Starting phenix.real_space_refine
on Thu Mar 13 18:17:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s1m_24805/03_2025/7s1m_24805.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s1m_24805/03_2025/7s1m_24805.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s1m_24805/03_2025/7s1m_24805.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s1m_24805/03_2025/7s1m_24805.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s1m_24805/03_2025/7s1m_24805.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s1m_24805/03_2025/7s1m_24805.cif"
  }
  resolution = 2.41
  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      57      5.16       5
     C    5825      2.51       5
     N    1592      2.21       5
     O    1686      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9160
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1929
          Classifications: {'peptide': 233}
          Link IDs: {'PTRANS': 6, 'TRANS': 226}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2615
          Classifications: {'peptide': 340}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "P"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 23
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
    Chain: "P"
      Number of atoms: 213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 213
          Classifications: {'peptide': 26}
          Modifications used: {'PEPT-D': 1}
          Link IDs: {'TRANS': 25}
    Chain: "R"
      Number of atoms: 2963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 2963
          Classifications: {'peptide': 381}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'PTRANS': 13, 'TRANS': 367}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 204
          Unresolved non-hydrogen angles: 261
          Unresolved non-hydrogen dihedrals: 167
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 143
  Time building chain proxies: 5.67, per 1000 atoms: 0.62
  Number of scatterers: 9160
  At special positions: 0
  Unit cell: (87.15, 171.81, 97.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O    1686      8.00
     N    1592      7.00
     C    5825      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  46 " - pdb=" SG  CYS R  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  62 " - pdb=" SG  CYS R 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " 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
  Links applied
    TRANS
      " DAL P   4 " - " GLU P   3 "
  Time building additional restraints: 2.39
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DAL P   4 "
  Number of C-beta restraints generated:  2202

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 11 sheets defined
      44.8% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
      removed outlier: 3.745A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 58
      removed outlier: 3.503A  pdb=" N   LYS A  58 " --> pdb=" O   ASN A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.556A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 279
    Processing helix  chain 'A' and resid 280 through 283
      removed outlier: 3.622A  pdb=" N   ARG A 283 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 280 through 283'
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 4.037A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.274A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.644A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 2 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.546A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'P' and resid 2 through 29
      No H-bonds generated for 'chain 'P' and resid 2 through 29'
    Processing helix  chain 'R' and resid 32 through 52
    Processing helix  chain 'R' and resid 91 through 95
    Processing helix  chain 'R' and resid 139 through 169
    Processing helix  chain 'R' and resid 170 through 173
    Processing helix  chain 'R' and resid 174 through 205
      removed outlier: 3.508A  pdb=" N   TYR R 205 " --> pdb=" O   LEU R 201 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 206 through 215
      removed outlier: 3.574A  pdb=" N   GLN R 213 " --> pdb=" O   ALA R 209 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   TRP R 214 " --> pdb=" O   GLN R 210 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ASP R 215 " --> pdb=" O   GLN R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 223 through 255
      removed outlier: 4.157A  pdb=" N   ARG R 227 " --> pdb=" O   SER R 223 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 291
      removed outlier: 3.695A  pdb=" N   ARG R 267 " --> pdb=" O   GLN R 263 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   VAL R 276 " --> pdb=" O   ILE R 272 " (cutoff:3.500A)
      Proline residue:  R 277  - end of helix
      removed outlier: 4.056A  pdb=" N   PHE R 280 " --> pdb=" O   VAL R 276 " (cutoff:3.500A)
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 294 through 298
    Processing helix  chain 'R' and resid 302 through 338
      removed outlier: 3.894A  pdb=" N   ILE R 308 " --> pdb=" O   ASN R 304 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   ILE R 309 " --> pdb=" O   TYR R 305 " (cutoff:3.500A)
      Proline residue:  R 312  - end of helix
    Processing helix  chain 'R' and resid 342 through 361
      Proline residue:  R 358  - end of helix
    Processing helix  chain 'R' and resid 364 through 369
      removed outlier: 4.712A  pdb=" N   PHE R 369 " --> pdb=" O   VAL R 365 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 376 through 404
      removed outlier: 4.153A  pdb=" N   GLY R 395 " --> pdb=" O   THR R 391 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   LEU R 396 " --> pdb=" O   SER R 392 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 406 through 422
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.235A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.159A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.691A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.079A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.537A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.732A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.452A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ASN B 125 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 4.458A  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 153
      removed outlier: 3.501A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.291A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.478A  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: 6.575A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.894A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.266A  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 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.830A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 80 through 84

    469 hydrogen bonds defined for protein.
    1335 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: 2.78

  Time building geometry restraints manager: 2.78 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: 2978
        1.34 -     1.45: 1441
        1.45 -     1.57: 4865
        1.57 -     1.69: 0
        1.69 -     1.81: 77
  Bond restraints: 9361
  Sorted by residual:
  bond pdb=" N   SER R 258 "
       pdb=" CA  SER R 258 "
    ideal  model  delta    sigma   weight residual
    1.457  1.475 -0.017 1.29e-02 6.01e+03 1.77e+00
  bond pdb=" CA  ASP R 372 "
       pdb=" C   ASP R 372 "
    ideal  model  delta    sigma   weight residual
    1.524  1.508  0.016 1.27e-02 6.20e+03 1.50e+00
  bond pdb=" CG  GLN R  37 "
       pdb=" CD  GLN R  37 "
    ideal  model  delta    sigma   weight residual
    1.516  1.486  0.030 2.50e-02 1.60e+03 1.45e+00
  bond pdb=" CA  SER R 261 "
       pdb=" C   SER R 261 "
    ideal  model  delta    sigma   weight residual
    1.524  1.509  0.015 1.29e-02 6.01e+03 1.34e+00
  bond pdb=" CA  MET R 371 "
       pdb=" C   MET R 371 "
    ideal  model  delta    sigma   weight residual
    1.525  1.511  0.013 1.28e-02 6.10e+03 1.09e+00
  ... (remaining 9356 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 12450
        1.49 -     2.97: 196
        2.97 -     4.46: 33
        4.46 -     5.95: 14
        5.95 -     7.44: 2
  Bond angle restraints: 12695
  Sorted by residual:
  angle pdb=" N   TYR B 105 "
        pdb=" CA  TYR B 105 "
        pdb=" C   TYR B 105 "
      ideal   model   delta    sigma   weight residual
     109.59  102.48    7.11 1.61e+00 3.86e-01 1.95e+01
  angle pdb=" N   MET R 371 "
        pdb=" CA  MET R 371 "
        pdb=" C   MET R 371 "
      ideal   model   delta    sigma   weight residual
     110.35  115.98   -5.63 1.36e+00 5.41e-01 1.71e+01
  angle pdb=" N   SER R 258 "
        pdb=" CA  SER R 258 "
        pdb=" C   SER R 258 "
      ideal   model   delta    sigma   weight residual
     110.80  118.24   -7.44 2.13e+00 2.20e-01 1.22e+01
  angle pdb=" N   PHE R 257 "
        pdb=" CA  PHE R 257 "
        pdb=" C   PHE R 257 "
      ideal   model   delta    sigma   weight residual
     111.30  115.38   -4.08 1.43e+00 4.89e-01 8.14e+00
  angle pdb=" N   SER R 261 "
        pdb=" CA  SER R 261 "
        pdb=" C   SER R 261 "
      ideal   model   delta    sigma   weight residual
     109.15  105.08    4.07 1.44e+00 4.82e-01 7.97e+00
  ... (remaining 12690 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 5081
       17.91 -    35.82: 373
       35.82 -    53.74: 65
       53.74 -    71.65: 9
       71.65 -    89.56: 15
  Dihedral angle restraints: 5543
    sinusoidal: 2139
      harmonic: 3404
  Sorted by residual:
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.85  -24.15     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CB  CYS R  62 "
           pdb=" SG  CYS R  62 "
           pdb=" SG  CYS R 104 "
           pdb=" CB  CYS R 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -116.56   30.56     1      1.00e+01 1.00e-02 1.33e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.37   17.63     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 5540 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1216
       0.060 -    0.121: 178
       0.121 -    0.181: 14
       0.181 -    0.242: 1
       0.242 -    0.302: 2
  Chirality restraints: 1411
  Sorted by residual:
  chirality pdb=" CA  TYR B 105 "
            pdb=" N   TYR B 105 "
            pdb=" C   TYR B 105 "
            pdb=" CB  TYR B 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" CA  SER R 258 "
            pdb=" N   SER R 258 "
            pdb=" C   SER R 258 "
            pdb=" CB  SER R 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.28 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CA  PHE R 257 "
            pdb=" N   PHE R 257 "
            pdb=" C   PHE R 257 "
            pdb=" CB  PHE R 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 1408 not shown)

  Planarity restraints: 1620
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 214 "   -0.016 2.00e-02 2.50e+03   1.46e-02 5.30e+00
        pdb=" CG  TRP R 214 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 214 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 214 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 214 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 214 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 214 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 214 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 214 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 214 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 259 "    0.010 2.00e-02 2.50e+03   1.95e-02 3.79e+00
        pdb=" C   VAL R 259 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   VAL R 259 "    0.012 2.00e-02 2.50e+03
        pdb=" N   PHE R 260 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 276 "   -0.029 5.00e-02 4.00e+02   4.31e-02 2.97e+00
        pdb=" N   PRO R 277 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO R 277 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO R 277 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1617 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1631
        2.77 -     3.30: 8876
        3.30 -     3.83: 15680
        3.83 -     4.37: 18882
        4.37 -     4.90: 31874
  Nonbonded interactions: 76943
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 260 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   TYR A 318 "
            pdb=" NH1 ARG A 336 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OG1 THR R 175 "
            pdb=" OE2 GLU R 262 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OH  TYR A 253 "
            pdb=" OG  SER A 306 "
     model   vdw
     2.293 3.040
  ... (remaining 76938 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.870
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:15.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
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   0.030   9361  Z= 0.219
  Angle     :  0.513   7.435  12695  Z= 0.288
  Chirality :  0.044   0.302   1411
  Planarity :  0.004   0.050   1619
  Dihedral  : 13.540  89.560   3320
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.52 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.25), residues: 1146
  helix:  2.62 (0.24), residues: 456
  sheet:  0.99 (0.36), residues: 225
  loop : -0.05 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.001   TRP R 214 
 HIS   0.015   0.001   HIS A 357 
 PHE   0.014   0.001   PHE R 230 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.009   0.000   ARG G  62 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 1.040 
Fit side-chains
REVERT: P   17 GLU cc_start: 0.8520 (tp30) cc_final: 0.8037 (tp30)
REVERT: R  211 GLN cc_start: 0.8678 (tp-100) cc_final: 0.8331 (tp40)
  outliers start: 1
  outliers final: 0
  residues processed: 132
  average time/residue: 1.5620
  time to fit residues: 218.1044
Evaluate side-chains
  109 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 89 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 103 optimal weight:    0.8980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
B 268 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   3 GLN
R 338 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.116027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.081681 restraints weight = 14278.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 2.19
r_work: 0.2963 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9361  Z= 0.193
  Angle     :  0.501   5.019  12695  Z= 0.278
  Chirality :  0.042   0.156   1411
  Planarity :  0.004   0.039   1619
  Dihedral  :  4.250  21.809   1269
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  7.22 %
    Favored  : 91.42 %
  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:  1.88 (0.25), residues: 1146
  helix:  2.71 (0.23), residues: 467
  sheet:  0.78 (0.36), residues: 226
  loop : -0.04 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.011   0.001   HIS A 357 
 PHE   0.012   0.001   PHE R 230 
 TYR   0.033   0.001   TYR R 148 
 ARG   0.005   0.000   ARG R 421 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 1.132 
Fit side-chains
REVERT: N    5 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7227 (mp10)
REVERT: N   46 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7620 (mm-30)
REVERT: P   17 GLU cc_start: 0.8984 (tp30) cc_final: 0.8341 (tp30)
REVERT: R   33 TRP cc_start: 0.8194 (t60) cc_final: 0.7954 (t60)
REVERT: R   71 CYS cc_start: 0.6068 (t) cc_final: 0.5358 (p)
REVERT: R  211 GLN cc_start: 0.8910 (tp-100) cc_final: 0.8552 (tp40)
REVERT: R  218 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6694 (tp)
  outliers start: 13
  outliers final: 2
  residues processed: 126
  average time/residue: 1.4527
  time to fit residues: 194.0133
Evaluate side-chains
  121 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 117
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain R residue  218 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 110 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 103 optimal weight:    0.8980
   chunk 94 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
B   6 GLN
B 268 ASN
** B 340 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 = 0.3623 r_free = 0.3623 target = 0.114584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.079905 restraints weight = 14408.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 2.23
r_work: 0.2929 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2810 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9361  Z= 0.260
  Angle     :  0.518   7.618  12695  Z= 0.286
  Chirality :  0.043   0.162   1411
  Planarity :  0.004   0.040   1619
  Dihedral  :  4.357  20.006   1269
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  9.31 %
    Favored  : 89.54 %
  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:  1.72 (0.25), residues: 1146
  helix:  2.63 (0.23), residues: 466
  sheet:  0.57 (0.35), residues: 226
  loop : -0.11 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.010   0.001   HIS A 357 
 PHE   0.013   0.001   PHE R 230 
 TYR   0.028   0.002   TYR R 148 
 ARG   0.002   0.000   ARG A 336 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 1.134 
Fit side-chains
REVERT: B    6 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8077 (pp30)
REVERT: N   46 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7714 (mm-30)
REVERT: P   17 GLU cc_start: 0.8982 (tp30) cc_final: 0.8335 (tp30)
REVERT: R   33 TRP cc_start: 0.8128 (t60) cc_final: 0.7890 (t60)
REVERT: R  210 GLN cc_start: 0.8593 (pt0) cc_final: 0.8269 (pt0)
REVERT: R  211 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8375 (tp40)
  outliers start: 11
  outliers final: 2
  residues processed: 121
  average time/residue: 1.9182
  time to fit residues: 245.5069
Evaluate side-chains
  116 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 113
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain G residue   14 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 80 optimal weight:   50.0000
   chunk 36 optimal weight:    0.0870
   chunk 87 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 67 optimal weight:    6.9990
   chunk 106 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0670
   overall best weight:    0.5696

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
B   6 GLN
B 268 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.116557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.082315 restraints weight = 14250.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 2.19
r_work: 0.2975 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9361  Z= 0.145
  Angle     :  0.468   8.397  12695  Z= 0.257
  Chirality :  0.040   0.165   1411
  Planarity :  0.003   0.038   1619
  Dihedral  :  4.089  19.352   1269
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 11.51 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.25), residues: 1146
  helix:  2.80 (0.24), residues: 467
  sheet:  0.37 (0.34), residues: 228
  loop : -0.15 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.010   0.001   PHE A 212 
 TYR   0.025   0.001   TYR R 148 
 ARG   0.002   0.000   ARG A 265 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 1.076 
Fit side-chains
REVERT: B    6 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8058 (pp30)
REVERT: N   43 LYS cc_start: 0.8353 (ptpt) cc_final: 0.8140 (ptpp)
REVERT: N   46 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7743 (mm-30)
REVERT: P   17 GLU cc_start: 0.8980 (tp30) cc_final: 0.8321 (tp30)
REVERT: P   24 GLU cc_start: 0.9151 (tp30) cc_final: 0.8377 (tm-30)
REVERT: R   33 TRP cc_start: 0.8067 (t60) cc_final: 0.7843 (t60)
REVERT: R   71 CYS cc_start: 0.6122 (t) cc_final: 0.5496 (p)
REVERT: R  211 GLN cc_start: 0.8741 (tp-100) cc_final: 0.8262 (tp40)
REVERT: R  218 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6588 (tp)
REVERT: R  320 ASN cc_start: 0.8849 (m-40) cc_final: 0.8624 (t0)
  outliers start: 11
  outliers final: 3
  residues processed: 123
  average time/residue: 1.4751
  time to fit residues: 192.1397
Evaluate side-chains
  115 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 110
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain R residue  218 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 92 optimal weight:    6.9990
   chunk 105 optimal weight:    3.9990
   chunk 98 optimal weight:    4.9990
   chunk 79 optimal weight:   20.0000
   chunk 23 optimal weight:    0.1980
   chunk 102 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   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 390 GLN
B   6 GLN
B 268 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.115441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.081004 restraints weight = 14318.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 2.19
r_work: 0.2952 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9361  Z= 0.210
  Angle     :  0.491   8.866  12695  Z= 0.269
  Chirality :  0.041   0.157   1411
  Planarity :  0.003   0.038   1619
  Dihedral  :  4.161  19.462   1269
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 12.45 %
    Favored  : 86.19 %
  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:  1.72 (0.25), residues: 1146
  helix:  2.75 (0.23), residues: 467
  sheet:  0.41 (0.34), residues: 226
  loop : -0.18 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.012   0.001   PHE B 151 
 TYR   0.025   0.001   TYR R 148 
 ARG   0.002   0.000   ARG G  62 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 2.824 
Fit side-chains
REVERT: B    6 GLN cc_start: 0.8460 (pt0) cc_final: 0.8027 (pp30)
REVERT: N   43 LYS cc_start: 0.8417 (ptpt) cc_final: 0.8188 (ptpp)
REVERT: N   46 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7836 (mm-30)
REVERT: P   17 GLU cc_start: 0.8984 (tp30) cc_final: 0.8328 (tp30)
REVERT: P   24 GLU cc_start: 0.9152 (tp30) cc_final: 0.8375 (tm-30)
REVERT: R   33 TRP cc_start: 0.8057 (t60) cc_final: 0.7842 (t60)
REVERT: R   71 CYS cc_start: 0.6196 (t) cc_final: 0.5552 (p)
REVERT: R  211 GLN cc_start: 0.8700 (tp-100) cc_final: 0.8253 (tp40)
REVERT: R  218 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6594 (tp)
REVERT: R  320 ASN cc_start: 0.8822 (m-40) cc_final: 0.8590 (t0)
  outliers start: 13
  outliers final: 5
  residues processed: 121
  average time/residue: 2.2137
  time to fit residues: 284.7200
Evaluate side-chains
  120 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain R residue  218 LEU
Chi-restraints excluded: chain R residue  228 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 81 optimal weight:    8.9990
   chunk 45 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0370
   chunk 93 optimal weight:    8.9990
   chunk 60 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.9260

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN
R 210 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.115882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.081535 restraints weight = 14295.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 2.19
r_work: 0.2961 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9361  Z= 0.180
  Angle     :  0.479   9.661  12695  Z= 0.263
  Chirality :  0.041   0.151   1411
  Planarity :  0.003   0.037   1619
  Dihedral  :  4.094  19.150   1269
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.76 %
    Favored  : 85.67 %
  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:  1.72 (0.25), residues: 1146
  helix:  2.73 (0.23), residues: 473
  sheet:  0.32 (0.34), residues: 229
  loop : -0.13 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.011   0.001   PHE R 230 
 TYR   0.024   0.001   TYR R 148 
 ARG   0.003   0.000   ARG G  62 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 1.107 
Fit side-chains
REVERT: B    6 GLN cc_start: 0.8404 (pt0) cc_final: 0.8031 (pp30)
REVERT: P   17 GLU cc_start: 0.8979 (tp30) cc_final: 0.8319 (tp30)
REVERT: P   24 GLU cc_start: 0.9158 (tp30) cc_final: 0.8359 (tm-30)
REVERT: R   33 TRP cc_start: 0.8045 (t60) cc_final: 0.7840 (t60)
REVERT: R   71 CYS cc_start: 0.6078 (t) cc_final: 0.5500 (p)
REVERT: R  211 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8088 (tp40)
REVERT: R  320 ASN cc_start: 0.8778 (m-40) cc_final: 0.8539 (t0)
  outliers start: 15
  outliers final: 6
  residues processed: 122
  average time/residue: 1.6672
  time to fit residues: 215.2400
Evaluate side-chains
  117 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  228 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 80 optimal weight:   40.0000
   chunk 18 optimal weight:    1.9990
   chunk 97 optimal weight:    0.4980
   chunk 51 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   chunk 109 optimal weight:    8.9990
   chunk 20 optimal weight:    0.4980
   chunk 29 optimal weight:    0.8980
   chunk 105 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.116549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.082292 restraints weight = 14442.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 2.20
r_work: 0.2976 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2858 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9361  Z= 0.156
  Angle     :  0.472  10.688  12695  Z= 0.257
  Chirality :  0.040   0.146   1411
  Planarity :  0.003   0.037   1619
  Dihedral  :  3.987  18.953   1269
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.97 %
    Favored  : 85.36 %
  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:  1.77 (0.25), residues: 1146
  helix:  2.80 (0.23), residues: 474
  sheet:  0.48 (0.35), residues: 222
  loop : -0.22 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.011   0.001   PHE R 280 
 TYR   0.024   0.001   TYR R 148 
 ARG   0.001   0.000   ARG N  38 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 1.139 
Fit side-chains
REVERT: A   50 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7305 (pp20)
REVERT: B    6 GLN cc_start: 0.8383 (pt0) cc_final: 0.8046 (pp30)
REVERT: B  234 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8513 (m-80)
REVERT: N   46 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7776 (mt-10)
REVERT: N   89 GLU cc_start: 0.7950 (pt0) cc_final: 0.7689 (pm20)
REVERT: P   17 GLU cc_start: 0.8982 (tp30) cc_final: 0.8321 (tp30)
REVERT: P   24 GLU cc_start: 0.9152 (tp30) cc_final: 0.8328 (tm-30)
REVERT: R   71 CYS cc_start: 0.6199 (t) cc_final: 0.5711 (p)
REVERT: R  211 GLN cc_start: 0.8611 (tp-100) cc_final: 0.8085 (tp40)
REVERT: R  218 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6517 (tp)
REVERT: R  320 ASN cc_start: 0.8768 (m-40) cc_final: 0.8559 (t0)
  outliers start: 16
  outliers final: 6
  residues processed: 121
  average time/residue: 1.4842
  time to fit residues: 189.9107
Evaluate side-chains
  115 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  218 LEU
Chi-restraints excluded: chain R residue  228 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 79 optimal weight:   20.0000
   chunk 100 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 94 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 101 optimal weight:    4.9990
   chunk 3 optimal weight:    0.3980
   chunk 57 optimal weight:    1.9990
   chunk 52 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN
R 210 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.116441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.082176 restraints weight = 14535.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 2.21
r_work: 0.2974 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9361  Z= 0.162
  Angle     :  0.477  10.551  12695  Z= 0.260
  Chirality :  0.040   0.146   1411
  Planarity :  0.003   0.037   1619
  Dihedral  :  3.975  18.902   1269
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 13.39 %
    Favored  : 84.94 %
  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:  1.76 (0.25), residues: 1146
  helix:  2.78 (0.23), residues: 474
  sheet:  0.45 (0.35), residues: 223
  loop : -0.21 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.011   0.001   PHE R 260 
 TYR   0.024   0.001   TYR R 148 
 ARG   0.001   0.000   ARG N  72 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 1.077 
Fit side-chains
REVERT: B  234 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8515 (m-80)
REVERT: N   89 GLU cc_start: 0.7922 (pt0) cc_final: 0.7657 (pm20)
REVERT: P   17 GLU cc_start: 0.8987 (tp30) cc_final: 0.8325 (tp30)
REVERT: P   24 GLU cc_start: 0.9155 (tp30) cc_final: 0.8338 (tm-30)
REVERT: R   71 CYS cc_start: 0.6133 (t) cc_final: 0.5701 (p)
REVERT: R  211 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8284 (tp40)
REVERT: R  218 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6580 (tp)
REVERT: R  320 ASN cc_start: 0.8773 (m-40) cc_final: 0.8563 (t0)
REVERT: R  369 PHE cc_start: 0.7285 (m-80) cc_final: 0.6062 (t80)
  outliers start: 16
  outliers final: 7
  residues processed: 121
  average time/residue: 1.4906
  time to fit residues: 190.9561
Evaluate side-chains
  118 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain P residue   21 LEU
Chi-restraints excluded: chain R residue  218 LEU
Chi-restraints excluded: chain R residue  228 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 93 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0170
   chunk 100 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0470
   chunk 69 optimal weight:    0.9990
   chunk 49 optimal weight:    0.1980
   chunk 82 optimal weight:    3.9990
   overall best weight:    0.3916

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

Flipped N/Q/H residues before XYZ refinement:
B   6 GLN
B 268 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.117653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.083813 restraints weight = 14263.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 2.21
r_work: 0.3003 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   9361  Z= 0.133
  Angle     :  0.468  11.382  12695  Z= 0.255
  Chirality :  0.039   0.141   1411
  Planarity :  0.003   0.036   1619
  Dihedral  :  3.830  18.575   1269
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 14.44 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.89 (0.25), residues: 1146
  helix:  2.93 (0.24), residues: 468
  sheet:  0.46 (0.35), residues: 223
  loop : -0.11 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP R  33 
 HIS   0.004   0.000   HIS A 357 
 PHE   0.010   0.001   PHE R 260 
 TYR   0.023   0.001   TYR R 148 
 ARG   0.002   0.000   ARG R 310 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 1.021 
Fit side-chains
REVERT: B  217 MET cc_start: 0.9018 (pmm) cc_final: 0.8767 (pmm)
REVERT: B  234 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8582 (m-80)
REVERT: N   89 GLU cc_start: 0.7879 (pt0) cc_final: 0.7628 (pm20)
REVERT: P   17 GLU cc_start: 0.8984 (tp30) cc_final: 0.8313 (tp30)
REVERT: P   24 GLU cc_start: 0.9146 (tp30) cc_final: 0.8326 (tm-30)
REVERT: R   71 CYS cc_start: 0.6100 (t) cc_final: 0.5680 (p)
REVERT: R  211 GLN cc_start: 0.8608 (tp-100) cc_final: 0.8059 (tp40)
REVERT: R  218 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6564 (tp)
REVERT: R  320 ASN cc_start: 0.8750 (m-40) cc_final: 0.8547 (t0)
REVERT: R  369 PHE cc_start: 0.7240 (m-80) cc_final: 0.6086 (t80)
  outliers start: 13
  outliers final: 6
  residues processed: 125
  average time/residue: 1.4980
  time to fit residues: 198.8590
Evaluate side-chains
  119 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  218 LEU
Chi-restraints excluded: chain R residue  228 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 112 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9990
   chunk 102 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0050
   overall best weight:    0.7396

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.116931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.082741 restraints weight = 14521.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 2.21
r_work: 0.2984 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9361  Z= 0.164
  Angle     :  0.488  11.932  12695  Z= 0.265
  Chirality :  0.040   0.145   1411
  Planarity :  0.003   0.037   1619
  Dihedral  :  3.885  18.811   1269
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 14.96 %
    Favored  : 84.00 %
  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:  1.78 (0.25), residues: 1146
  helix:  2.78 (0.24), residues: 474
  sheet:  0.46 (0.35), residues: 223
  loop : -0.17 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP R  33 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.012   0.001   PHE R 260 
 TYR   0.023   0.001   TYR R 148 
 ARG   0.002   0.000   ARG R 310 

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 112
  time to evaluate  : 1.090 
Fit side-chains
REVERT: B  217 MET cc_start: 0.9032 (pmm) cc_final: 0.8784 (pmm)
REVERT: B  234 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.8506 (m-80)
REVERT: N   89 GLU cc_start: 0.7881 (pt0) cc_final: 0.7626 (pm20)
REVERT: P   17 GLU cc_start: 0.8979 (tp30) cc_final: 0.8304 (tp30)
REVERT: P   24 GLU cc_start: 0.9154 (tp30) cc_final: 0.8319 (tm-30)
REVERT: R   71 CYS cc_start: 0.6202 (t) cc_final: 0.5810 (p)
REVERT: R  211 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8044 (tp40)
REVERT: R  218 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6582 (tp)
REVERT: R  320 ASN cc_start: 0.8767 (m-40) cc_final: 0.8563 (t0)
REVERT: R  369 PHE cc_start: 0.7250 (m-80) cc_final: 0.6092 (t80)
  outliers start: 10
  outliers final: 6
  residues processed: 119
  average time/residue: 1.5712
  time to fit residues: 197.7564
Evaluate side-chains
  117 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   14 LYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain R residue  218 LEU
Chi-restraints excluded: chain R residue  228 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 100 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 83 optimal weight:   30.0000
   chunk 66 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.115733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.081457 restraints weight = 14284.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 2.19
r_work: 0.2960 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9361  Z= 0.209
  Angle     :  0.511  12.062  12695  Z= 0.278
  Chirality :  0.041   0.151   1411
  Planarity :  0.003   0.037   1619
  Dihedral  :  4.040  18.940   1269
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 15.17 %
    Favored  : 83.68 %
  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:  1.71 (0.25), residues: 1146
  helix:  2.68 (0.23), residues: 474
  sheet:  0.45 (0.35), residues: 223
  loop : -0.17 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP R  33 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.013   0.001   PHE R 260 
 TYR   0.024   0.001   TYR R 148 
 ARG   0.001   0.000   ARG R 310 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9919.44 seconds
wall clock time: 173 minutes 46.70 seconds (10426.70 seconds total)