Starting phenix.real_space_refine
on Thu Mar 13 04:14:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jiq_36324/03_2025/8jiq_36324.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jiq_36324/03_2025/8jiq_36324.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jiq_36324/03_2025/8jiq_36324.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jiq_36324/03_2025/8jiq_36324.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jiq_36324/03_2025/8jiq_36324.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jiq_36324/03_2025/8jiq_36324.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      55      5.16       5
     C    5527      2.51       5
     N    1524      2.21       5
     O    1601      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8707
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1817
          Classifications: {'peptide': 219}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 212}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 2510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2510
          Classifications: {'peptide': 332}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 5, 'TRANS': 326}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 28
    Chain: "C"
      Number of atoms: 363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 363
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 4, 'TRANS': 42}
    Chain: "E"
      Number of atoms: 234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 234
          Classifications: {'peptide': 29}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 28}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 2810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 379, 2810
          Classifications: {'peptide': 379}
          Incomplete info: {'truncation_to_alanine': 68}
          Link IDs: {'PTRANS': 15, 'TRANS': 363}
          Chain breaks: 3
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 291
          Unresolved non-hydrogen angles: 379
          Unresolved non-hydrogen dihedrals: 259
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 190
  Time building chain proxies: 5.99, per 1000 atoms: 0.69
  Number of scatterers: 8707
  At special positions: 0
  Unit cell: (92.13, 98.77, 161.02, 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      55     16.00
     O    1601      8.00
     N    1524      7.00
     C    5527      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R  58 " - pdb=" SG  CYS R 100 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  81 " - pdb=" SG  CYS R 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 224 " - pdb=" SG  CYS R 294 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.25
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2124

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 12 sheets defined
      42.0% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 38
      removed outlier: 5.010A  pdb=" N   GLU A  15 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 241
      removed outlier: 4.417A  pdb=" N   ASP A 240 " --> pdb=" O   CYS A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.770A  pdb=" N   ALA A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 4.038A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   LEU A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.513A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.796A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 17 through 23
      removed outlier: 3.563A  pdb=" N   ALA C  23 " --> pdb=" O   LEU C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'E' and resid 2 through 29
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.660A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 28 through 50
      removed outlier: 4.306A  pdb=" N   GLN R  42 " --> pdb=" O   LEU R  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 85 through 89
      removed outlier: 3.514A  pdb=" N   HIS R  89 " --> pdb=" O   PRO R  86 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 124 through 131
      removed outlier: 4.278A  pdb=" N   GLU R 129 " --> pdb=" O   GLU R 126 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 133 through 164
      removed outlier: 4.256A  pdb=" N   MET R 137 " --> pdb=" O   GLU R 133 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL R 147 " --> pdb=" O   VAL R 143 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 203
      removed outlier: 3.619A  pdb=" N   TYR R 202 " --> pdb=" O   LEU R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 255
      removed outlier: 3.719A  pdb=" N   VAL R 221 " --> pdb=" O   SER R 217 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ALA R 222 " --> pdb=" O   ASP R 218 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLY R 223 " --> pdb=" O   GLY R 219 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 263 through 277
      removed outlier: 3.991A  pdb=" N   ALA R 274 " --> pdb=" O   ILE R 270 " (cutoff:3.500A)
      Proline residue:  R 275  - end of helix
    Processing helix  chain 'R' and resid 278 through 290
    Processing helix  chain 'R' and resid 301 through 335
      removed outlier: 3.975A  pdb=" N   ILE R 306 " --> pdb=" O   GLY R 302 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   LEU R 307 " --> pdb=" O   PHE R 303 " (cutoff:3.500A)
      Proline residue:  R 310  - end of helix
      removed outlier: 3.674A  pdb=" N   ALA R 331 " --> pdb=" O   GLN R 327 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ALA R 335 " --> pdb=" O   ALA R 331 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 344 through 353
    Processing helix  chain 'R' and resid 354 through 359
    Processing helix  chain 'R' and resid 361 through 368
      removed outlier: 3.588A  pdb=" N   PHE R 365 " --> pdb=" O   HIS R 361 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 378 through 402
      removed outlier: 4.601A  pdb=" N   GLY R 393 " --> pdb=" O   SER R 389 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   LEU R 394 " --> pdb=" O   SER R 390 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   PHE R 402 " --> pdb=" O   VAL R 398 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 404 through 418
      removed outlier: 4.098A  pdb=" N   GLU R 410 " --> pdb=" O   GLU R 406 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 3.764A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 9.359A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.252A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50
      removed outlier: 6.666A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.105A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.222A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.794A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.758A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.481A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.680A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.950A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8
      removed outlier: 3.721A  pdb=" N   SER N  21 " --> pdb=" O   SER N   7 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.832A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 57 through 58
      removed outlier: 3.675A  pdb=" N   THR R  71 " --> pdb=" O   CYS R  58 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'R' and resid 77 through 80

    449 hydrogen bonds defined for protein.
    1260 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.39

  Time building geometry restraints manager: 2.64 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1509
        1.32 -     1.44: 2410
        1.44 -     1.57: 4897
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 8892
  Sorted by residual:
  bond pdb=" C   ARG R 199 "
       pdb=" O   ARG R 199 "
    ideal  model  delta    sigma   weight residual
    1.237  1.201  0.036 1.17e-02 7.31e+03 9.53e+00
  bond pdb=" C   GLY R 101 "
       pdb=" N   PRO R 102 "
    ideal  model  delta    sigma   weight residual
    1.335  1.374 -0.039 1.28e-02 6.10e+03 9.33e+00
  bond pdb=" CA  ARG R 116 "
       pdb=" C   ARG R 116 "
    ideal  model  delta    sigma   weight residual
    1.528  1.511  0.017 8.80e-03 1.29e+04 3.59e+00
  bond pdb=" CA  ASP R 208 "
       pdb=" C   ASP R 208 "
    ideal  model  delta    sigma   weight residual
    1.522  1.497  0.026 1.40e-02 5.10e+03 3.32e+00
  bond pdb=" C   THR R  71 "
       pdb=" O   THR R  71 "
    ideal  model  delta    sigma   weight residual
    1.238  1.215  0.023 1.28e-02 6.10e+03 3.30e+00
  ... (remaining 8887 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.63: 11949
        2.63 -     5.26: 103
        5.26 -     7.88: 5
        7.88 -    10.51: 1
       10.51 -    13.14: 2
  Bond angle restraints: 12060
  Sorted by residual:
  angle pdb=" N   ARG R 201 "
        pdb=" CA  ARG R 201 "
        pdb=" C   ARG R 201 "
      ideal   model   delta    sigma   weight residual
     113.97  100.83   13.14 1.28e+00 6.10e-01 1.05e+02
  angle pdb=" N   ASP R 208 "
        pdb=" CA  ASP R 208 "
        pdb=" C   ASP R 208 "
      ideal   model   delta    sigma   weight residual
     113.17  102.84   10.33 1.26e+00 6.30e-01 6.73e+01
  angle pdb=" C   THR R  71 "
        pdb=" N   PRO R  72 "
        pdb=" CA  PRO R  72 "
      ideal   model   delta    sigma   weight residual
     119.85  113.94    5.91 1.01e+00 9.80e-01 3.43e+01
  angle pdb=" C   GLY R 101 "
        pdb=" N   PRO R 102 "
        pdb=" CA  PRO R 102 "
      ideal   model   delta    sigma   weight residual
     119.28  113.44    5.84 1.10e+00 8.26e-01 2.82e+01
  angle pdb=" CA  GLN R 113 "
        pdb=" C   GLN R 113 "
        pdb=" N   PRO R 114 "
      ideal   model   delta    sigma   weight residual
     120.79  116.76    4.03 9.70e-01 1.06e+00 1.72e+01
  ... (remaining 12055 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 4625
       17.44 -    34.87: 496
       34.87 -    52.31: 94
       52.31 -    69.75: 27
       69.75 -    87.18: 10
  Dihedral angle restraints: 5252
    sinusoidal: 1969
      harmonic: 3283
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -37.12  -48.88     1      1.00e+01 1.00e-02 3.29e+01
  dihedral pdb=" CB  CYS R 224 "
           pdb=" SG  CYS R 224 "
           pdb=" SG  CYS R 294 "
           pdb=" CB  CYS R 294 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  137.50  -44.50     1      1.00e+01 1.00e-02 2.75e+01
  dihedral pdb=" CB  CYS R  81 "
           pdb=" SG  CYS R  81 "
           pdb=" SG  CYS R 121 "
           pdb=" CB  CYS R 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.66   39.34     1      1.00e+01 1.00e-02 2.18e+01
  ... (remaining 5249 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 993
       0.044 -    0.088: 271
       0.088 -    0.132: 78
       0.132 -    0.175: 7
       0.175 -    0.219: 4
  Chirality restraints: 1353
  Sorted by residual:
  chirality pdb=" CA  ASN R  74 "
            pdb=" N   ASN R  74 "
            pdb=" C   ASN R  74 "
            pdb=" CB  ASN R  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  ASP R 209 "
            pdb=" N   ASP R 209 "
            pdb=" C   ASP R 209 "
            pdb=" CB  ASP R 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  ARG R 201 "
            pdb=" N   ARG R 201 "
            pdb=" C   ARG R 201 "
            pdb=" CB  ARG R 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.19 2.00e-01 2.50e+01 9.49e-01
  ... (remaining 1350 not shown)

  Planarity restraints: 1546
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 241 "   -0.021 2.00e-02 2.50e+03   1.96e-02 9.61e+00
        pdb=" CG  TRP R 241 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 241 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 241 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 241 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 241 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 241 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 241 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 241 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 241 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 194 "    0.010 2.00e-02 2.50e+03   1.91e-02 3.65e+00
        pdb=" C   ILE R 194 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   ILE R 194 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ASP R 195 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG R 199 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.57e+00
        pdb=" C   ARG R 199 "    0.033 2.00e-02 2.50e+03
        pdb=" O   ARG R 199 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   THR R 200 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1543 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 836
        2.74 -     3.28: 8826
        3.28 -     3.82: 14736
        3.82 -     4.36: 16765
        4.36 -     4.90: 29215
  Nonbonded interactions: 70378
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OD2 ASP A 240 "
            pdb=" NZ  LYS B  57 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" OG1 THR R 172 "
            pdb=" OH  TYR R 248 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASN B 110 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.292 3.040
  ... (remaining 70373 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:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.490
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8892  Z= 0.214
  Angle     :  0.637  13.140  12060  Z= 0.388
  Chirality :  0.044   0.219   1353
  Planarity :  0.003   0.035   1546
  Dihedral  : 15.174  87.182   3113
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.14 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  :  1.35 %
    Favored  : 96.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.26), residues: 1112
  helix:  1.46 (0.27), residues: 402
  sheet: -0.75 (0.35), residues: 224
  loop : -0.87 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP R 241 
 HIS   0.005   0.001   HIS R  45 
 PHE   0.009   0.001   PHE A 212 
 TYR   0.016   0.001   TYR R 145 
 ARG   0.004   0.000   ARG B  96 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 154
  time to evaluate  : 1.035 
Fit side-chains
REVERT: R  376 THR cc_start: 0.4124 (OUTLIER) cc_final: 0.3439 (p)
REVERT: R  378 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.4137 (ptt90)
  outliers start: 22
  outliers final: 0
  residues processed: 171
  average time/residue: 0.2090
  time to fit residues: 48.7556
Evaluate side-chains
  125 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  376 THR
Chi-restraints excluded: chain R residue  378 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 82 optimal weight:   20.0000
   chunk 45 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0170
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 33 optimal weight:    8.9990
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    0.9022

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN
** B 295 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 = 0.4024 r_free = 0.4024 target = 0.125667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.088024 restraints weight = 17153.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 3.40
r_work: 0.3255 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8892  Z= 0.173
  Angle     :  0.537   6.621  12060  Z= 0.281
  Chirality :  0.041   0.154   1353
  Planarity :  0.003   0.033   1546
  Dihedral  :  4.192  49.657   1226
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.69 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.34 %
    Favored  : 87.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.26), residues: 1112
  helix:  1.59 (0.26), residues: 406
  sheet: -0.67 (0.35), residues: 220
  loop : -0.71 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP R 241 
 HIS   0.002   0.000   HIS B 183 
 PHE   0.024   0.001   PHE E  22 
 TYR   0.018   0.001   TYR B 111 
 ARG   0.003   0.000   ARG A 228 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
REVERT: B  130 GLU cc_start: 0.7677 (mp0) cc_final: 0.7384 (mp0)
REVERT: C   42 GLU cc_start: 0.8625 (tt0) cc_final: 0.8337 (pp20)
REVERT: E   11 SER cc_start: 0.8879 (t) cc_final: 0.8621 (p)
REVERT: N   73 ASP cc_start: 0.8810 (t0) cc_final: 0.8499 (t0)
REVERT: R  355 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8801 (mt)
  outliers start: 10
  outliers final: 6
  residues processed: 135
  average time/residue: 0.2032
  time to fit residues: 38.0940
Evaluate side-chains
  123 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain E residue   14 LEU
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  376 THR
Chi-restraints excluded: chain R residue  378 ARG
Chi-restraints excluded: chain R residue  386 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 80 optimal weight:   40.0000
   chunk 82 optimal weight:   20.0000
   chunk 89 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
A 390 GLN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 232 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.125408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.087810 restraints weight = 17277.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 3.39
r_work: 0.3248 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8892  Z= 0.177
  Angle     :  0.516   6.406  12060  Z= 0.269
  Chirality :  0.041   0.159   1353
  Planarity :  0.003   0.033   1546
  Dihedral  :  4.110  57.033   1226
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 14.03 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.26), residues: 1112
  helix:  1.68 (0.26), residues: 406
  sheet: -0.77 (0.34), residues: 222
  loop : -0.62 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP R 241 
 HIS   0.002   0.000   HIS B 183 
 PHE   0.012   0.001   PHE N 108 
 TYR   0.016   0.001   TYR R 145 
 ARG   0.002   0.000   ARG R 173 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
REVERT: C   42 GLU cc_start: 0.8615 (tt0) cc_final: 0.8334 (pp20)
REVERT: E   11 SER cc_start: 0.8880 (t) cc_final: 0.8591 (p)
REVERT: N   73 ASP cc_start: 0.8876 (t0) cc_final: 0.8551 (t0)
REVERT: R  355 ILE cc_start: 0.9087 (mt) cc_final: 0.8699 (mt)
  outliers start: 10
  outliers final: 6
  residues processed: 138
  average time/residue: 0.1989
  time to fit residues: 38.6279
Evaluate side-chains
  126 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain E residue   14 LEU
Chi-restraints excluded: chain R residue   28 VAL
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  378 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 50 optimal weight:    0.0980
   chunk 87 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 19 optimal weight:    0.1980
   chunk 107 optimal weight:    4.9990
   chunk 88 optimal weight:    0.7980
   chunk 89 optimal weight:    6.9990
   chunk 67 optimal weight:   10.0000
   chunk 82 optimal weight:   20.0000
   chunk 15 optimal weight:    0.0870
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.4360

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.123909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.088147 restraints weight = 17333.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 3.26
r_work: 0.3273 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.058   8892  Z= 0.134
  Angle     :  0.491   6.114  12060  Z= 0.257
  Chirality :  0.040   0.154   1353
  Planarity :  0.003   0.033   1546
  Dihedral  :  3.913  55.992   1225
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.81 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.26), residues: 1112
  helix:  1.82 (0.26), residues: 406
  sheet: -0.60 (0.35), residues: 218
  loop : -0.58 (0.30), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.001   TRP R 241 
 HIS   0.002   0.000   HIS A 357 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.017   0.001   TYR A 360 
 ARG   0.002   0.000   ARG A 228 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.987 
Fit side-chains
REVERT: B  130 GLU cc_start: 0.7665 (mp0) cc_final: 0.7343 (mp0)
REVERT: C   42 GLU cc_start: 0.8557 (tt0) cc_final: 0.8276 (pp20)
REVERT: E   11 SER cc_start: 0.8797 (t) cc_final: 0.8529 (p)
REVERT: E   27 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8455 (tpt)
REVERT: N   73 ASP cc_start: 0.8903 (t0) cc_final: 0.8561 (t0)
REVERT: R  355 ILE cc_start: 0.9023 (mt) cc_final: 0.8655 (mt)
REVERT: R  378 ARG cc_start: 0.6014 (OUTLIER) cc_final: 0.4214 (ppt170)
  outliers start: 16
  outliers final: 11
  residues processed: 139
  average time/residue: 0.1998
  time to fit residues: 39.1543
Evaluate side-chains
  133 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain E residue    9 ASP
Chi-restraints excluded: chain E residue   14 LEU
Chi-restraints excluded: chain E residue   27 MET
Chi-restraints excluded: chain R residue   28 VAL
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  378 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0470
   chunk 41 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0670
   chunk 49 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   chunk 92 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0570
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.3334

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 232 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.127874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.090771 restraints weight = 16894.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 3.37
r_work: 0.3314 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   8892  Z= 0.128
  Angle     :  0.488   6.871  12060  Z= 0.252
  Chirality :  0.040   0.156   1353
  Planarity :  0.003   0.033   1546
  Dihedral  :  3.705  49.032   1225
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.61 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.26), residues: 1112
  helix:  1.89 (0.26), residues: 405
  sheet: -0.54 (0.35), residues: 218
  loop : -0.49 (0.30), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP R 241 
 HIS   0.003   0.000   HIS A 357 
 PHE   0.010   0.001   PHE A 212 
 TYR   0.019   0.001   TYR A 360 
 ARG   0.002   0.000   ARG A 228 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.950 
Fit side-chains
REVERT: B   42 ARG cc_start: 0.7207 (mmt-90) cc_final: 0.6817 (tpp-160)
REVERT: B  130 GLU cc_start: 0.7627 (mp0) cc_final: 0.7348 (mp0)
REVERT: C   42 GLU cc_start: 0.8562 (tt0) cc_final: 0.8258 (pp20)
REVERT: E   11 SER cc_start: 0.8786 (t) cc_final: 0.8536 (p)
REVERT: N   73 ASP cc_start: 0.8903 (t0) cc_final: 0.8597 (t70)
REVERT: R  291 ASN cc_start: 0.8131 (t0) cc_final: 0.7699 (t0)
REVERT: R  355 ILE cc_start: 0.8907 (mt) cc_final: 0.8553 (mt)
REVERT: R  378 ARG cc_start: 0.5863 (OUTLIER) cc_final: 0.4157 (ppt170)
  outliers start: 18
  outliers final: 10
  residues processed: 148
  average time/residue: 0.1927
  time to fit residues: 40.4188
Evaluate side-chains
  134 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain E residue    9 ASP
Chi-restraints excluded: chain E residue   27 MET
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  378 ARG
Chi-restraints excluded: chain R residue  395 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 54 optimal weight:    0.0970
   chunk 2 optimal weight:    0.5980
   chunk 88 optimal weight:    0.5980
   chunk 97 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 86 optimal weight:    7.9990
   chunk 66 optimal weight:    0.3980
   chunk 36 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.124580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.089181 restraints weight = 17252.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 3.24
r_work: 0.3289 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8892  Z= 0.139
  Angle     :  0.503   8.542  12060  Z= 0.258
  Chirality :  0.041   0.199   1353
  Planarity :  0.003   0.033   1546
  Dihedral  :  3.673  44.348   1225
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.73 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.26), residues: 1112
  helix:  1.92 (0.26), residues: 407
  sheet: -0.53 (0.35), residues: 218
  loop : -0.52 (0.30), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP R 295 
 HIS   0.002   0.000   HIS R  44 
 PHE   0.010   0.001   PHE E  22 
 TYR   0.019   0.001   TYR A 360 
 ARG   0.002   0.000   ARG R 336 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.985 
Fit side-chains
REVERT: B   42 ARG cc_start: 0.7316 (mmt-90) cc_final: 0.6937 (tpp-160)
REVERT: B  130 GLU cc_start: 0.7607 (mp0) cc_final: 0.7334 (mp0)
REVERT: C   42 GLU cc_start: 0.8549 (tt0) cc_final: 0.8246 (pp20)
REVERT: E   11 SER cc_start: 0.8783 (t) cc_final: 0.8532 (p)
REVERT: N   73 ASP cc_start: 0.8905 (t0) cc_final: 0.8602 (t70)
REVERT: R  291 ASN cc_start: 0.8084 (t0) cc_final: 0.7603 (t0)
REVERT: R  355 ILE cc_start: 0.8923 (mt) cc_final: 0.8588 (mt)
REVERT: R  378 ARG cc_start: 0.5886 (OUTLIER) cc_final: 0.4180 (ppt170)
  outliers start: 18
  outliers final: 15
  residues processed: 144
  average time/residue: 0.2071
  time to fit residues: 42.1633
Evaluate side-chains
  135 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain E residue    9 ASP
Chi-restraints excluded: chain E residue   25 TRP
Chi-restraints excluded: chain E residue   27 MET
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue   28 VAL
Chi-restraints excluded: chain R residue  185 VAL
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  378 ARG
Chi-restraints excluded: chain R residue  395 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 103 optimal weight:    0.4980
   chunk 16 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 84 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 232 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.126082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.088238 restraints weight = 17421.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 3.44
r_work: 0.3266 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8892  Z= 0.178
  Angle     :  0.526   8.281  12060  Z= 0.268
  Chirality :  0.041   0.167   1353
  Planarity :  0.003   0.033   1546
  Dihedral  :  3.687  38.567   1225
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.28 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.26), residues: 1112
  helix:  1.92 (0.26), residues: 407
  sheet: -0.61 (0.35), residues: 220
  loop : -0.51 (0.30), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP R 241 
 HIS   0.002   0.000   HIS B 183 
 PHE   0.012   0.001   PHE N 108 
 TYR   0.018   0.001   TYR A 360 
 ARG   0.002   0.000   ARG R 173 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 1.048 
Fit side-chains
REVERT: A  343 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7914 (p0)
REVERT: B   45 MET cc_start: 0.8486 (mmm) cc_final: 0.8139 (mmt)
REVERT: B  130 GLU cc_start: 0.7638 (mp0) cc_final: 0.7366 (mp0)
REVERT: C   42 GLU cc_start: 0.8565 (tt0) cc_final: 0.8219 (pp20)
REVERT: E   11 SER cc_start: 0.8793 (t) cc_final: 0.8539 (p)
REVERT: R  291 ASN cc_start: 0.8249 (t0) cc_final: 0.7759 (t0)
REVERT: R  355 ILE cc_start: 0.8959 (mt) cc_final: 0.8603 (mt)
REVERT: R  378 ARG cc_start: 0.5826 (OUTLIER) cc_final: 0.4189 (ppt170)
  outliers start: 24
  outliers final: 15
  residues processed: 138
  average time/residue: 0.1935
  time to fit residues: 37.7766
Evaluate side-chains
  136 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain E residue    9 ASP
Chi-restraints excluded: chain E residue   25 TRP
Chi-restraints excluded: chain E residue   27 MET
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  185 VAL
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  378 ARG
Chi-restraints excluded: chain R residue  395 LEU
Chi-restraints excluded: chain R residue  406 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 73 optimal weight:    8.9990
   chunk 103 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   chunk 74 optimal weight:   10.0000
   chunk 86 optimal weight:    7.9990
   chunk 102 optimal weight:    3.9990
   chunk 68 optimal weight:    8.9990
   chunk 84 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
A 390 GLN
** B 295 ASN ** 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 = 0.3934 r_free = 0.3934 target = 0.119446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.081126 restraints weight = 17759.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 3.40
r_work: 0.3129 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050   8892  Z= 0.442
  Angle     :  0.676   8.777  12060  Z= 0.351
  Chirality :  0.046   0.276   1353
  Planarity :  0.004   0.035   1546
  Dihedral  :  4.472  34.028   1225
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 18.97 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.26), residues: 1112
  helix:  1.54 (0.26), residues: 407
  sheet: -0.83 (0.35), residues: 224
  loop : -0.66 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP R 295 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.029   0.002   PHE N 108 
 TYR   0.018   0.002   TYR B 111 
 ARG   0.006   0.001   ARG R 173 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.990 
Fit side-chains
REVERT: C   42 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8377 (pp20)
REVERT: E   11 SER cc_start: 0.8849 (t) cc_final: 0.8586 (p)
REVERT: N   73 ASP cc_start: 0.9049 (t70) cc_final: 0.8639 (t0)
REVERT: R  355 ILE cc_start: 0.9154 (mt) cc_final: 0.8764 (mt)
  outliers start: 21
  outliers final: 15
  residues processed: 133
  average time/residue: 0.2173
  time to fit residues: 39.7780
Evaluate side-chains
  129 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain E residue    9 ASP
Chi-restraints excluded: chain E residue   14 LEU
Chi-restraints excluded: chain E residue   25 TRP
Chi-restraints excluded: chain E residue   27 MET
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  395 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 99 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 108 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 90 optimal weight:    9.9990
   chunk 89 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.120723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.085269 restraints weight = 17612.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 3.25
r_work: 0.3214 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8892  Z= 0.173
  Angle     :  0.572   9.597  12060  Z= 0.292
  Chirality :  0.043   0.283   1353
  Planarity :  0.003   0.049   1546
  Dihedral  :  3.914  25.658   1221
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 19.98 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.26), residues: 1112
  helix:  1.71 (0.26), residues: 407
  sheet: -0.77 (0.35), residues: 222
  loop : -0.58 (0.30), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP R 295 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.012   0.001   PHE N 103 
 TYR   0.018   0.001   TYR A 360 
 ARG   0.012   0.000   ARG B  96 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 1.033 
Fit side-chains
REVERT: C   42 GLU cc_start: 0.8514 (tt0) cc_final: 0.8264 (pp20)
REVERT: E   11 SER cc_start: 0.8792 (t) cc_final: 0.8495 (p)
REVERT: N   73 ASP cc_start: 0.9026 (t70) cc_final: 0.8586 (t0)
REVERT: R   35 LYS cc_start: 0.8069 (mttt) cc_final: 0.7055 (tptp)
REVERT: R  290 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7920 (mm-30)
REVERT: R  355 ILE cc_start: 0.9035 (mt) cc_final: 0.8635 (mt)
  outliers start: 15
  outliers final: 12
  residues processed: 138
  average time/residue: 0.1909
  time to fit residues: 37.3218
Evaluate side-chains
  137 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain E residue    9 ASP
Chi-restraints excluded: chain E residue   25 TRP
Chi-restraints excluded: chain E residue   27 MET
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  395 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 82 optimal weight:   20.0000
   chunk 63 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 33 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0570
   chunk 43 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
** B 295 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 = 0.3970 r_free = 0.3970 target = 0.121681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.086191 restraints weight = 17494.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 3.26
r_work: 0.3232 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   8892  Z= 0.156
  Angle     :  0.570   9.510  12060  Z= 0.289
  Chirality :  0.042   0.273   1353
  Planarity :  0.003   0.058   1546
  Dihedral  :  3.772  21.506   1221
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 20.09 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.26), residues: 1112
  helix:  1.73 (0.26), residues: 407
  sheet: -0.69 (0.35), residues: 222
  loop : -0.55 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP R 295 
 HIS   0.002   0.000   HIS B 183 
 PHE   0.012   0.001   PHE R 312 
 TYR   0.018   0.001   TYR A 360 
 ARG   0.013   0.000   ARG B  96 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 1.026 
Fit side-chains
REVERT: C   42 GLU cc_start: 0.8570 (tt0) cc_final: 0.8271 (pp20)
REVERT: E   11 SER cc_start: 0.8778 (t) cc_final: 0.8496 (p)
REVERT: N   73 ASP cc_start: 0.9018 (t70) cc_final: 0.8599 (t0)
REVERT: R  290 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7946 (mm-30)
REVERT: R  355 ILE cc_start: 0.8994 (mt) cc_final: 0.8571 (mt)
  outliers start: 15
  outliers final: 14
  residues processed: 136
  average time/residue: 0.2002
  time to fit residues: 38.6385
Evaluate side-chains
  139 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain E residue    9 ASP
Chi-restraints excluded: chain E residue   25 TRP
Chi-restraints excluded: chain E residue   27 MET
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue  185 VAL
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  395 LEU
Chi-restraints excluded: chain R residue  406 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 54 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 29 optimal weight:    0.1980
   chunk 8 optimal weight:    0.7980
   chunk 107 optimal weight:    2.9990
   chunk 92 optimal weight:    0.7980
   chunk 94 optimal weight:    0.0770
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 295 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 = 0.3985 r_free = 0.3985 target = 0.123002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.086550 restraints weight = 17428.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 3.34
r_work: 0.3241 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8892  Z= 0.158
  Angle     :  0.571   9.309  12060  Z= 0.289
  Chirality :  0.042   0.267   1353
  Planarity :  0.003   0.054   1546
  Dihedral  :  3.695  19.774   1221
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 19.98 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.26), residues: 1112
  helix:  1.73 (0.26), residues: 407
  sheet: -0.64 (0.35), residues: 222
  loop : -0.57 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP R 295 
 HIS   0.002   0.000   HIS R 361 
 PHE   0.011   0.001   PHE R 312 
 TYR   0.020   0.001   TYR R 145 
 ARG   0.013   0.000   ARG B  96 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4959.76 seconds
wall clock time: 85 minutes 29.08 seconds (5129.08 seconds total)