Starting phenix.real_space_refine
on Wed Mar 12 19:05:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wa3_37390/03_2025/8wa3_37390.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wa3_37390/03_2025/8wa3_37390.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wa3_37390/03_2025/8wa3_37390.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wa3_37390/03_2025/8wa3_37390.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wa3_37390/03_2025/8wa3_37390.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wa3_37390/03_2025/8wa3_37390.cif"
  }
  resolution = 2.86
  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=   0.019
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      48      5.16       5
     C    5156      2.51       5
     N    1458      2.21       5
     O    1501      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 8163
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2222
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2222
          Classifications: {'peptide': 274}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 6, 'TRANS': 267}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 34
    Chain: "A"
      Number of atoms: 1922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1922
          Classifications: {'peptide': 232}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2616
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
  Time building chain proxies: 5.46, per 1000 atoms: 0.67
  Number of scatterers: 8163
  At special positions: 0
  Unit cell: (80.325, 100.674, 128.52, 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      48     16.00
     O    1501      8.00
     N    1458      7.00
     C    5156      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 216 " - pdb=" SG  CYS R 286 " distance=2.03
    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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.84
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1934

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 10 sheets defined
      41.4% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'R' and resid 128 through 161
      removed outlier: 3.607A  pdb=" N   LEU R 161 " --> pdb=" O   LEU R 157 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 167 through 194
    Processing helix  chain 'R' and resid 211 through 247
      removed outlier: 3.637A  pdb=" N   TYR R 231 " --> pdb=" O   VAL R 227 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 255 through 265
    Processing helix  chain 'R' and resid 265 through 281
      Proline residue:  R 273  - end of helix
    Processing helix  chain 'R' and resid 292 through 329
      removed outlier: 3.989A  pdb=" N   TRP R 296 " --> pdb=" O   VAL R 292 " (cutoff:3.500A)
      Proline residue:  R 302  - end of helix
    Processing helix  chain 'R' and resid 331 through 347
      removed outlier: 3.685A  pdb=" N   ARG R 338 " --> pdb=" O   ASP R 334 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   LEU R 339 " --> pdb=" O   TYR R 335 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU R 344 " --> pdb=" O   ALA R 340 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   PHE R 345 " --> pdb=" O   ARG R 341 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 350 through 357
      removed outlier: 4.208A  pdb=" N   PHE R 357 " --> pdb=" O   HIS R 353 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 367 through 394
      removed outlier: 3.584A  pdb=" N   PHE R 371 " --> pdb=" O   GLY R 367 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLY R 385 " --> pdb=" O   SER R 381 " (cutoff:3.500A)
      removed outlier: 4.926A  pdb=" N   VAL R 388 " --> pdb=" O   GLN R 384 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   CYS R 393 " --> pdb=" O   SER R 389 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 398 through 415
    Processing helix  chain 'A' and resid 10 through 40
      removed outlier: 3.557A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.563A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 331 through 350
    Processing helix  chain 'A' and resid 369 through 391
      removed outlier: 3.911A  pdb=" N   ARG A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.748A  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 55 through 59
    Processing helix  chain 'N' and resid 28 through 32
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 6.279A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51
      removed outlier: 6.894A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.521A  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: 3.787A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.849A  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: 4.380A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.502A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.322A  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: 7.084A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.403A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.817A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.580A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 6
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 7.058A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1233 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: 2.22

  Time building geometry restraints manager: 2.22 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: 2703
        1.34 -     1.46: 1550
        1.46 -     1.58: 4002
        1.58 -     1.70: 0
        1.70 -     1.82: 66
  Bond restraints: 8321
  Sorted by residual:
  bond pdb=" CA  LEU A  46 "
       pdb=" C   LEU A  46 "
    ideal  model  delta    sigma   weight residual
    1.528  1.487  0.042 1.28e-02 6.10e+03 1.06e+01
  bond pdb=" CA  GLN R 384 "
       pdb=" C   GLN R 384 "
    ideal  model  delta    sigma   weight residual
    1.522  1.481  0.040 1.45e-02 4.76e+03 7.68e+00
  bond pdb=" CA  LEU A  45 "
       pdb=" C   LEU A  45 "
    ideal  model  delta    sigma   weight residual
    1.524  1.489  0.035 1.27e-02 6.20e+03 7.66e+00
  bond pdb=" CA  SER R 382 "
       pdb=" C   SER R 382 "
    ideal  model  delta    sigma   weight residual
    1.524  1.497  0.027 1.24e-02 6.50e+03 4.84e+00
  bond pdb=" CA  PHE R 379 "
       pdb=" C   PHE R 379 "
    ideal  model  delta    sigma   weight residual
    1.524  1.501  0.023 1.24e-02 6.50e+03 3.38e+00
  ... (remaining 8316 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 11146
        2.41 -     4.81: 91
        4.81 -     7.22: 18
        7.22 -     9.63: 2
        9.63 -    12.03: 3
  Bond angle restraints: 11260
  Sorted by residual:
  angle pdb=" N   GLN R 384 "
        pdb=" CA  GLN R 384 "
        pdb=" C   GLN R 384 "
      ideal   model   delta    sigma   weight residual
     112.34  102.20   10.14 1.30e+00 5.92e-01 6.09e+01
  angle pdb=" N   LYS A 307 "
        pdb=" CA  LYS A 307 "
        pdb=" C   LYS A 307 "
      ideal   model   delta    sigma   weight residual
     113.89  101.86   12.03 1.58e+00 4.01e-01 5.80e+01
  angle pdb=" N   LEU A  46 "
        pdb=" CA  LEU A  46 "
        pdb=" C   LEU A  46 "
      ideal   model   delta    sigma   weight residual
     109.86  103.86    6.00 1.55e+00 4.16e-01 1.50e+01
  angle pdb=" N   SER A  51 "
        pdb=" CA  SER A  51 "
        pdb=" C   SER A  51 "
      ideal   model   delta    sigma   weight residual
     114.64  109.14    5.50 1.52e+00 4.33e-01 1.31e+01
  angle pdb=" N   GLU A 309 "
        pdb=" CA  GLU A 309 "
        pdb=" C   GLU A 309 "
      ideal   model   delta    sigma   weight residual
     113.12  108.90    4.22 1.25e+00 6.40e-01 1.14e+01
  ... (remaining 11255 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 4471
       17.29 -    34.59: 404
       34.59 -    51.88: 81
       51.88 -    69.18: 8
       69.18 -    86.47: 12
  Dihedral angle restraints: 4976
    sinusoidal: 1984
      harmonic: 2992
  Sorted by residual:
  dihedral pdb=" CA  CYS N  99 "
           pdb=" C   CYS N  99 "
           pdb=" N   PRO N 100 "
           pdb=" CA  PRO N 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.70  -29.30     0      5.00e+00 4.00e-02 3.43e+01
  dihedral pdb=" CA  CYS N 107 "
           pdb=" C   CYS N 107 "
           pdb=" N   PHE N 108 "
           pdb=" CA  PHE N 108 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.39  -25.61     0      5.00e+00 4.00e-02 2.62e+01
  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 -160.41  -19.59     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 4973 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 944
       0.044 -    0.088: 242
       0.088 -    0.132: 73
       0.132 -    0.177: 6
       0.177 -    0.221: 1
  Chirality restraints: 1266
  Sorted by residual:
  chirality pdb=" CA  LYS A 307 "
            pdb=" N   LYS A 307 "
            pdb=" C   LYS A 307 "
            pdb=" CB  LYS A 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CG  LEU R 387 "
            pdb=" CB  LEU R 387 "
            pdb=" CD1 LEU R 387 "
            pdb=" CD2 LEU R 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.22e-01
  chirality pdb=" CA  GLU A  15 "
            pdb=" N   GLU A  15 "
            pdb=" C   GLU A  15 "
            pdb=" CB  GLU A  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.33e-01
  ... (remaining 1263 not shown)

  Planarity restraints: 1440
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  44 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.69e+00
        pdb=" C   LEU A  44 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   LEU A  44 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LEU A  45 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A  11 "    0.011 2.00e-02 2.50e+03   2.15e-02 4.63e+00
        pdb=" C   ASP A  11 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   ASP A  11 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLN A  12 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL G  54 "   -0.029 5.00e-02 4.00e+02   4.35e-02 3.03e+00
        pdb=" N   PRO G  55 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO G  55 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO G  55 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1437 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 112
        2.65 -     3.21: 7635
        3.21 -     3.78: 12854
        3.78 -     4.34: 17503
        4.34 -     4.90: 28618
  Nonbonded interactions: 66722
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP N  50 "
            pdb=" OG  SER N  59 "
     model   vdw
     2.090 3.040
  nonbonded pdb=" OG  SER G  57 "
            pdb=" OE1 GLU G  58 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" NE2 GLN B  75 "
            pdb=" O   VAL B 100 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.207 3.040
  ... (remaining 66717 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     21.990
  Find NCS groups from input model:        0.070
  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:14.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8321  Z= 0.195
  Angle     :  0.646  12.032  11260  Z= 0.378
  Chirality :  0.043   0.221   1266
  Planarity :  0.003   0.043   1440
  Dihedral  : 14.056  86.470   3033
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  0.91 %
    Favored  : 98.06 %
  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:  0.71 (0.27), residues: 1015
  helix:  1.95 (0.27), residues: 410
  sheet:  0.37 (0.35), residues: 219
  loop : -1.11 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 296 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.014   0.001   PHE R 371 
 TYR   0.027   0.001   TYR B  59 
 ARG   0.006   0.000   ARG B 129 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 171
  time to evaluate  : 0.864 
Fit side-chains
REVERT: R  408 HIS cc_start: 0.8077 (m170) cc_final: 0.7755 (m-70)
REVERT: A  300 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7142 (ttpt)
REVERT: A  356 ARG cc_start: 0.7823 (mtp-110) cc_final: 0.7361 (mtp-110)
REVERT: B    7 LEU cc_start: 0.9270 (mm) cc_final: 0.8922 (mm)
REVERT: B    8 ARG cc_start: 0.9019 (mpt-90) cc_final: 0.8743 (mpt-90)
REVERT: G   16 VAL cc_start: 0.9371 (p) cc_final: 0.9089 (p)
REVERT: G   18 GLN cc_start: 0.9232 (tp40) cc_final: 0.8709 (tp40)
REVERT: G   20 LYS cc_start: 0.8942 (ptpp) cc_final: 0.8654 (pttp)
REVERT: N    5 GLN cc_start: 0.8428 (tp-100) cc_final: 0.8107 (tp40)
REVERT: N   43 LYS cc_start: 0.7882 (mmpt) cc_final: 0.7664 (mmmm)
REVERT: N   73 ASP cc_start: 0.7819 (t0) cc_final: 0.7354 (t0)
REVERT: N   87 LYS cc_start: 0.9319 (mttp) cc_final: 0.8853 (mttm)
  outliers start: 9
  outliers final: 4
  residues processed: 180
  average time/residue: 1.3279
  time to fit residues: 252.2549
Evaluate side-chains
  146 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 141
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  270 PHE
Chi-restraints excluded: chain R residue  381 SER
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  308 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
R 230 ASN
R 384 GLN
A 387 HIS
B 266 HIS
B 268 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.105531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.074647 restraints weight = 15940.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 3.57
r_work: 0.2893 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8321  Z= 0.226
  Angle     :  0.631  10.070  11260  Z= 0.325
  Chirality :  0.042   0.151   1266
  Planarity :  0.004   0.053   1440
  Dihedral  :  4.798  44.573   1147
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 12.44 %
    Favored  : 85.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.27), residues: 1015
  helix:  2.18 (0.27), residues: 411
  sheet:  0.32 (0.35), residues: 219
  loop : -1.31 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 287 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.019   0.001   PHE R 371 
 TYR   0.015   0.001   TYR R 141 
 ARG   0.005   0.000   ARG A  38 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 158
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  170 ASN cc_start: 0.8414 (m110) cc_final: 0.8182 (m-40)
REVERT: R  181 MET cc_start: 0.8511 (mmm) cc_final: 0.8171 (mmt)
REVERT: R  282 GLU cc_start: 0.7427 (pp20) cc_final: 0.7214 (pp20)
REVERT: R  408 HIS cc_start: 0.8305 (m170) cc_final: 0.7956 (m-70)
REVERT: A  311 TYR cc_start: 0.7369 (m-10) cc_final: 0.7035 (m-10)
REVERT: A  356 ARG cc_start: 0.8094 (mtp-110) cc_final: 0.7546 (mtp-110)
REVERT: B    7 LEU cc_start: 0.9002 (mm) cc_final: 0.8437 (mm)
REVERT: B    8 ARG cc_start: 0.8994 (mpt-90) cc_final: 0.8636 (mpt-90)
REVERT: B   15 LYS cc_start: 0.9206 (mtmm) cc_final: 0.8737 (tmtm)
REVERT: B   23 LYS cc_start: 0.9478 (tmmm) cc_final: 0.9258 (tptp)
REVERT: G   13 ARG cc_start: 0.9356 (ptp-110) cc_final: 0.9077 (ptp-110)
REVERT: G   18 GLN cc_start: 0.9046 (tp40) cc_final: 0.8496 (tp40)
REVERT: G   20 LYS cc_start: 0.8990 (ptpp) cc_final: 0.8616 (ptpp)
REVERT: N    5 GLN cc_start: 0.8402 (tp-100) cc_final: 0.8044 (tp40)
REVERT: N   46 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8324 (pt0)
REVERT: N   53 GLN cc_start: 0.7860 (mp10) cc_final: 0.7521 (mp10)
REVERT: N   73 ASP cc_start: 0.7727 (t0) cc_final: 0.7335 (t0)
REVERT: N   87 LYS cc_start: 0.9128 (mttp) cc_final: 0.8761 (mttm)
  outliers start: 19
  outliers final: 7
  residues processed: 165
  average time/residue: 1.4855
  time to fit residues: 258.1768
Evaluate side-chains
  157 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 149
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  270 PHE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain N residue   46 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 51 optimal weight:    0.3980
   chunk 23 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0060
   chunk 2 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
R 384 GLN
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.106839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.074969 restraints weight = 15909.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 3.61
r_work: 0.2912 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8321  Z= 0.184
  Angle     :  0.598  10.477  11260  Z= 0.307
  Chirality :  0.042   0.155   1266
  Planarity :  0.004   0.055   1440
  Dihedral  :  4.490  45.971   1141
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 17.01 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.27), residues: 1015
  helix:  2.10 (0.26), residues: 412
  sheet:  0.47 (0.36), residues: 205
  loop : -1.27 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP R 287 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.017   0.001   PHE R 371 
 TYR   0.015   0.001   TYR R 141 
 ARG   0.004   0.000   ARG A  38 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 164
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
REVERT: R  170 ASN cc_start: 0.8435 (m110) cc_final: 0.8153 (m-40)
REVERT: R  181 MET cc_start: 0.8744 (mmm) cc_final: 0.8526 (tpp)
REVERT: R  255 HIS cc_start: 0.7176 (m170) cc_final: 0.6936 (m-70)
REVERT: R  293 LYS cc_start: 0.6576 (pptt) cc_final: 0.6332 (pptt)
REVERT: R  408 HIS cc_start: 0.8303 (m170) cc_final: 0.7959 (m-70)
REVERT: A   27 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8603 (mm-30)
REVERT: A  311 TYR cc_start: 0.7533 (m-10) cc_final: 0.7202 (m-10)
REVERT: A  356 ARG cc_start: 0.8107 (mtp-110) cc_final: 0.7720 (mtp-110)
REVERT: B    8 ARG cc_start: 0.9023 (mpt-90) cc_final: 0.8595 (mpt-90)
REVERT: B   15 LYS cc_start: 0.9208 (mtmm) cc_final: 0.8748 (tmmt)
REVERT: B   23 LYS cc_start: 0.9524 (tmmm) cc_final: 0.9259 (tptp)
REVERT: B  217 MET cc_start: 0.8455 (ppp) cc_final: 0.8219 (ppp)
REVERT: G   13 ARG cc_start: 0.9357 (ptp-110) cc_final: 0.8914 (ptp-110)
REVERT: G   17 GLU cc_start: 0.9554 (tp30) cc_final: 0.9128 (mm-30)
REVERT: G   18 GLN cc_start: 0.8997 (tp40) cc_final: 0.8460 (tp40)
REVERT: G   20 LYS cc_start: 0.8983 (ptpp) cc_final: 0.8393 (pttm)
REVERT: N    5 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8050 (tp40)
REVERT: N   43 LYS cc_start: 0.7992 (mmmm) cc_final: 0.7651 (tptt)
REVERT: N   46 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8420 (pt0)
REVERT: N   53 GLN cc_start: 0.7975 (mp10) cc_final: 0.7615 (mp10)
REVERT: N   70 ILE cc_start: 0.8654 (pt) cc_final: 0.8320 (pp)
REVERT: N   73 ASP cc_start: 0.7850 (t0) cc_final: 0.7369 (t0)
REVERT: N   87 LYS cc_start: 0.9150 (mttp) cc_final: 0.8757 (mttm)
  outliers start: 16
  outliers final: 7
  residues processed: 172
  average time/residue: 1.2969
  time to fit residues: 236.3632
Evaluate side-chains
  158 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 150
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  270 PHE
Chi-restraints excluded: chain R residue  379 PHE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   46 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0040
   chunk 95 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 50 optimal weight:    6.9990
   chunk 58 optimal weight:    0.4980
   chunk 44 optimal weight:    1.9990
   chunk 23 optimal weight:   10.0000
   chunk 63 optimal weight:    0.0010
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.1002

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

Flipped N/Q/H residues before XYZ refinement:
** R 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 384 GLN
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.105306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.072636 restraints weight = 15597.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 3.59
r_work: 0.2883 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8321  Z= 0.237
  Angle     :  0.626  10.162  11260  Z= 0.322
  Chirality :  0.044   0.247   1266
  Planarity :  0.004   0.057   1440
  Dihedral  :  4.531  45.345   1141
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.84 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.27), residues: 1015
  helix:  2.01 (0.26), residues: 410
  sheet:  0.51 (0.37), residues: 205
  loop : -1.31 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP R 287 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.020   0.001   PHE R 371 
 TYR   0.013   0.001   TYR R 141 
 ARG   0.003   0.000   ARG N  38 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 153
  time to evaluate  : 1.253 
Fit side-chains
   revert: symmetry clash
REVERT: R  170 ASN cc_start: 0.8454 (m110) cc_final: 0.8196 (m-40)
REVERT: R  293 LYS cc_start: 0.6615 (pptt) cc_final: 0.6341 (pptt)
REVERT: R  396 ASN cc_start: 0.8251 (t0) cc_final: 0.7864 (t0)
REVERT: R  408 HIS cc_start: 0.8334 (m170) cc_final: 0.7988 (m-70)
REVERT: A   27 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8623 (mm-30)
REVERT: A  311 TYR cc_start: 0.7696 (m-10) cc_final: 0.7282 (m-10)
REVERT: A  356 ARG cc_start: 0.8158 (mtp-110) cc_final: 0.7648 (mtp-110)
REVERT: B    8 ARG cc_start: 0.9085 (mpt-90) cc_final: 0.8740 (mpt-90)
REVERT: B   12 GLU cc_start: 0.8915 (pp20) cc_final: 0.8712 (pp20)
REVERT: B   15 LYS cc_start: 0.9285 (mtmm) cc_final: 0.8779 (tmmt)
REVERT: B   23 LYS cc_start: 0.9535 (tmmm) cc_final: 0.9263 (tptp)
REVERT: B  217 MET cc_start: 0.8371 (ppp) cc_final: 0.8057 (ppp)
REVERT: G   13 ARG cc_start: 0.9362 (ptp-110) cc_final: 0.9040 (mtm110)
REVERT: G   14 LYS cc_start: 0.9487 (mmmm) cc_final: 0.9123 (mmpt)
REVERT: G   18 GLN cc_start: 0.8954 (tp40) cc_final: 0.8438 (tp40)
REVERT: G   20 LYS cc_start: 0.8986 (ptpp) cc_final: 0.8562 (ptpp)
REVERT: N    5 GLN cc_start: 0.8407 (tp-100) cc_final: 0.8048 (tp40)
REVERT: N   46 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8489 (pt0)
REVERT: N   53 GLN cc_start: 0.8054 (mp10) cc_final: 0.7691 (mp10)
REVERT: N   70 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8342 (pp)
REVERT: N   73 ASP cc_start: 0.7892 (t0) cc_final: 0.7404 (t0)
REVERT: N   87 LYS cc_start: 0.9119 (mttp) cc_final: 0.8758 (mttm)
  outliers start: 29
  outliers final: 9
  residues processed: 165
  average time/residue: 1.2395
  time to fit residues: 218.0935
Evaluate side-chains
  152 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 141
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  260 LEU
Chi-restraints excluded: chain R residue  270 PHE
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   70 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 82 optimal weight:    0.8980
   chunk 83 optimal weight:    0.0570
   chunk 20 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
R 384 GLN
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.106210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.073786 restraints weight = 15494.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 3.58
r_work: 0.2902 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8321  Z= 0.189
  Angle     :  0.623  10.682  11260  Z= 0.317
  Chirality :  0.044   0.256   1266
  Planarity :  0.004   0.059   1440
  Dihedral  :  4.438  46.091   1141
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.09 %
    Favored  : 76.83 %
  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:  0.70 (0.27), residues: 1015
  helix:  2.02 (0.26), residues: 410
  sheet:  0.56 (0.37), residues: 211
  loop : -1.33 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP R 287 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.024   0.001   PHE R 379 
 TYR   0.014   0.001   TYR R 141 
 ARG   0.003   0.000   ARG N  38 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 159
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
REVERT: R  170 ASN cc_start: 0.8388 (m110) cc_final: 0.8116 (m-40)
REVERT: R  293 LYS cc_start: 0.6708 (pptt) cc_final: 0.6399 (pptt)
REVERT: R  396 ASN cc_start: 0.8248 (t0) cc_final: 0.7733 (t0)
REVERT: R  408 HIS cc_start: 0.8319 (m170) cc_final: 0.7982 (m-70)
REVERT: A   27 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8622 (mm-30)
REVERT: A  311 TYR cc_start: 0.7794 (m-10) cc_final: 0.7386 (m-10)
REVERT: A  356 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7596 (mtp-110)
REVERT: A  390 GLN cc_start: 0.8733 (tt0) cc_final: 0.8316 (tp-100)
REVERT: B    8 ARG cc_start: 0.9110 (mpt-90) cc_final: 0.8741 (mpt-90)
REVERT: B   15 LYS cc_start: 0.9261 (mtmm) cc_final: 0.8793 (tmmt)
REVERT: B   23 LYS cc_start: 0.9525 (tmmm) cc_final: 0.9272 (tptp)
REVERT: B  217 MET cc_start: 0.8385 (ppp) cc_final: 0.8055 (ppp)
REVERT: G   13 ARG cc_start: 0.9387 (ptp-110) cc_final: 0.9023 (mtm110)
REVERT: G   14 LYS cc_start: 0.9530 (mmmm) cc_final: 0.9161 (mmpt)
REVERT: G   18 GLN cc_start: 0.8971 (tp40) cc_final: 0.8448 (tp40)
REVERT: G   32 LYS cc_start: 0.8659 (ttpp) cc_final: 0.8433 (tppp)
REVERT: G   36 ASP cc_start: 0.8836 (m-30) cc_final: 0.8632 (m-30)
REVERT: N    5 GLN cc_start: 0.8404 (tp-100) cc_final: 0.8069 (tp40)
REVERT: N   46 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8409 (pt0)
REVERT: N   53 GLN cc_start: 0.8138 (mp10) cc_final: 0.7800 (mp10)
REVERT: N   70 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8391 (pp)
REVERT: N   73 ASP cc_start: 0.7875 (t0) cc_final: 0.7395 (t0)
REVERT: N   87 LYS cc_start: 0.9112 (mttp) cc_final: 0.8746 (mttm)
  outliers start: 27
  outliers final: 16
  residues processed: 170
  average time/residue: 1.0639
  time to fit residues: 193.1739
Evaluate side-chains
  163 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  213 LEU
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  248 VAL
Chi-restraints excluded: chain R residue  270 PHE
Chi-restraints excluded: chain R residue  379 PHE
Chi-restraints excluded: chain R residue  384 GLN
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   70 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
R 384 GLN
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.105522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.073512 restraints weight = 15518.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 3.54
r_work: 0.2888 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8321  Z= 0.213
  Angle     :  0.634   9.748  11260  Z= 0.325
  Chirality :  0.044   0.275   1266
  Planarity :  0.004   0.060   1440
  Dihedral  :  4.456  45.460   1141
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 22.26 %
    Favored  : 74.43 %
  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:  0.70 (0.27), residues: 1015
  helix:  2.04 (0.26), residues: 405
  sheet:  0.62 (0.38), residues: 205
  loop : -1.31 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP R 287 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.021   0.001   PHE R 371 
 TYR   0.013   0.001   TYR R 141 
 ARG   0.003   0.000   ARG N  38 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  170 ASN cc_start: 0.8419 (m110) cc_final: 0.8142 (m-40)
REVERT: R  293 LYS cc_start: 0.6725 (pptt) cc_final: 0.6404 (pptt)
REVERT: R  384 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7812 (tt0)
REVERT: R  396 ASN cc_start: 0.8224 (t0) cc_final: 0.7656 (t0)
REVERT: R  408 HIS cc_start: 0.8318 (m170) cc_final: 0.7975 (m-70)
REVERT: A   27 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8619 (mm-30)
REVERT: A  311 TYR cc_start: 0.7841 (m-10) cc_final: 0.7409 (m-10)
REVERT: A  356 ARG cc_start: 0.8113 (mtp-110) cc_final: 0.7586 (mtp-110)
REVERT: A  390 GLN cc_start: 0.8766 (tt0) cc_final: 0.8335 (tp-100)
REVERT: B    8 ARG cc_start: 0.9074 (mpt-90) cc_final: 0.8690 (mpt-90)
REVERT: B   12 GLU cc_start: 0.8948 (pp20) cc_final: 0.8722 (pp20)
REVERT: B   15 LYS cc_start: 0.9272 (mtmm) cc_final: 0.8817 (tmmt)
REVERT: B   23 LYS cc_start: 0.9540 (tmmm) cc_final: 0.9272 (tptp)
REVERT: B  217 MET cc_start: 0.8446 (ppp) cc_final: 0.8080 (ppp)
REVERT: G   13 ARG cc_start: 0.9385 (ptp-110) cc_final: 0.8743 (mtm110)
REVERT: G   14 LYS cc_start: 0.9527 (mmmm) cc_final: 0.9045 (mmpt)
REVERT: G   16 VAL cc_start: 0.9365 (t) cc_final: 0.9146 (p)
REVERT: G   18 GLN cc_start: 0.8945 (tp40) cc_final: 0.8409 (tp40)
REVERT: G   20 LYS cc_start: 0.9043 (ptpp) cc_final: 0.8837 (ptpp)
REVERT: G   29 LYS cc_start: 0.8296 (mmtm) cc_final: 0.8066 (tppp)
REVERT: G   32 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8528 (tppp)
REVERT: G   36 ASP cc_start: 0.8852 (m-30) cc_final: 0.8637 (m-30)
REVERT: N    5 GLN cc_start: 0.8447 (tp-100) cc_final: 0.8107 (tp40)
REVERT: N   43 LYS cc_start: 0.8026 (mmmm) cc_final: 0.7643 (tptt)
REVERT: N   46 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8435 (pt0)
REVERT: N   53 GLN cc_start: 0.8149 (mp10) cc_final: 0.7803 (mp10)
REVERT: N   70 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8404 (pp)
REVERT: N   73 ASP cc_start: 0.7932 (t0) cc_final: 0.7410 (t0)
REVERT: N   76 LYS cc_start: 0.9471 (mmmm) cc_final: 0.9194 (mmmm)
REVERT: N   87 LYS cc_start: 0.9113 (mttp) cc_final: 0.8755 (mttm)
REVERT: N  105 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8571 (mtm180)
  outliers start: 29
  outliers final: 18
  residues processed: 165
  average time/residue: 1.1103
  time to fit residues: 195.3107
Evaluate side-chains
  173 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 151
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  213 LEU
Chi-restraints excluded: chain R residue  248 VAL
Chi-restraints excluded: chain R residue  260 LEU
Chi-restraints excluded: chain R residue  270 PHE
Chi-restraints excluded: chain R residue  379 PHE
Chi-restraints excluded: chain R residue  384 GLN
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  105 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 14 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
R 384 GLN
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.106379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.073621 restraints weight = 15544.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 3.60
r_work: 0.2890 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8321  Z= 0.216
  Angle     :  0.630   9.978  11260  Z= 0.325
  Chirality :  0.045   0.304   1266
  Planarity :  0.004   0.062   1440
  Dihedral  :  4.495  46.138   1141
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 23.17 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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:  0.73 (0.27), residues: 1015
  helix:  2.07 (0.26), residues: 405
  sheet:  0.62 (0.37), residues: 210
  loop : -1.32 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP R 287 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.022   0.001   PHE R 371 
 TYR   0.012   0.001   TYR R 141 
 ARG   0.003   0.000   ARG N  38 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  135 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8507 (mp0)
REVERT: R  170 ASN cc_start: 0.8400 (m110) cc_final: 0.8119 (m-40)
REVERT: R  293 LYS cc_start: 0.6697 (pptt) cc_final: 0.6388 (pptt)
REVERT: R  377 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8878 (mt-10)
REVERT: R  396 ASN cc_start: 0.8201 (t0) cc_final: 0.7545 (t0)
REVERT: R  408 HIS cc_start: 0.8326 (m170) cc_final: 0.7983 (m-70)
REVERT: A  311 TYR cc_start: 0.7895 (m-10) cc_final: 0.7429 (m-10)
REVERT: A  356 ARG cc_start: 0.8096 (mtp-110) cc_final: 0.7535 (mtp-110)
REVERT: A  390 GLN cc_start: 0.8769 (tt0) cc_final: 0.8343 (tp-100)
REVERT: B    8 ARG cc_start: 0.9091 (mpt-90) cc_final: 0.8704 (mpt-90)
REVERT: B   15 LYS cc_start: 0.9270 (mtmm) cc_final: 0.8813 (tmmt)
REVERT: B   23 LYS cc_start: 0.9538 (tmmm) cc_final: 0.9270 (tptp)
REVERT: B  217 MET cc_start: 0.8416 (ppp) cc_final: 0.8033 (ppp)
REVERT: G   13 ARG cc_start: 0.9426 (ptp-110) cc_final: 0.8751 (mtm110)
REVERT: G   14 LYS cc_start: 0.9529 (mmmm) cc_final: 0.9034 (mmpt)
REVERT: G   18 GLN cc_start: 0.8943 (tp40) cc_final: 0.8379 (tp40)
REVERT: G   24 ASN cc_start: 0.9238 (p0) cc_final: 0.9009 (p0)
REVERT: G   32 LYS cc_start: 0.8703 (ttpp) cc_final: 0.8435 (tppp)
REVERT: G   36 ASP cc_start: 0.8883 (m-30) cc_final: 0.8650 (m-30)
REVERT: N    5 GLN cc_start: 0.8442 (tp-100) cc_final: 0.8082 (tp40)
REVERT: N   46 GLU cc_start: 0.8789 (tt0) cc_final: 0.8460 (pt0)
REVERT: N   53 GLN cc_start: 0.8155 (mp10) cc_final: 0.7803 (mp10)
REVERT: N   70 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8398 (pp)
REVERT: N   73 ASP cc_start: 0.7898 (t0) cc_final: 0.7386 (t0)
REVERT: N   76 LYS cc_start: 0.9476 (mmmm) cc_final: 0.9210 (mmmm)
REVERT: N   87 LYS cc_start: 0.9121 (mttp) cc_final: 0.8780 (mttm)
  outliers start: 21
  outliers final: 16
  residues processed: 164
  average time/residue: 1.1619
  time to fit residues: 202.7621
Evaluate side-chains
  159 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  213 LEU
Chi-restraints excluded: chain R residue  260 LEU
Chi-restraints excluded: chain R residue  270 PHE
Chi-restraints excluded: chain R residue  379 PHE
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   70 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 43 optimal weight:    8.9990
   chunk 35 optimal weight:    0.7980
   chunk 68 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 78 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
R 329 GLN
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.103578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.071151 restraints weight = 15812.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 3.60
r_work: 0.2838 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8321  Z= 0.305
  Angle     :  0.682  10.792  11260  Z= 0.354
  Chirality :  0.046   0.336   1266
  Planarity :  0.004   0.064   1440
  Dihedral  :  4.606  45.092   1141
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 23.86 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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:  0.60 (0.27), residues: 1015
  helix:  1.97 (0.26), residues: 404
  sheet:  0.42 (0.37), residues: 206
  loop : -1.30 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP R 287 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.023   0.001   PHE R 371 
 TYR   0.011   0.001   TYR R 141 
 ARG   0.004   0.000   ARG N  38 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 148
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  164 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8561 (tmm-80)
REVERT: R  170 ASN cc_start: 0.8517 (m110) cc_final: 0.8251 (m-40)
REVERT: R  293 LYS cc_start: 0.6790 (pptt) cc_final: 0.6438 (pptt)
REVERT: R  335 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.6340 (m-10)
REVERT: R  396 ASN cc_start: 0.8184 (t0) cc_final: 0.7670 (t0)
REVERT: R  408 HIS cc_start: 0.8344 (m170) cc_final: 0.8004 (m-70)
REVERT: A  311 TYR cc_start: 0.8026 (m-10) cc_final: 0.7591 (m-10)
REVERT: A  356 ARG cc_start: 0.8167 (mtp-110) cc_final: 0.7601 (mtp-110)
REVERT: B    8 ARG cc_start: 0.9113 (mpt-90) cc_final: 0.8792 (mmt90)
REVERT: B   12 GLU cc_start: 0.8984 (pp20) cc_final: 0.8771 (pp20)
REVERT: B   15 LYS cc_start: 0.9298 (mtmm) cc_final: 0.8848 (tmmt)
REVERT: B   23 LYS cc_start: 0.9533 (tmmm) cc_final: 0.9246 (tptp)
REVERT: B  217 MET cc_start: 0.8431 (ppp) cc_final: 0.8055 (ppp)
REVERT: G   13 ARG cc_start: 0.9427 (ptp-110) cc_final: 0.8804 (mtm110)
REVERT: G   14 LYS cc_start: 0.9538 (mmmm) cc_final: 0.9088 (mmpt)
REVERT: G   17 GLU cc_start: 0.9541 (tp30) cc_final: 0.9297 (mm-30)
REVERT: G   18 GLN cc_start: 0.8963 (tp40) cc_final: 0.8329 (tp40)
REVERT: G   22 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8471 (mm-30)
REVERT: G   24 ASN cc_start: 0.9174 (p0) cc_final: 0.8921 (p0)
REVERT: G   28 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8094 (tp)
REVERT: G   29 LYS cc_start: 0.8222 (tppp) cc_final: 0.8009 (tppp)
REVERT: N    1 GLN cc_start: 0.7302 (tp40) cc_final: 0.6993 (tp40)
REVERT: N    5 GLN cc_start: 0.8467 (tp-100) cc_final: 0.8114 (tp40)
REVERT: N   46 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8575 (pt0)
REVERT: N   53 GLN cc_start: 0.8232 (mp10) cc_final: 0.7869 (mp10)
REVERT: N   70 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8573 (pt)
REVERT: N   73 ASP cc_start: 0.8016 (t0) cc_final: 0.7501 (t0)
REVERT: N   76 LYS cc_start: 0.9510 (mmmm) cc_final: 0.9269 (mmmm)
REVERT: N   87 LYS cc_start: 0.9166 (mttp) cc_final: 0.8814 (mttm)
  outliers start: 27
  outliers final: 15
  residues processed: 164
  average time/residue: 1.3315
  time to fit residues: 231.9289
Evaluate side-chains
  160 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  164 ARG
Chi-restraints excluded: chain R residue  213 LEU
Chi-restraints excluded: chain R residue  260 LEU
Chi-restraints excluded: chain R residue  270 PHE
Chi-restraints excluded: chain R residue  335 TYR
Chi-restraints excluded: chain R residue  379 PHE
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   70 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 88 optimal weight:    0.6980
   chunk 6 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0370
   chunk 47 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 100 optimal weight:    0.0970
   chunk 70 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 78 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.4256

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.105640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.073403 restraints weight = 15871.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 3.60
r_work: 0.2889 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8321  Z= 0.201
  Angle     :  0.694  11.555  11260  Z= 0.355
  Chirality :  0.045   0.277   1266
  Planarity :  0.004   0.066   1440
  Dihedral  :  4.522  46.690   1141
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 24.54 %
    Favored  : 72.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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:  0.66 (0.27), residues: 1015
  helix:  1.99 (0.26), residues: 405
  sheet:  0.62 (0.38), residues: 204
  loop : -1.32 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP R 287 
 HIS   0.003   0.000   HIS A 357 
 PHE   0.022   0.001   PHE R 371 
 TYR   0.012   0.001   TYR R 141 
 ARG   0.013   0.000   ARG R 326 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 158
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
REVERT: R  170 ASN cc_start: 0.8425 (m110) cc_final: 0.8168 (m-40)
REVERT: R  293 LYS cc_start: 0.6711 (pptt) cc_final: 0.6393 (pptt)
REVERT: R  396 ASN cc_start: 0.8132 (t0) cc_final: 0.6844 (t0)
REVERT: R  408 HIS cc_start: 0.8338 (m170) cc_final: 0.7948 (m-70)
REVERT: A  311 TYR cc_start: 0.7947 (m-10) cc_final: 0.7504 (m-10)
REVERT: A  356 ARG cc_start: 0.8098 (mtp-110) cc_final: 0.7518 (mtp-110)
REVERT: A  390 GLN cc_start: 0.8780 (tt0) cc_final: 0.8425 (tp-100)
REVERT: B    8 ARG cc_start: 0.9094 (mpt-90) cc_final: 0.8764 (mmt90)
REVERT: B   12 GLU cc_start: 0.8993 (pp20) cc_final: 0.8741 (pp20)
REVERT: B   15 LYS cc_start: 0.9273 (mtmm) cc_final: 0.8829 (tmmt)
REVERT: B   23 LYS cc_start: 0.9512 (tmmm) cc_final: 0.9218 (tptp)
REVERT: B   61 MET cc_start: 0.9497 (pp-130) cc_final: 0.9152 (pp-130)
REVERT: B  217 MET cc_start: 0.8415 (ppp) cc_final: 0.8071 (ppp)
REVERT: G   13 ARG cc_start: 0.9409 (ptp-110) cc_final: 0.9096 (ptp-110)
REVERT: G   18 GLN cc_start: 0.8863 (tp40) cc_final: 0.8338 (tp40)
REVERT: G   24 ASN cc_start: 0.9157 (p0) cc_final: 0.8888 (p0)
REVERT: G   29 LYS cc_start: 0.8156 (tppp) cc_final: 0.7926 (tppp)
REVERT: G   47 GLU cc_start: 0.8693 (mp0) cc_final: 0.7760 (mp0)
REVERT: N    1 GLN cc_start: 0.7149 (tp40) cc_final: 0.6858 (tp40)
REVERT: N    5 GLN cc_start: 0.8428 (tp-100) cc_final: 0.8081 (tp40)
REVERT: N   46 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8481 (pt0)
REVERT: N   53 GLN cc_start: 0.8151 (mp10) cc_final: 0.7790 (mp10)
REVERT: N   70 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8394 (pp)
REVERT: N   73 ASP cc_start: 0.7917 (t0) cc_final: 0.7451 (t0)
REVERT: N   76 LYS cc_start: 0.9488 (mmmm) cc_final: 0.9232 (mmmm)
REVERT: N   87 LYS cc_start: 0.9124 (mttp) cc_final: 0.8782 (mttm)
REVERT: N  105 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8580 (mtm180)
  outliers start: 22
  outliers final: 12
  residues processed: 169
  average time/residue: 1.0966
  time to fit residues: 197.4189
Evaluate side-chains
  163 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  157 LEU
Chi-restraints excluded: chain R residue  270 PHE
Chi-restraints excluded: chain R residue  379 PHE
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  105 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0370
   chunk 64 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 94 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.106461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.073718 restraints weight = 15472.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 3.63
r_work: 0.2873 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8321  Z= 0.217
  Angle     :  0.708  11.047  11260  Z= 0.361
  Chirality :  0.045   0.332   1266
  Planarity :  0.004   0.067   1440
  Dihedral  :  4.524  46.210   1141
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 25.23 %
    Favored  : 72.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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:  0.66 (0.27), residues: 1015
  helix:  1.93 (0.27), residues: 404
  sheet:  0.62 (0.37), residues: 210
  loop : -1.28 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP R 287 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.023   0.001   PHE R 371 
 TYR   0.012   0.001   TYR R 141 
 ARG   0.013   0.000   ARG R 326 

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 154
  time to evaluate  : 0.856 
Fit side-chains
REVERT: R  170 ASN cc_start: 0.8437 (m110) cc_final: 0.8178 (m-40)
REVERT: R  293 LYS cc_start: 0.6717 (pptt) cc_final: 0.6422 (pptt)
REVERT: R  335 TYR cc_start: 0.6503 (OUTLIER) cc_final: 0.5973 (m-10)
REVERT: R  408 HIS cc_start: 0.8354 (m170) cc_final: 0.7966 (m-70)
REVERT: A   27 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8642 (mm-30)
REVERT: A  311 TYR cc_start: 0.7992 (m-10) cc_final: 0.7553 (m-10)
REVERT: A  356 ARG cc_start: 0.8119 (mtp-110) cc_final: 0.7539 (mtp-110)
REVERT: A  390 GLN cc_start: 0.8871 (tt0) cc_final: 0.8275 (tp-100)
REVERT: B    8 ARG cc_start: 0.9133 (mpt-90) cc_final: 0.8739 (mpt-90)
REVERT: B   12 GLU cc_start: 0.8932 (pp20) cc_final: 0.8627 (pp20)
REVERT: B   15 LYS cc_start: 0.9277 (mtmm) cc_final: 0.8837 (tmmt)
REVERT: B   23 LYS cc_start: 0.9511 (tmmm) cc_final: 0.9208 (tptp)
REVERT: B   61 MET cc_start: 0.9506 (pp-130) cc_final: 0.9129 (pp-130)
REVERT: B  217 MET cc_start: 0.8461 (ppp) cc_final: 0.8146 (ppp)
REVERT: G   13 ARG cc_start: 0.9394 (ptp-110) cc_final: 0.9095 (mtm110)
REVERT: G   18 GLN cc_start: 0.8885 (tp40) cc_final: 0.8331 (tp40)
REVERT: G   24 ASN cc_start: 0.9154 (p0) cc_final: 0.8896 (p0)
REVERT: G   29 LYS cc_start: 0.8183 (tppp) cc_final: 0.7941 (tppp)
REVERT: N    1 GLN cc_start: 0.7190 (tp40) cc_final: 0.6902 (tp40)
REVERT: N    5 GLN cc_start: 0.8428 (tp-100) cc_final: 0.8072 (tp40)
REVERT: N   46 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8537 (pt0)
REVERT: N   53 GLN cc_start: 0.8231 (mp10) cc_final: 0.7865 (mp10)
REVERT: N   70 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8417 (pp)
REVERT: N   73 ASP cc_start: 0.8095 (t0) cc_final: 0.7479 (t0)
REVERT: N   76 LYS cc_start: 0.9488 (mmmm) cc_final: 0.9235 (mmmm)
REVERT: N   87 LYS cc_start: 0.9163 (mttp) cc_final: 0.8802 (mttm)
REVERT: N  105 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8595 (mtm180)
  outliers start: 18
  outliers final: 10
  residues processed: 160
  average time/residue: 1.0935
  time to fit residues: 186.7461
Evaluate side-chains
  162 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  157 LEU
Chi-restraints excluded: chain R residue  270 PHE
Chi-restraints excluded: chain R residue  335 TYR
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  105 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 94 optimal weight:    6.9990
   chunk 84 optimal weight:   20.0000
   chunk 65 optimal weight:    0.6980
   chunk 85 optimal weight:   10.0000
   chunk 4 optimal weight:    0.4980
   chunk 80 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
R 255 HIS
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.105497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.073522 restraints weight = 15817.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 3.57
r_work: 0.2881 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8321  Z= 0.221
  Angle     :  0.701  12.164  11260  Z= 0.359
  Chirality :  0.045   0.349   1266
  Planarity :  0.004   0.067   1440
  Dihedral  :  4.477  45.853   1141
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 25.68 %
    Favored  : 72.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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:  0.63 (0.27), residues: 1015
  helix:  1.94 (0.27), residues: 405
  sheet:  0.59 (0.38), residues: 204
  loop : -1.30 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP R 287 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.023   0.001   PHE R 371 
 TYR   0.012   0.001   TYR R 141 
 ARG   0.012   0.000   ARG R 326 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6379.82 seconds
wall clock time: 111 minutes 43.65 seconds (6703.65 seconds total)