Starting phenix.real_space_refine
on Tue May  7 01:22:28 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unz_42422/05_2024/8unz_42422_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unz_42422/05_2024/8unz_42422.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unz_42422/05_2024/8unz_42422.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unz_42422/05_2024/8unz_42422.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unz_42422/05_2024/8unz_42422_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unz_42422/05_2024/8unz_42422_updated.pdb"
  }
  resolution = 3.8
  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=   0.017
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      38      5.16       5
     C    4059      2.51       5
     N    1097      2.21       5
     O    1132      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "R TYR  199": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE  332": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib"
  Total number of atoms: 6329
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1554
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 80}
          Link IDs: {'PTRANS': 6, 'TRANS': 217}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 321
          Unresolved non-hydrogen angles: 394
          Unresolved non-hydrogen dihedrals: 261
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 16, 'ARG:plan': 14}
          Unresolved non-hydrogen planarities: 228
    Chain: "B"
      Number of atoms: 2376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2376
          Classifications: {'peptide': 335}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 57}
          Link IDs: {'PTRANS': 5, 'TRANS': 329}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 201
          Unresolved non-hydrogen angles: 248
          Unresolved non-hydrogen dihedrals: 154
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 14}
          Unresolved non-hydrogen planarities: 146
    Chain: "G"
      Number of atoms: 348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 348
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 83
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 43
    Chain: "R"
      Number of atoms: 2004
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2004
          Classifications: {'peptide': 283}
          Incomplete info: {'truncation_to_alanine': 78}
          Link IDs: {'PTRANS': 7, 'TRANS': 275}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 281
          Unresolved non-hydrogen angles: 351
          Unresolved non-hydrogen dihedrals: 225
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 163
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.77, per 1000 atoms: 0.60
  Number of scatterers: 6329
  At special positions: 0
  Unit cell: (85.0346, 136.229, 98.9178, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P       3     15.00
     O    1132      8.00
     N    1097      7.00
     C    4059      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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 1.3 seconds
  

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1704

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      26 helices and 9 sheets defined
      42.5% alpha, 15.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.614A  pdb=" N   ASN A  23 " --> pdb=" O   GLN A  19 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 56
      No H-bonds generated for 'chain 'A' and resid 53 through 56'
    Processing helix  chain 'A' and resid 235 through 238
    Processing helix  chain 'A' and resid 251 through 253
      No H-bonds generated for 'chain 'A' and resid 251 through 253'
    Processing helix  chain 'A' and resid 266 through 277
    Processing helix  chain 'A' and resid 295 through 301
      removed outlier: 3.774A  pdb=" N   ALA A 298 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 310
      No H-bonds generated for 'chain 'A' and resid 308 through 310'
    Processing helix  chain 'A' and resid 332 through 353
      removed outlier: 3.740A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 390
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.715A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 33
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'G' and resid 8 through 23
      removed outlier: 3.774A  pdb=" N   LYS G  20 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 30 through 43
    Processing helix  chain 'R' and resid 31 through 60
      removed outlier: 3.695A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 96
      removed outlier: 4.405A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 103 through 136
      removed outlier: 4.158A  pdb=" N   ILE R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   GLU R 122 " --> pdb=" O   THR R 118 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 141 through 144
      No H-bonds generated for 'chain 'R' and resid 141 through 144'
    Processing helix  chain 'R' and resid 147 through 164
      removed outlier: 3.930A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 167 through 170
      No H-bonds generated for 'chain 'R' and resid 167 through 170'
    Processing helix  chain 'R' and resid 179 through 186
    Processing helix  chain 'R' and resid 197 through 207
      removed outlier: 3.522A  pdb=" N   ILE R 201 " --> pdb=" O   GLN R 197 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 210 through 236
      removed outlier: 4.040A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   MET R 215 " --> pdb=" O   PRO R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 286
      removed outlier: 4.768A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 289 through 298
      removed outlier: 4.842A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 305 through 325
      removed outlier: 3.693A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ASN R 322 " --> pdb=" O   ASN R 318 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 330 through 338
      removed outlier: 3.584A  pdb=" N   ALA R 335 " --> pdb=" O   ASP R 331 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 286 through 292
      removed outlier: 4.163A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A  45 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 91 through 94
      removed outlier: 3.755A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   SER B  72 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 111 through 115
      removed outlier: 3.690A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 179 through 181
      removed outlier: 4.512A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.885A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.429A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 250 through 252
      removed outlier: 3.627A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 307 through 309
      removed outlier: 5.061A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.964A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.999A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)

    309 hydrogen bonds defined for protein.
    903 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.74

  Time building geometry restraints manager: 2.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2039
        1.34 -     1.46: 1305
        1.46 -     1.58: 3065
        1.58 -     1.70: 5
        1.70 -     1.82: 50
  Bond restraints: 6464
  Sorted by residual:
  bond pdb=" N   VAL R  39 "
       pdb=" CA  VAL R  39 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.035 1.21e-02 6.83e+03 8.18e+00
  bond pdb=" N   THR R  66 "
       pdb=" CA  THR R  66 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.16e-02 7.43e+03 7.96e+00
  bond pdb=" N   VAL R  48 "
       pdb=" CA  VAL R  48 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.21e-02 6.83e+03 7.86e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.451 -0.054 2.00e-02 2.50e+03 7.22e+00
  bond pdb=" N   ASN A 254 "
       pdb=" CA  ASN A 254 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.036 1.33e-02 5.65e+03 7.15e+00
  ... (remaining 6459 not shown)

  Histogram of bond angle deviations from ideal:
      100.33 -   107.07: 156
      107.07 -   113.82: 3704
      113.82 -   120.56: 2595
      120.56 -   127.31: 2334
      127.31 -   134.05: 79
  Bond angle restraints: 8868
  Sorted by residual:
  angle pdb=" N   SER G   8 "
        pdb=" CA  SER G   8 "
        pdb=" C   SER G   8 "
      ideal   model   delta    sigma   weight residual
     111.28  105.00    6.28 1.09e+00 8.42e-01 3.32e+01
  angle pdb=" N   MET R  40 "
        pdb=" CA  MET R  40 "
        pdb=" C   MET R  40 "
      ideal   model   delta    sigma   weight residual
     111.28  105.47    5.81 1.09e+00 8.42e-01 2.85e+01
  angle pdb=" N   GLN A  19 "
        pdb=" CA  GLN A  19 "
        pdb=" C   GLN A  19 "
      ideal   model   delta    sigma   weight residual
     111.71  105.92    5.79 1.15e+00 7.56e-01 2.54e+01
  angle pdb=" N   ASN A 371 "
        pdb=" CA  ASN A 371 "
        pdb=" C   ASN A 371 "
      ideal   model   delta    sigma   weight residual
     113.72  107.41    6.31 1.30e+00 5.92e-01 2.36e+01
  angle pdb=" N   ARG G  13 "
        pdb=" CA  ARG G  13 "
        pdb=" C   ARG G  13 "
      ideal   model   delta    sigma   weight residual
     111.28  106.44    4.84 1.09e+00 8.42e-01 1.97e+01
  ... (remaining 8863 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.04: 3641
       34.04 -    68.08: 64
       68.08 -   102.11: 3
      102.11 -   136.15: 1
      136.15 -   170.19: 2
  Dihedral angle restraints: 3711
    sinusoidal: 1094
      harmonic: 2617
  Sorted by residual:
  dihedral pdb=" CB  CYS R 106 "
           pdb=" SG  CYS R 106 "
           pdb=" SG  CYS R 191 "
           pdb=" CB  CYS R 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.05   71.05     1      1.00e+01 1.00e-02 6.48e+01
  dihedral pdb=" CB  CYS R 184 "
           pdb=" SG  CYS R 184 "
           pdb=" SG  CYS R 190 "
           pdb=" CB  CYS R 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.49  -60.49     1      1.00e+01 1.00e-02 4.87e+01
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -85.22 -170.19     1      2.00e+01 2.50e-03 4.76e+01
  ... (remaining 3708 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 860
       0.060 -    0.120: 166
       0.120 -    0.180: 44
       0.180 -    0.241: 6
       0.241 -    0.301: 5
  Chirality restraints: 1081
  Sorted by residual:
  chirality pdb=" CA  GLN B  17 "
            pdb=" N   GLN B  17 "
            pdb=" C   GLN B  17 "
            pdb=" CB  GLN B  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CA  ILE G   9 "
            pdb=" N   ILE G   9 "
            pdb=" C   ILE G   9 "
            pdb=" CB  ILE G   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CA  LEU B   4 "
            pdb=" N   LEU B   4 "
            pdb=" C   LEU B   4 "
            pdb=" CB  LEU B   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.71e+00
  ... (remaining 1078 not shown)

  Planarity restraints: 1111
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU R  62 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" C   GLU R  62 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   GLU R  62 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ARG R  63 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A  14 "   -0.010 2.00e-02 2.50e+03   1.98e-02 3.92e+00
        pdb=" C   ASN A  14 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ASN A  14 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLU A  15 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R  35 "   -0.010 2.00e-02 2.50e+03   1.97e-02 3.89e+00
        pdb=" C   GLY R  35 "    0.034 2.00e-02 2.50e+03
        pdb=" O   GLY R  35 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   MET R  36 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1108 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1165
        2.77 -     3.30: 6060
        3.30 -     3.84: 9879
        3.84 -     4.37: 10362
        4.37 -     4.90: 18658
  Nonbonded interactions: 46124
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 111 "
            pdb=" O   SER R 165 "
     model   vdw
     2.238 2.440
  nonbonded pdb=" OG1 THR A  55 "
            pdb=" O1A GTP A 401 "
     model   vdw
     2.267 2.440
  nonbonded pdb=" OG  SER A  54 "
            pdb=" O1A GTP A 401 "
     model   vdw
     2.319 2.440
  nonbonded pdb=" ND2 ASN B 230 "
            pdb=" OD1 ASP B 246 "
     model   vdw
     2.373 2.520
  nonbonded pdb=" OD1 ASP A 223 "
            pdb=" N   VAL A 224 "
     model   vdw
     2.396 2.520
  ... (remaining 46119 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          7.510
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.970
  Find NCS groups from input model:        0.170
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   6464  Z= 0.335
  Angle     :  0.811  10.276   8868  Z= 0.542
  Chirality :  0.056   0.301   1081
  Planarity :  0.003   0.036   1111
  Dihedral  : 13.666 170.188   2001
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.29), residues: 878
  helix:  2.35 (0.28), residues: 377
  sheet: -0.17 (0.44), residues: 145
  loop : -0.85 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 109 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.018   0.001   TYR R 185 
 ARG   0.002   0.000   ARG A 380 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.701 
Fit side-chains
REVERT: B  143 THR cc_start: 0.8413 (p) cc_final: 0.8154 (t)
REVERT: B  233 CYS cc_start: 0.9348 (t) cc_final: 0.9011 (t)
REVERT: G   38 MET cc_start: 0.7924 (ptp) cc_final: 0.7678 (ptp)
REVERT: G   48 ASP cc_start: 0.8558 (t70) cc_final: 0.8130 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1617
  time to fit residues: 21.7224
Evaluate side-chains
  67 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   chunk 37 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 44 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 68 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    0.4980
   chunk 51 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A  23 ASN
R 178 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.1022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6464  Z= 0.176
  Angle     :  0.477   7.131   8868  Z= 0.259
  Chirality :  0.040   0.157   1081
  Planarity :  0.003   0.037   1111
  Dihedral  :  9.594 174.547    969
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  8.94 %
    Favored  : 89.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.29), residues: 878
  helix:  2.31 (0.27), residues: 381
  sheet: -0.28 (0.41), residues: 158
  loop : -0.62 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 109 
 HIS   0.007   0.001   HIS R 178 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.036   0.001   TYR R 185 
 ARG   0.001   0.000   ARG A 342 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.599 
Fit side-chains
REVERT: B  143 THR cc_start: 0.8527 (p) cc_final: 0.8288 (t)
REVERT: G   38 MET cc_start: 0.7871 (ptp) cc_final: 0.7566 (ptp)
REVERT: G   48 ASP cc_start: 0.8589 (t70) cc_final: 0.8082 (t0)
  outliers start: 7
  outliers final: 7
  residues processed: 83
  average time/residue: 0.1223
  time to fit residues: 15.2362
Evaluate side-chains
  79 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  275 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0040
   chunk 66 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 22 optimal weight:   10.0000
   chunk 80 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 71 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6464  Z= 0.141
  Angle     :  0.447   6.074   8868  Z= 0.240
  Chirality :  0.039   0.149   1081
  Planarity :  0.003   0.037   1111
  Dihedral  :  9.206 178.936    969
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 12.85 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.29), residues: 878
  helix:  2.43 (0.27), residues: 381
  sheet: -0.33 (0.41), residues: 163
  loop : -0.60 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 109 
 HIS   0.013   0.001   HIS R 178 
 PHE   0.009   0.001   PHE B 199 
 TYR   0.025   0.001   TYR R 185 
 ARG   0.001   0.000   ARG A 347 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 0.742 
Fit side-chains
REVERT: B  143 THR cc_start: 0.8706 (p) cc_final: 0.8459 (t)
REVERT: G   38 MET cc_start: 0.7867 (ptp) cc_final: 0.7540 (ptp)
  outliers start: 2
  outliers final: 2
  residues processed: 77
  average time/residue: 0.1162
  time to fit residues: 14.0583
Evaluate side-chains
  72 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain R residue  201 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 70 optimal weight:    5.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 178 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6464  Z= 0.241
  Angle     :  0.490   6.119   8868  Z= 0.265
  Chirality :  0.040   0.152   1081
  Planarity :  0.003   0.041   1111
  Dihedral  :  8.880 178.079    969
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 14.34 %
    Favored  : 84.54 %
  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:  1.04 (0.29), residues: 878
  helix:  2.39 (0.27), residues: 381
  sheet: -0.39 (0.42), residues: 157
  loop : -0.73 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 109 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.015   0.001   PHE B 151 
 TYR   0.022   0.001   TYR R 185 
 ARG   0.002   0.000   ARG B 304 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.705 
Fit side-chains
REVERT: B  143 THR cc_start: 0.8889 (p) cc_final: 0.8678 (t)
REVERT: G   38 MET cc_start: 0.8044 (ptp) cc_final: 0.7659 (ptp)
  outliers start: 6
  outliers final: 3
  residues processed: 77
  average time/residue: 0.1399
  time to fit residues: 15.8241
Evaluate side-chains
  70 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue  201 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0370
   chunk 72 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 0 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 76 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.9460

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6464  Z= 0.163
  Angle     :  0.447   5.995   8868  Z= 0.240
  Chirality :  0.039   0.150   1081
  Planarity :  0.003   0.040   1111
  Dihedral  :  8.569 177.981    969
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 15.46 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.99 (0.29), residues: 878
  helix:  2.43 (0.27), residues: 378
  sheet: -0.51 (0.41), residues: 162
  loop : -0.79 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 109 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.018   0.001   TYR R 185 
 ARG   0.001   0.000   ARG B  49 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.717 
Fit side-chains
REVERT: G   38 MET cc_start: 0.7974 (ptp) cc_final: 0.7560 (ptp)
  outliers start: 5
  outliers final: 3
  residues processed: 78
  average time/residue: 0.1387
  time to fit residues: 15.9985
Evaluate side-chains
  70 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue  201 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 76 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 49 optimal weight:    0.2980
   chunk 20 optimal weight:    2.9990
   chunk 85 optimal weight:    5.9990
   chunk 70 optimal weight:    0.2980
   chunk 39 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6464  Z= 0.188
  Angle     :  0.464   6.109   8868  Z= 0.249
  Chirality :  0.039   0.147   1081
  Planarity :  0.003   0.040   1111
  Dihedral  :  8.338 177.700    969
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 15.08 %
    Favored  : 83.80 %
  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:  0.95 (0.30), residues: 878
  helix:  2.45 (0.28), residues: 378
  sheet: -0.63 (0.41), residues: 162
  loop : -0.83 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 109 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.016   0.001   TYR R 185 
 ARG   0.004   0.000   ARG A 342 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.741 
Fit side-chains
REVERT: G   38 MET cc_start: 0.8052 (ptp) cc_final: 0.7626 (ptp)
  outliers start: 6
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1289
  time to fit residues: 14.4002
Evaluate side-chains
  72 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue  201 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    8.9990
   chunk 48 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.7988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6464  Z= 0.276
  Angle     :  0.511   6.042   8868  Z= 0.277
  Chirality :  0.041   0.146   1081
  Planarity :  0.003   0.042   1111
  Dihedral  :  8.323 178.266    969
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.90 %
    Favored  : 82.68 %
  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:  0.74 (0.29), residues: 878
  helix:  2.36 (0.28), residues: 373
  sheet: -0.85 (0.41), residues: 160
  loop : -0.94 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 109 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.012   0.001   TYR R 185 
 ARG   0.004   0.000   ARG A 342 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.711 
Fit side-chains
REVERT: A  362 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.7352 (m-70)
REVERT: B   59 TYR cc_start: 0.8591 (m-80) cc_final: 0.8178 (m-80)
REVERT: G   38 MET cc_start: 0.8112 (ptp) cc_final: 0.7616 (ptp)
  outliers start: 13
  outliers final: 8
  residues processed: 76
  average time/residue: 0.1181
  time to fit residues: 13.8300
Evaluate side-chains
  71 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  275 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 41 optimal weight:    0.4980
   chunk 7 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 81 optimal weight:    4.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    1.0786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6464  Z= 0.187
  Angle     :  0.468   6.468   8868  Z= 0.252
  Chirality :  0.040   0.151   1081
  Planarity :  0.003   0.041   1111
  Dihedral  :  8.107 177.777    969
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.46 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.30), residues: 878
  helix:  2.40 (0.28), residues: 373
  sheet: -0.77 (0.43), residues: 155
  loop : -0.93 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 109 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.017   0.001   TYR R 316 
 ARG   0.004   0.000   ARG A 342 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.755 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.8584 (m-80) cc_final: 0.8157 (m-80)
REVERT: G   38 MET cc_start: 0.8076 (ptp) cc_final: 0.7597 (ptp)
  outliers start: 9
  outliers final: 8
  residues processed: 75
  average time/residue: 0.1311
  time to fit residues: 14.5711
Evaluate side-chains
  74 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 24 optimal weight:    6.9990
   chunk 71 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 83 optimal weight:    0.5980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
R 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6464  Z= 0.163
  Angle     :  0.463   6.589   8868  Z= 0.248
  Chirality :  0.039   0.149   1081
  Planarity :  0.003   0.040   1111
  Dihedral  :  7.914 176.858    969
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.83 %
    Favored  : 82.50 %
  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:  0.82 (0.30), residues: 878
  helix:  2.41 (0.28), residues: 372
  sheet: -0.78 (0.42), residues: 161
  loop : -0.88 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 109 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.023   0.001   PHE R 289 
 TYR   0.017   0.001   TYR R 316 
 ARG   0.005   0.000   ARG A 342 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.759 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.8593 (m-80) cc_final: 0.8152 (m-80)
REVERT: G   38 MET cc_start: 0.8073 (ptp) cc_final: 0.7587 (ptp)
  outliers start: 9
  outliers final: 8
  residues processed: 72
  average time/residue: 0.1628
  time to fit residues: 16.5938
Evaluate side-chains
  69 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 39 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 87 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 55 optimal weight:    0.3980
   chunk 74 optimal weight:    8.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
R 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6464  Z= 0.221
  Angle     :  0.482   6.715   8868  Z= 0.259
  Chirality :  0.040   0.146   1081
  Planarity :  0.003   0.041   1111
  Dihedral  :  7.885 176.495    969
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 16.01 %
    Favored  : 82.50 %
  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:  0.77 (0.30), residues: 878
  helix:  2.39 (0.28), residues: 371
  sheet: -0.80 (0.43), residues: 155
  loop : -0.93 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 109 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.029   0.001   PHE R 289 
 TYR   0.015   0.001   TYR R 316 
 ARG   0.001   0.000   ARG A 342 

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.652 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.8623 (m-80) cc_final: 0.8181 (m-80)
REVERT: G   38 MET cc_start: 0.8099 (ptp) cc_final: 0.7630 (ptp)
  outliers start: 8
  outliers final: 8
  residues processed: 69
  average time/residue: 0.1453
  time to fit residues: 14.8213
Evaluate side-chains
  69 residues out of total 776 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue  201 ILE
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 21 optimal weight:    0.4980
   chunk 64 optimal weight:    0.2980
   chunk 10 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 69 optimal weight:    0.2980
   chunk 29 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 12 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
R 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.120314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.094432 restraints weight = 13158.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.096831 restraints weight = 7899.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.098381 restraints weight = 5634.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6464  Z= 0.128
  Angle     :  0.447   6.752   8868  Z= 0.239
  Chirality :  0.039   0.151   1081
  Planarity :  0.003   0.039   1111
  Dihedral  :  7.729 175.863    969
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 17.32 %
    Favored  : 81.94 %
  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:  0.90 (0.30), residues: 878
  helix:  2.44 (0.28), residues: 372
  sheet: -0.66 (0.42), residues: 160
  loop : -0.83 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 109 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.025   0.001   PHE R 289 
 TYR   0.015   0.001   TYR R 185 
 ARG   0.001   0.000   ARG B  49 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1489.27 seconds
wall clock time: 27 minutes 58.16 seconds (1678.16 seconds total)