p0)
REVERT: B  215 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6326 (mt-10)
REVERT: B  217 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7193 (pmm)
REVERT: B  226 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6288 (mp0)
REVERT: G   28 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6760 (pt)
REVERT: G   42 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6904 (mp0)
REVERT: P    3 MET cc_start: 0.6219 (mtm) cc_final: 0.5684 (ttm)
REVERT: R  105 LYS cc_start: 0.7532 (mttp) cc_final: 0.6733 (mmtm)
REVERT: R  153 GLN cc_start: 0.8415 (mt0) cc_final: 0.8080 (tt0)
REVERT: R  226 MET cc_start: 0.7346 (mtm) cc_final: 0.7129 (mtp)
REVERT: A  343 LYS cc_start: 0.7147 (tttm) cc_final: 0.6817 (tttm)
  outliers start: 25
  outliers final: 8
  residues processed: 116
  average time/residue: 0.7201
  time to fit residues: 87.0549
Evaluate side-chains
  102 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue  171 THR
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  214 LEU
Chi-restraints excluded: chain R residue  376 ARG
Chi-restraints excluded: chain A residue  210 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 0 optimal weight:   30.0000
   chunk 83 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 70 optimal weight:    5.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.184663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.134035 restraints weight = 7133.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 2.11
r_work: 0.3569 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3439 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6932  Z= 0.117
  Angle     :  0.539   7.617   9422  Z= 0.277
  Chirality :  0.042   0.149   1114
  Planarity :  0.004   0.037   1178
  Dihedral  :  5.061  49.388    949
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 14.71 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.29), residues: 869
  helix:  2.51 (0.26), residues: 385
  sheet:  0.24 (0.39), residues: 173
  loop : -0.97 (0.33), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 219 
 TYR   0.010   0.001   TYR R  48 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.011   0.001   TRP R 209 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 6930)
  covalent geometry    : angle       0.53726 ( 9420)
  SS BOND              : bond        0.00669 (    1)
  SS BOND              : angle       2.89166 (    2)
  hydrogen bonds       : bond        0.04102 (  382)
  hydrogen bonds       : angle       4.08127 ( 1101)
  Misc. bond           : bond        0.00064 (    1)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.7969 (m-80) cc_final: 0.7437 (m-80)
REVERT: B  215 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6274 (mt-10)
REVERT: B  217 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.6696 (pmm)
REVERT: G   42 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6800 (mp0)
REVERT: P    3 MET cc_start: 0.6164 (mtm) cc_final: 0.5562 (ttm)
REVERT: R  226 MET cc_start: 0.7301 (mtm) cc_final: 0.7053 (mtp)
REVERT: R  313 ARG cc_start: 0.6858 (ptp90) cc_final: 0.6535 (ptp90)
  outliers start: 22
  outliers final: 7
  residues processed: 106
  average time/residue: 0.6856
  time to fit residues: 76.0538
Evaluate side-chains
  98 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  214 LEU
Chi-restraints excluded: chain R residue  376 ARG
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  297 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 62 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 266 HIS
B 268 ASN
** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 HIS ** 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 = 0.4256 r_free = 0.4256 target = 0.185002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.134365 restraints weight = 7205.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 2.12
r_work: 0.3575 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6932  Z= 0.114
  Angle     :  0.515   7.934   9422  Z= 0.267
  Chirality :  0.041   0.158   1114
  Planarity :  0.003   0.037   1178
  Dihedral  :  4.873  48.188    949
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 14.85 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.29), residues: 869
  helix:  2.76 (0.26), residues: 379
  sheet:  0.30 (0.40), residues: 173
  loop : -0.82 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 310 
 TYR   0.009   0.001   TYR A 391 
 PHE   0.016   0.001   PHE R  79 
 TRP   0.010   0.001   TRP R 209 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 6930)
  covalent geometry    : angle       0.51372 ( 9420)
  SS BOND              : bond        0.00644 (    1)
  SS BOND              : angle       2.68608 (    2)
  hydrogen bonds       : bond        0.03868 (  382)
  hydrogen bonds       : angle       3.93455 ( 1101)
  Misc. bond           : bond        0.00063 (    1)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: B  215 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6835 (mt-10)
REVERT: B  226 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6315 (mp0)
REVERT: G   42 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6792 (mp0)
REVERT: P    3 MET cc_start: 0.6125 (mtm) cc_final: 0.5514 (ttm)
REVERT: R  226 MET cc_start: 0.7279 (mtm) cc_final: 0.7038 (mtp)
REVERT: R  313 ARG cc_start: 0.6852 (ptp90) cc_final: 0.6613 (ptp90)
  outliers start: 22
  outliers final: 7
  residues processed: 104
  average time/residue: 0.7498
  time to fit residues: 81.2657
Evaluate side-chains
  98 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  225 MET
Chi-restraints excluded: chain R residue  376 ARG
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  297 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 78 optimal weight:    9.9990
   chunk 74 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 63 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0570
   chunk 69 optimal weight:    0.0670
   chunk 5 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.187628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.137399 restraints weight = 7248.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 2.12
r_work: 0.3613 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3483 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6932  Z= 0.096
  Angle     :  0.489   8.044   9422  Z= 0.252
  Chirality :  0.041   0.168   1114
  Planarity :  0.003   0.038   1178
  Dihedral  :  4.623  45.988    949
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 15.13 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.30), residues: 869
  helix:  2.84 (0.27), residues: 384
  sheet:  0.38 (0.40), residues: 173
  loop : -0.73 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 310 
 TYR   0.007   0.001   TYR A 391 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.008   0.001   TRP R 209 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00193 ( 6930)
  covalent geometry    : angle       0.48900 ( 9420)
  SS BOND              : bond        0.00769 (    1)
  SS BOND              : angle       1.55319 (    2)
  hydrogen bonds       : bond        0.03448 (  382)
  hydrogen bonds       : angle       3.71570 ( 1101)
  Misc. bond           : bond        0.00030 (    1)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: B  215 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6833 (mt-10)
REVERT: B  226 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6257 (mp0)
REVERT: G   42 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6721 (mp0)
REVERT: P    3 MET cc_start: 0.6156 (mtm) cc_final: 0.5568 (ttm)
REVERT: R  195 MET cc_start: 0.4515 (ptp) cc_final: 0.3896 (ptp)
REVERT: R  313 ARG cc_start: 0.6876 (ptp90) cc_final: 0.6597 (ptp90)
REVERT: R  327 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7851 (ttp)
REVERT: R  369 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8093 (mp)
REVERT: A  343 LYS cc_start: 0.7057 (tttm) cc_final: 0.6591 (tttm)
  outliers start: 23
  outliers final: 6
  residues processed: 110
  average time/residue: 0.6898
  time to fit residues: 79.3704
Evaluate side-chains
  97 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  327 MET
Chi-restraints excluded: chain R residue  369 ILE
Chi-restraints excluded: chain R residue  376 ARG
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  358 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0970
   chunk 9 optimal weight:    0.2980
   chunk 27 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 79 optimal weight:    0.1980
   chunk 26 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.188157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.137642 restraints weight = 7288.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 2.14
r_work: 0.3617 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3488 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6932  Z= 0.097
  Angle     :  0.490   8.276   9422  Z= 0.252
  Chirality :  0.041   0.168   1114
  Planarity :  0.003   0.037   1178
  Dihedral  :  4.540  45.278    949
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 16.55 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.30), residues: 869
  helix:  2.90 (0.26), residues: 384
  sheet:  0.32 (0.40), residues: 174
  loop : -0.63 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 310 
 TYR   0.011   0.001   TYR A 360 
 PHE   0.016   0.001   PHE R 185 
 TRP   0.007   0.001   TRP R 326 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 ( 6930)
  covalent geometry    : angle       0.48973 ( 9420)
  SS BOND              : bond        0.00820 (    1)
  SS BOND              : angle       1.75211 (    2)
  hydrogen bonds       : bond        0.03386 (  382)
  hydrogen bonds       : angle       3.62479 ( 1101)
  Misc. bond           : bond        0.00032 (    1)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.7927 (m-80) cc_final: 0.7368 (m-80)
REVERT: B  146 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7966 (mt)
REVERT: B  215 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6854 (mt-10)
REVERT: G   28 ILE cc_start: 0.6455 (OUTLIER) cc_final: 0.5892 (pp)
REVERT: G   42 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6733 (mp0)
REVERT: P    3 MET cc_start: 0.6231 (mtm) cc_final: 0.5650 (ttm)
REVERT: R  195 MET cc_start: 0.4444 (ptp) cc_final: 0.3892 (ptp)
REVERT: R  226 MET cc_start: 0.7240 (mtm) cc_final: 0.7000 (mtp)
REVERT: R  313 ARG cc_start: 0.6851 (ptp90) cc_final: 0.6561 (ptp90)
REVERT: R  327 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7831 (ttp)
REVERT: R  369 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8096 (mp)
REVERT: A  343 LYS cc_start: 0.7073 (tttm) cc_final: 0.6607 (tttm)
  outliers start: 21
  outliers final: 8
  residues processed: 104
  average time/residue: 0.6805
  time to fit residues: 74.0339
Evaluate side-chains
  101 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  225 MET
Chi-restraints excluded: chain R residue  327 MET
Chi-restraints excluded: chain R residue  369 ILE
Chi-restraints excluded: chain R residue  376 ARG
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  358 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 21 optimal weight:    0.1980
   chunk 49 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 33 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0670
   chunk 66 optimal weight:    0.6980
   chunk 47 optimal weight:    0.5980
   chunk 6 optimal weight:    0.3980
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.189135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.138986 restraints weight = 7130.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 2.11
r_work: 0.3632 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3504 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6932  Z= 0.094
  Angle     :  0.497   9.574   9422  Z= 0.252
  Chirality :  0.041   0.175   1114
  Planarity :  0.004   0.064   1178
  Dihedral  :  4.451  44.535    949
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 17.54 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.30), residues: 869
  helix:  2.92 (0.26), residues: 386
  sheet:  0.37 (0.40), residues: 173
  loop : -0.55 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 310 
 TYR   0.009   0.001   TYR A 360 
 PHE   0.014   0.001   PHE R 185 
 TRP   0.007   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 ( 6930)
  covalent geometry    : angle       0.49688 ( 9420)
  SS BOND              : bond        0.01110 (    1)
  SS BOND              : angle       1.70061 (    2)
  hydrogen bonds       : bond        0.03257 (  382)
  hydrogen bonds       : angle       3.56469 ( 1101)
  Misc. bond           : bond        0.00024 (    1)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.7771 (m-80) cc_final: 0.7417 (m-80)
REVERT: B  215 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6918 (mt-10)
REVERT: G   42 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6765 (mp0)
REVERT: P    3 MET cc_start: 0.6212 (mtm) cc_final: 0.5656 (ttm)
REVERT: R  195 MET cc_start: 0.4223 (ptp) cc_final: 0.3714 (ptp)
REVERT: R  226 MET cc_start: 0.7215 (mtm) cc_final: 0.6975 (mtp)
REVERT: R  313 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6580 (ptp90)
REVERT: R  327 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7789 (ttp)
REVERT: R  369 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8004 (mp)
  outliers start: 22
  outliers final: 8
  residues processed: 105
  average time/residue: 0.6523
  time to fit residues: 71.7624
Evaluate side-chains
  98 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  225 MET
Chi-restraints excluded: chain R residue  313 ARG
Chi-restraints excluded: chain R residue  327 MET
Chi-restraints excluded: chain R residue  369 ILE
Chi-restraints excluded: chain R residue  376 ARG
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  358 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 18 optimal weight:    0.2980
   chunk 17 optimal weight:    6.9990
   chunk 37 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0030
   chunk 24 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.188564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.137957 restraints weight = 7266.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 2.14
r_work: 0.3614 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3486 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6932  Z= 0.101
  Angle     :  0.517   9.643   9422  Z= 0.260
  Chirality :  0.041   0.180   1114
  Planarity :  0.004   0.057   1178
  Dihedral  :  4.474  44.603    949
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 18.10 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.30), residues: 869
  helix:  2.89 (0.27), residues: 384
  sheet:  0.40 (0.40), residues: 174
  loop : -0.52 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 310 
 TYR   0.010   0.001   TYR A 360 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.008   0.001   TRP R 326 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 6930)
  covalent geometry    : angle       0.51666 ( 9420)
  SS BOND              : bond        0.00934 (    1)
  SS BOND              : angle       1.55468 (    2)
  hydrogen bonds       : bond        0.03338 (  382)
  hydrogen bonds       : angle       3.61965 ( 1101)
  Misc. bond           : bond        0.00035 (    1)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.7839 (m-80) cc_final: 0.7396 (m-80)
REVERT: B   61 MET cc_start: 0.8759 (ppp) cc_final: 0.8554 (ppp)
REVERT: B  215 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6836 (mt-10)
REVERT: G   28 ILE cc_start: 0.6440 (OUTLIER) cc_final: 0.5871 (pp)
REVERT: G   42 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6742 (mp0)
REVERT: P    3 MET cc_start: 0.6213 (mtm) cc_final: 0.5653 (ttm)
REVERT: R  195 MET cc_start: 0.4177 (ptp) cc_final: 0.3618 (ptp)
REVERT: R  226 MET cc_start: 0.7213 (mtm) cc_final: 0.6973 (mtp)
REVERT: R  313 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6527 (ptp90)
REVERT: R  327 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7783 (ttp)
REVERT: R  369 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7982 (mp)
  outliers start: 20
  outliers final: 9
  residues processed: 96
  average time/residue: 0.6581
  time to fit residues: 66.0220
Evaluate side-chains
  100 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  225 MET
Chi-restraints excluded: chain R residue  313 ARG
Chi-restraints excluded: chain R residue  327 MET
Chi-restraints excluded: chain R residue  369 ILE
Chi-restraints excluded: chain R residue  376 ARG
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  358 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 69 optimal weight:    0.1980
   chunk 67 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 21 optimal weight:    0.3980
   chunk 46 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.188682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.138206 restraints weight = 7282.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 2.14
r_work: 0.3617 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3490 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   6932  Z= 0.104
  Angle     :  0.532   9.613   9422  Z= 0.268
  Chirality :  0.042   0.182   1114
  Planarity :  0.004   0.052   1178
  Dihedral  :  4.465  45.051    949
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.82 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.75 (0.30), residues: 869
  helix:  2.73 (0.27), residues: 390
  sheet:  0.37 (0.39), residues: 181
  loop : -0.46 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 310 
 TYR   0.009   0.001   TYR A 360 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.007   0.001   TRP R 326 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 6930)
  covalent geometry    : angle       0.53161 ( 9420)
  SS BOND              : bond        0.00675 (    1)
  SS BOND              : angle       1.35720 (    2)
  hydrogen bonds       : bond        0.03340 (  382)
  hydrogen bonds       : angle       3.67521 ( 1101)
  Misc. bond           : bond        0.00034 (    1)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.7888 (m-80) cc_final: 0.7351 (m-80)
REVERT: B  215 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6901 (mt-10)
REVERT: G   28 ILE cc_start: 0.6490 (OUTLIER) cc_final: 0.5925 (pp)
REVERT: G   42 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6746 (mp0)
REVERT: P    3 MET cc_start: 0.6189 (mtm) cc_final: 0.5629 (ttm)
REVERT: R  195 MET cc_start: 0.3918 (ptp) cc_final: 0.3363 (ptp)
REVERT: R  226 MET cc_start: 0.7216 (mtm) cc_final: 0.6978 (mtp)
REVERT: R  327 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7752 (ttp)
REVERT: R  369 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7953 (mp)
  outliers start: 21
  outliers final: 10
  residues processed: 93
  average time/residue: 0.6473
  time to fit residues: 62.8433
Evaluate side-chains
  101 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  225 MET
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain R residue  327 MET
Chi-restraints excluded: chain R residue  369 ILE
Chi-restraints excluded: chain R residue  376 ARG
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  358 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 0 optimal weight:   30.0000
   chunk 80 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0010
   chunk 29 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    1.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.185818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.134742 restraints weight = 7177.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.12
r_work: 0.3579 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6932  Z= 0.135
  Angle     :  0.581  10.288   9422  Z= 0.291
  Chirality :  0.043   0.190   1114
  Planarity :  0.004   0.057   1178
  Dihedral  :  4.745  47.275    949
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.10 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.30), residues: 869
  helix:  2.68 (0.27), residues: 384
  sheet:  0.38 (0.40), residues: 175
  loop : -0.59 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 310 
 TYR   0.011   0.001   TYR A 360 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.011   0.001   TRP R 209 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6930)
  covalent geometry    : angle       0.58040 ( 9420)
  SS BOND              : bond        0.00912 (    1)
  SS BOND              : angle       1.57457 (    2)
  hydrogen bonds       : bond        0.03843 (  382)
  hydrogen bonds       : angle       3.86209 ( 1101)
  Misc. bond           : bond        0.00081 (    1)

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: B  262 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7554 (ttm)
REVERT: G   28 ILE cc_start: 0.6498 (OUTLIER) cc_final: 0.5917 (pp)
REVERT: G   42 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6759 (mp0)
REVERT: P    3 MET cc_start: 0.6116 (mtm) cc_final: 0.5519 (ttm)
REVERT: R  195 MET cc_start: 0.3976 (ptp) cc_final: 0.3363 (ptp)
REVERT: R  226 MET cc_start: 0.7240 (mtm) cc_final: 0.7005 (mtp)
REVERT: R  327 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7749 (ttp)
REVERT: A  209 GLU cc_start: 0.6366 (mm-30) cc_final: 0.5956 (mm-30)
  outliers start: 19
  outliers final: 8
  residues processed: 95
  average time/residue: 0.7161
  time to fit residues: 70.9927
Evaluate side-chains
  98 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue  182 LEU
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain R residue  327 MET
Chi-restraints excluded: chain R residue  376 ARG
Chi-restraints excluded: chain A residue  210 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 75 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 42 optimal weight:    9.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.187360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.136527 restraints weight = 7162.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 2.13
r_work: 0.3598 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   6932  Z= 0.112
  Angle     :  0.556  10.306   9422  Z= 0.276
  Chirality :  0.043   0.204   1114
  Planarity :  0.004   0.053   1178
  Dihedral  :  4.666  47.880    949
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 18.67 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.30), residues: 869
  helix:  2.70 (0.27), residues: 384
  sheet:  0.36 (0.39), residues: 180
  loop : -0.50 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 219 
 TYR   0.008   0.001   TYR A 391 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.008   0.001   TRP R 209 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6930)
  covalent geometry    : angle       0.55546 ( 9420)
  SS BOND              : bond        0.00908 (    1)
  SS BOND              : angle       1.52337 (    2)
  hydrogen bonds       : bond        0.03602 (  382)
  hydrogen bonds       : angle       3.80484 ( 1101)
  Misc. bond           : bond        0.00052 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3444.85 seconds
wall clock time: 59 minutes 23.41 seconds (3563.41 seconds total)