Starting phenix.real_space_refine
on Thu Feb 13 02:35:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jiq_36324/02_2025/8jiq_36324.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jiq_36324/02_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_36324/02_2025/8jiq_36324.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jiq_36324/02_2025/8jiq_36324.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jiq_36324/02_2025/8jiq_36324.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jiq_36324/02_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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.27, per 1000 atoms: 0.61
  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: 2.29
  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: 0.91
  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: 2.61

  Time building geometry restraints manager: 2.67 seconds

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

  Histogram of bond lengths:
        1.20 -     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:             0.960
  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:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     22.830
  Find NCS groups from input model:        0.100
  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:             0.010
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.380
-------------------------------------------------------------------------------
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  : 0.948 
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: 0.2285
  time to fit residues: 53.2894
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  : 1.027 
-------------------------------------------------------------------------------
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 = 0.125666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.088026 restraints weight = 17152.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 3.40
r_work: 0.3256 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8892  Z= 0.173
  Angle     :  0.537   6.648  12060  Z= 0.281
  Chirality :  0.041   0.155   1353
  Planarity :  0.003   0.033   1546
  Dihedral  :  4.191  49.741   1226
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.99
  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  : 0.986 
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: 0.8338 (pp20)
REVERT: E   11 SER cc_start: 0.8872 (t) cc_final: 0.8611 (p)
REVERT: N   73 ASP cc_start: 0.8812 (t0) cc_final: 0.8500 (t0)
REVERT: R  355 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8794 (mt)
  outliers start: 10
  outliers final: 6
  residues processed: 135
  average time/residue: 0.2118
  time to fit residues: 39.5299
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  : 0.938 
-------------------------------------------------------------------------------
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:    0.0870
   chunk 34 optimal weight:    7.9990
   chunk 30 optimal weight:    0.8980
   chunk 80 optimal weight:   40.0000
   chunk 82 optimal weight:   20.0000
   chunk 89 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.7758

-------------------------------------------------------------------------------
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**
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 = 0.4034 r_free = 0.4034 target = 0.126297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.088873 restraints weight = 17277.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 3.37
r_work: 0.3268 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8892  Z= 0.156
  Angle     :  0.507   6.645  12060  Z= 0.264
  Chirality :  0.041   0.182   1353
  Planarity :  0.003   0.033   1546
  Dihedral  :  4.048  57.962   1226
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 13.80 %
    Favored  : 85.19 %
  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:  1.73 (0.26), residues: 406
  sheet: -0.74 (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   0.011   0.001   PHE A 212 
 TYR   0.016   0.001   TYR R 145 
 ARG   0.002   0.000   ARG A 228 

*********************** 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
  142 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 0.967 
Fit side-chains
REVERT: C   42 GLU cc_start: 0.8605 (tt0) cc_final: 0.8327 (pp20)
REVERT: E   11 SER cc_start: 0.8882 (t) cc_final: 0.8582 (p)
REVERT: N   73 ASP cc_start: 0.8886 (t0) cc_final: 0.8557 (t0)
REVERT: R  355 ILE cc_start: 0.9110 (mt) cc_final: 0.8741 (mt)
REVERT: R  378 ARG cc_start: 0.6018 (OUTLIER) cc_final: 0.4274 (ppt170)
  outliers start: 9
  outliers final: 4
  residues processed: 140
  average time/residue: 0.2039
  time to fit residues: 39.8783
Evaluate side-chains
  126 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 121
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
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  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:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   chunk 67 optimal weight:    0.8980
   chunk 82 optimal weight:   20.0000
   chunk 15 optimal weight:    7.9990
   chunk 103 optimal weight:    0.7980
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3975 r_free = 0.3975 target = 0.122080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.086200 restraints weight = 17438.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 3.25
r_work: 0.3234 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8892  Z= 0.182
  Angle     :  0.511   6.501  12060  Z= 0.266
  Chirality :  0.041   0.153   1353
  Planarity :  0.003   0.033   1546
  Dihedral  :  3.987  54.731   1225
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 15.38 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.26), residues: 1112
  helix:  1.77 (0.26), residues: 406
  sheet: -0.76 (0.34), residues: 222
  loop : -0.60 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   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 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
  144 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 1.012 
Fit side-chains
REVERT: B  130 GLU cc_start: 0.7688 (mp0) cc_final: 0.7361 (mp0)
REVERT: C   42 GLU cc_start: 0.8582 (tt0) cc_final: 0.8315 (pp20)
REVERT: E   11 SER cc_start: 0.8810 (t) cc_final: 0.8551 (p)
REVERT: E   27 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8473 (tpt)
REVERT: N   73 ASP cc_start: 0.8910 (t0) cc_final: 0.8548 (t0)
REVERT: R  291 ASN cc_start: 0.8271 (t0) cc_final: 0.7909 (t0)
REVERT: R  355 ILE cc_start: 0.9062 (mt) cc_final: 0.8688 (mt)
REVERT: R  378 ARG cc_start: 0.6081 (OUTLIER) cc_final: 0.4245 (ppt170)
  outliers start: 17
  outliers final: 12
  residues processed: 138
  average time/residue: 0.2040
  time to fit residues: 39.5400
Evaluate side-chains
  135 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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
Chi-restraints excluded: chain R residue  386 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 37 optimal weight:    0.0020
   chunk 72 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 92 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   overall best weight:    0.7588

-------------------------------------------------------------------------------
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 = 0.4033 r_free = 0.4033 target = 0.126211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.088687 restraints weight = 16968.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 3.34
r_work: 0.3269 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8892  Z= 0.154
  Angle     :  0.498   6.635  12060  Z= 0.260
  Chirality :  0.040   0.155   1353
  Planarity :  0.003   0.033   1546
  Dihedral  :  3.836  48.870   1225
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.84 %
    Favored  : 81.14 %
  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:  1.84 (0.26), residues: 406
  sheet: -0.68 (0.34), residues: 220
  loop : -0.55 (0.30), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP R 241 
 HIS   0.002   0.000   HIS B 311 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.019   0.001   TYR A 360 
 ARG   0.002   0.000   ARG R 173 

*********************** 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
  147 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.918 
Fit side-chains
REVERT: B  130 GLU cc_start: 0.7673 (mp0) cc_final: 0.7350 (mp0)
REVERT: C   42 GLU cc_start: 0.8568 (tt0) cc_final: 0.8303 (pp20)
REVERT: E   11 SER cc_start: 0.8806 (t) cc_final: 0.8538 (p)
REVERT: N   73 ASP cc_start: 0.8924 (t0) cc_final: 0.8594 (t70)
REVERT: R   29 MET cc_start: 0.7918 (tpp) cc_final: 0.7709 (mmm)
REVERT: R  142 GLN cc_start: 0.8472 (tp40) cc_final: 0.8271 (tp40)
REVERT: R  355 ILE cc_start: 0.8996 (mt) cc_final: 0.8633 (mt)
REVERT: R  378 ARG cc_start: 0.5891 (OUTLIER) cc_final: 0.4167 (ppt170)
  outliers start: 18
  outliers final: 12
  residues processed: 140
  average time/residue: 0.1986
  time to fit residues: 38.9398
Evaluate side-chains
  134 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
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 N residue   69 THR
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 97 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0670
   chunk 6 optimal weight:    0.9980
   chunk 86 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 60 optimal weight:    8.9990
   overall best weight:    0.9720

-------------------------------------------------------------------------------
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 = 0.3977 r_free = 0.3977 target = 0.122141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.086476 restraints weight = 17426.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 3.24
r_work: 0.3239 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8892  Z= 0.167
  Angle     :  0.506   8.303  12060  Z= 0.263
  Chirality :  0.041   0.204   1353
  Planarity :  0.003   0.033   1546
  Dihedral  :  3.765  42.426   1225
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.51 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.26), residues: 1112
  helix:  1.82 (0.26), residues: 407
  sheet: -0.66 (0.34), residues: 220
  loop : -0.55 (0.30), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP R 241 
 HIS   0.002   0.000   HIS B 183 
 PHE   0.010   0.001   PHE N 108 
 TYR   0.019   0.001   TYR A 360 
 ARG   0.002   0.000   ARG R 173 

*********************** 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
  149 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 1.064 
Fit side-chains
REVERT: B  130 GLU cc_start: 0.7703 (mp0) cc_final: 0.7383 (mp0)
REVERT: C   42 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8290 (pp20)
REVERT: E   11 SER cc_start: 0.8810 (t) cc_final: 0.8541 (p)
REVERT: R  291 ASN cc_start: 0.8155 (t0) cc_final: 0.7796 (t0)
REVERT: R  295 TRP cc_start: 0.8007 (m-10) cc_final: 0.7462 (m-10)
REVERT: R  355 ILE cc_start: 0.8957 (mt) cc_final: 0.8571 (mt)
REVERT: R  378 ARG cc_start: 0.5861 (OUTLIER) cc_final: 0.4120 (ppt170)
  outliers start: 21
  outliers final: 14
  residues processed: 141
  average time/residue: 0.2131
  time to fit residues: 41.8612
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  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  255 LEU
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   69 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   chunk 84 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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**
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 = 0.4013 r_free = 0.4013 target = 0.124694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.086853 restraints weight = 17565.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 3.43
r_work: 0.3240 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8892  Z= 0.186
  Angle     :  0.534   9.495  12060  Z= 0.276
  Chirality :  0.041   0.168   1353
  Planarity :  0.003   0.050   1546
  Dihedral  :  3.795  36.966   1225
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.73 %
    Favored  : 79.80 %
  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:  0.39 (0.26), residues: 1112
  helix:  1.80 (0.26), residues: 407
  sheet: -0.66 (0.34), residues: 220
  loop : -0.56 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP R 241 
 HIS   0.002   0.001   HIS B 183 
 PHE   0.013   0.001   PHE N 108 
 TYR   0.019   0.001   TYR A 360 
 ARG   0.010   0.000   ARG B  96 

*********************** 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
  149 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.941 
Fit side-chains
REVERT: B  130 GLU cc_start: 0.7699 (mp0) cc_final: 0.7349 (mp0)
REVERT: C   42 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8270 (pp20)
REVERT: E   11 SER cc_start: 0.8812 (t) cc_final: 0.8545 (p)
REVERT: N   73 ASP cc_start: 0.9046 (t70) cc_final: 0.8658 (t0)
REVERT: R  291 ASN cc_start: 0.8193 (t0) cc_final: 0.7810 (t0)
REVERT: R  295 TRP cc_start: 0.8067 (m-10) cc_final: 0.7580 (m-10)
REVERT: R  355 ILE cc_start: 0.8944 (mt) cc_final: 0.8557 (mt)
REVERT: R  378 ARG cc_start: 0.5809 (OUTLIER) cc_final: 0.4150 (ppt170)
  outliers start: 22
  outliers final: 14
  residues processed: 140
  average time/residue: 0.2290
  time to fit residues: 44.9117
Evaluate side-chains
  137 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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   69 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 47 optimal weight:    0.0980
   chunk 73 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 74 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 102 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    2.2186

-------------------------------------------------------------------------------
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**
R  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.121449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.083097 restraints weight = 17665.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 3.43
r_work: 0.3168 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8892  Z= 0.300
  Angle     :  0.594   9.321  12060  Z= 0.309
  Chirality :  0.043   0.187   1353
  Planarity :  0.004   0.049   1546
  Dihedral  :  4.118  29.702   1225
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 17.85 %
    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:  0.25 (0.26), residues: 1112
  helix:  1.69 (0.26), residues: 407
  sheet: -0.78 (0.34), residues: 230
  loop : -0.62 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP R 241 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.021   0.001   PHE N 108 
 TYR   0.017   0.002   TYR A 360 
 ARG   0.010   0.000   ARG B  96 

*********************** 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
  139 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 1.086 
Fit side-chains
REVERT: C   42 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8362 (pp20)
REVERT: E   11 SER cc_start: 0.8851 (t) cc_final: 0.8583 (p)
REVERT: N   73 ASP cc_start: 0.9058 (t70) cc_final: 0.8627 (t0)
REVERT: R  295 TRP cc_start: 0.8193 (m-10) cc_final: 0.7683 (m-10)
REVERT: R  355 ILE cc_start: 0.9004 (mt) cc_final: 0.8588 (mt)
  outliers start: 19
  outliers final: 13
  residues processed: 131
  average time/residue: 0.2028
  time to fit residues: 37.4404
Evaluate side-chains
  132 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 R residue   28 VAL
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  244 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 99 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9980
   chunk 1 optimal weight:    4.9990
   chunk 90 optimal weight:   20.0000
   chunk 89 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.123735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.085807 restraints weight = 17522.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 3.43
r_work: 0.3218 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8892  Z= 0.187
  Angle     :  0.553   9.879  12060  Z= 0.285
  Chirality :  0.042   0.158   1353
  Planarity :  0.003   0.037   1546
  Dihedral  :  3.832  23.843   1221
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 18.97 %
    Favored  : 79.24 %
  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:  0.33 (0.26), residues: 1112
  helix:  1.75 (0.26), residues: 407
  sheet: -0.72 (0.35), residues: 222
  loop : -0.58 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP R 241 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.012   0.001   PHE N 103 
 TYR   0.017   0.001   TYR A 360 
 ARG   0.009   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
  142 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 1.098 
Fit side-chains
REVERT: B  130 GLU cc_start: 0.7788 (mp0) cc_final: 0.7387 (mp0)
REVERT: C   42 GLU cc_start: 0.8552 (tt0) cc_final: 0.8293 (pp20)
REVERT: E   11 SER cc_start: 0.8848 (t) cc_final: 0.8571 (p)
REVERT: N   73 ASP cc_start: 0.9052 (t70) cc_final: 0.8628 (t0)
REVERT: R  295 TRP cc_start: 0.8178 (m-10) cc_final: 0.7683 (m-10)
REVERT: R  355 ILE cc_start: 0.8918 (mt) cc_final: 0.8480 (mt)
  outliers start: 16
  outliers final: 14
  residues processed: 136
  average time/residue: 0.1974
  time to fit residues: 38.1392
Evaluate side-chains
  138 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
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   14 LEU
Chi-restraints excluded: chain E residue   25 TRP
Chi-restraints excluded: chain E residue   27 MET
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain R residue   28 VAL
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  244 VAL
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:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0050
   chunk 4 optimal weight:    0.2980
   chunk 87 optimal weight:    0.9990
   chunk 67 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.6196

-------------------------------------------------------------------------------
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  75 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 = 0.4017 r_free = 0.4017 target = 0.124967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.087601 restraints weight = 17242.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 3.39
r_work: 0.3247 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   8892  Z= 0.157
  Angle     :  0.553  10.127  12060  Z= 0.283
  Chirality :  0.041   0.161   1353
  Planarity :  0.003   0.037   1546
  Dihedral  :  3.740  20.980   1221
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 19.75 %
    Favored  : 79.01 %
  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:  1.76 (0.26), residues: 407
  sheet: -0.68 (0.34), residues: 222
  loop : -0.55 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP R 241 
 HIS   0.002   0.000   HIS B 311 
 PHE   0.011   0.001   PHE R 312 
 TYR   0.018   0.001   TYR A 360 
 ARG   0.009   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
  141 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 1.063 
Fit side-chains
REVERT: C   42 GLU cc_start: 0.8573 (tt0) cc_final: 0.8281 (pp20)
REVERT: C   62 ARG cc_start: 0.6497 (ptp90) cc_final: 0.6295 (ptp90)
REVERT: E   11 SER cc_start: 0.8819 (t) cc_final: 0.8542 (p)
REVERT: N   73 ASP cc_start: 0.9051 (t70) cc_final: 0.8620 (t0)
REVERT: R  295 TRP cc_start: 0.8140 (m-10) cc_final: 0.7659 (m-10)
REVERT: R  355 ILE cc_start: 0.8905 (mt) cc_final: 0.8524 (mt)
  outliers start: 11
  outliers final: 10
  residues processed: 136
  average time/residue: 0.1975
  time to fit residues: 38.1645
Evaluate side-chains
  134 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
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  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   14 LEU
Chi-restraints excluded: chain E residue   25 TRP
Chi-restraints excluded: chain R residue   28 VAL
Chi-restraints excluded: chain R residue  230 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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  75 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 = 0.3959 r_free = 0.3959 target = 0.120978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.085119 restraints weight = 17572.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 3.26
r_work: 0.3212 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.2052

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= 0.196
  Angle     :  0.576  13.046  12060  Z= 0.290
  Chirality :  0.042   0.160   1353
  Planarity :  0.003   0.035   1546
  Dihedral  :  3.752  21.367   1221
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 20.09 %
    Favored  : 78.68 %
  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:  1.76 (0.26), residues: 407
  sheet: -0.66 (0.34), residues: 221
  loop : -0.59 (0.29), residues: 484

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   0.013   0.001   PHE N 108 
 TYR   0.017   0.001   TYR A 360 
 ARG   0.008   0.000   ARG B  96 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4755.83 seconds
wall clock time: 84 minutes 53.12 seconds (5093.12 seconds total)