Starting phenix.real_space_refine
on Wed Feb 12 18:23:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wa3_37390/02_2025/8wa3_37390.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wa3_37390/02_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_37390/02_2025/8wa3_37390.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wa3_37390/02_2025/8wa3_37390.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wa3_37390/02_2025/8wa3_37390.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wa3_37390/02_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.89, per 1000 atoms: 0.60
  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: 1.81
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.83
  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: 2.60

  Time building geometry restraints manager: 2.11 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:             1.130
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     21.360
  Find NCS groups from input model:        0.060
  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:14.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.570
-------------------------------------------------------------------------------
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  : 0.947 
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: 1.3107
  time to fit residues: 249.2212
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  : 0.938 
-------------------------------------------------------------------------------
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 = 45)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.074603 restraints weight = 15940.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 3.59
r_work: 0.2897 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
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  : 0.923 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  170 ASN cc_start: 0.8416 (m110) cc_final: 0.8184 (m-40)
REVERT: R  181 MET cc_start: 0.8512 (mmm) cc_final: 0.8172 (mmt)
REVERT: R  282 GLU cc_start: 0.7428 (pp20) cc_final: 0.7214 (pp20)
REVERT: R  408 HIS cc_start: 0.8303 (m170) cc_final: 0.7953 (m-70)
REVERT: A  311 TYR cc_start: 0.7370 (m-10) cc_final: 0.7036 (m-10)
REVERT: A  356 ARG cc_start: 0.8096 (mtp-110) cc_final: 0.7548 (mtp-110)
REVERT: B    7 LEU cc_start: 0.9007 (mm) cc_final: 0.8440 (mm)
REVERT: B    8 ARG cc_start: 0.8996 (mpt-90) cc_final: 0.8637 (mpt-90)
REVERT: B   15 LYS cc_start: 0.9207 (mtmm) cc_final: 0.8738 (tmtm)
REVERT: B   23 LYS cc_start: 0.9478 (tmmm) cc_final: 0.9257 (tptp)
REVERT: G   13 ARG cc_start: 0.9355 (ptp-110) cc_final: 0.9074 (ptp-110)
REVERT: G   18 GLN cc_start: 0.9048 (tp40) cc_final: 0.8498 (tp40)
REVERT: G   20 LYS cc_start: 0.8991 (ptpp) cc_final: 0.8616 (ptpp)
REVERT: N    5 GLN cc_start: 0.8403 (tp-100) cc_final: 0.8046 (tp40)
REVERT: N   46 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8326 (pt0)
REVERT: N   53 GLN cc_start: 0.7863 (mp10) cc_final: 0.7525 (mp10)
REVERT: N   73 ASP cc_start: 0.7728 (t0) cc_final: 0.7335 (t0)
REVERT: N   87 LYS cc_start: 0.9125 (mttp) cc_final: 0.8759 (mttm)
  outliers start: 19
  outliers final: 7
  residues processed: 165
  average time/residue: 1.3372
  time to fit residues: 232.9479
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  : 1.030 
-------------------------------------------------------------------------------
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:    0.0060
   chunk 51 optimal weight:    0.3980
   chunk 23 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0060
   chunk 2 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.4212

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

Flipped N/Q/H residues before XYZ refinement:
R 384 GLN
** R 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.107633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.075868 restraints weight = 15898.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 3.61
r_work: 0.2927 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.1838

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= 0.170
  Angle     :  0.596  10.595  11260  Z= 0.305
  Chirality :  0.041   0.148   1266
  Planarity :  0.004   0.055   1440
  Dihedral  :  4.467  46.218   1141
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 17.35 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.27), residues: 1015
  helix:  2.11 (0.26), residues: 412
  sheet:  0.48 (0.36), residues: 205
  loop : -1.27 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP R 287 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.017   0.001   PHE R 371 
 TYR   0.016   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
  187 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 172
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
REVERT: R  135 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8509 (mp0)
REVERT: R  170 ASN cc_start: 0.8395 (m110) cc_final: 0.8096 (m-40)
REVERT: R  181 MET cc_start: 0.8738 (mmm) cc_final: 0.8406 (mmt)
REVERT: R  255 HIS cc_start: 0.7140 (m170) cc_final: 0.6865 (m170)
REVERT: R  293 LYS cc_start: 0.6680 (pptt) cc_final: 0.6333 (pptt)
REVERT: R  377 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8789 (mt-10)
REVERT: R  408 HIS cc_start: 0.8302 (m170) cc_final: 0.7958 (m-70)
REVERT: A   27 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8582 (mm-30)
REVERT: A  311 TYR cc_start: 0.7476 (m-10) cc_final: 0.7124 (m-10)
REVERT: A  356 ARG cc_start: 0.8102 (mtp-110) cc_final: 0.7712 (mtp-110)
REVERT: B    8 ARG cc_start: 0.9026 (mpt-90) cc_final: 0.8595 (mpt-90)
REVERT: B   15 LYS cc_start: 0.9209 (mtmm) cc_final: 0.8754 (tmmt)
REVERT: B   23 LYS cc_start: 0.9521 (tmmm) cc_final: 0.9257 (tptp)
REVERT: B  217 MET cc_start: 0.8460 (ppp) cc_final: 0.8226 (ppp)
REVERT: G   13 ARG cc_start: 0.9359 (ptp-110) cc_final: 0.9003 (ptp-110)
REVERT: G   17 GLU cc_start: 0.9546 (tp30) cc_final: 0.9304 (mm-30)
REVERT: G   18 GLN cc_start: 0.9007 (tp40) cc_final: 0.8564 (tp40)
REVERT: N    5 GLN cc_start: 0.8403 (tp-100) cc_final: 0.8066 (tp40)
REVERT: N   38 ARG cc_start: 0.8770 (ttp-110) cc_final: 0.8478 (mtm110)
REVERT: N   43 LYS cc_start: 0.7974 (mmmm) cc_final: 0.7643 (tptt)
REVERT: N   46 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8362 (pt0)
REVERT: N   53 GLN cc_start: 0.7963 (mp10) cc_final: 0.7608 (mp10)
REVERT: N   70 ILE cc_start: 0.8620 (pt) cc_final: 0.8292 (pp)
REVERT: N   73 ASP cc_start: 0.7843 (t0) cc_final: 0.7364 (t0)
REVERT: N   87 LYS cc_start: 0.9164 (mttp) cc_final: 0.8776 (mttm)
  outliers start: 15
  outliers final: 8
  residues processed: 180
  average time/residue: 1.2199
  time to fit residues: 232.7929
Evaluate side-chains
  167 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 158
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  149 LEU
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:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0570
   chunk 95 optimal weight:    0.7980
   chunk 59 optimal weight:    0.6980
   chunk 50 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 23 optimal weight:    9.9990
   chunk 63 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0980
   overall best weight:    0.4498

-------------------------------------------------------------------------------
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 = 0.3650 r_free = 0.3650 target = 0.107771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.075975 restraints weight = 15618.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 3.59
r_work: 0.2929 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8321  Z= 0.177
  Angle     :  0.621  10.649  11260  Z= 0.317
  Chirality :  0.043   0.266   1266
  Planarity :  0.004   0.057   1440
  Dihedral  :  4.411  45.591   1141
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.18 %
    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:  0.68 (0.27), residues: 1015
  helix:  1.96 (0.26), residues: 412
  sheet:  0.56 (0.37), residues: 205
  loop : -1.27 (0.31), residues: 398

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   0.019   0.001   PHE R 371 
 TYR   0.015   0.001   TYR R 141 
 ARG   0.003   0.000   ARG A  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
  194 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
REVERT: R  135 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8462 (mp0)
REVERT: R  170 ASN cc_start: 0.8376 (m110) cc_final: 0.8100 (m-40)
REVERT: R  181 MET cc_start: 0.8719 (mmm) cc_final: 0.8409 (tpp)
REVERT: R  252 GLU cc_start: 0.7278 (pm20) cc_final: 0.6458 (pp20)
REVERT: R  293 LYS cc_start: 0.6673 (pptt) cc_final: 0.6410 (pptt)
REVERT: R  377 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8825 (mt-10)
REVERT: R  396 ASN cc_start: 0.8214 (t0) cc_final: 0.7678 (t0)
REVERT: R  408 HIS cc_start: 0.8332 (m170) cc_final: 0.7990 (m-70)
REVERT: A   27 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8583 (mm-30)
REVERT: A  311 TYR cc_start: 0.7519 (m-10) cc_final: 0.7137 (m-10)
REVERT: A  356 ARG cc_start: 0.8126 (mtp-110) cc_final: 0.7633 (mtp-110)
REVERT: A  390 GLN cc_start: 0.8709 (tt0) cc_final: 0.8367 (tp-100)
REVERT: B    8 ARG cc_start: 0.9068 (mpt-90) cc_final: 0.8750 (mpt-90)
REVERT: B   15 LYS cc_start: 0.9277 (mtmm) cc_final: 0.8781 (tmmt)
REVERT: B   23 LYS cc_start: 0.9520 (tmmm) cc_final: 0.9257 (tptp)
REVERT: B  217 MET cc_start: 0.8440 (ppp) cc_final: 0.8117 (ppp)
REVERT: G   13 ARG cc_start: 0.9353 (ptp-110) cc_final: 0.9078 (ptp-110)
REVERT: G   18 GLN cc_start: 0.8928 (tp40) cc_final: 0.8466 (tp40)
REVERT: N    5 GLN cc_start: 0.8391 (tp-100) cc_final: 0.8043 (tp40)
REVERT: N   38 ARG cc_start: 0.8721 (ttp-110) cc_final: 0.8467 (mtm110)
REVERT: N   46 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8367 (pt0)
REVERT: N   53 GLN cc_start: 0.7994 (mp10) cc_final: 0.7637 (mp10)
REVERT: N   70 ILE cc_start: 0.8660 (pt) cc_final: 0.8319 (pp)
REVERT: N   73 ASP cc_start: 0.7844 (t0) cc_final: 0.7339 (t0)
REVERT: N   87 LYS cc_start: 0.9152 (mttp) cc_final: 0.8759 (mttm)
  outliers start: 26
  outliers final: 8
  residues processed: 179
  average time/residue: 1.2753
  time to fit residues: 241.4948
Evaluate side-chains
  157 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 148
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  149 LEU
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  196 THR
Chi-restraints excluded: chain G residue   19 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 82 optimal weight:    4.9990
   chunk 83 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.106730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.074125 restraints weight = 15544.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 3.60
r_work: 0.2907 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2261

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= 0.213
  Angle     :  0.636   9.786  11260  Z= 0.327
  Chirality :  0.044   0.264   1266
  Planarity :  0.004   0.058   1440
  Dihedral  :  4.404  45.673   1141
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 19.63 %
    Favored  : 76.71 %
  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:  0.72 (0.27), residues: 1015
  helix:  1.98 (0.26), residues: 412
  sheet:  0.64 (0.37), residues: 205
  loop : -1.27 (0.31), residues: 398

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 379 
 TYR   0.013   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
  184 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 152
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
REVERT: R  170 ASN cc_start: 0.8410 (m110) cc_final: 0.8139 (m-40)
REVERT: R  293 LYS cc_start: 0.6706 (pptt) cc_final: 0.6409 (pptt)
REVERT: R  396 ASN cc_start: 0.8235 (t0) cc_final: 0.7727 (t0)
REVERT: R  408 HIS cc_start: 0.8320 (m170) cc_final: 0.7983 (m-70)
REVERT: A   27 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8621 (mm-30)
REVERT: A  311 TYR cc_start: 0.7670 (m-10) cc_final: 0.7297 (m-10)
REVERT: A  356 ARG cc_start: 0.8132 (mtp-110) cc_final: 0.7602 (mtp-110)
REVERT: A  390 GLN cc_start: 0.8740 (tt0) cc_final: 0.8321 (tp-100)
REVERT: B    8 ARG cc_start: 0.9107 (mpt-90) cc_final: 0.8734 (mpt-90)
REVERT: B   10 GLU cc_start: 0.8192 (pp20) cc_final: 0.7912 (pp20)
REVERT: B   12 GLU cc_start: 0.8994 (pp20) cc_final: 0.8791 (pp20)
REVERT: B   15 LYS cc_start: 0.9260 (mtmm) cc_final: 0.8788 (tmmt)
REVERT: B   23 LYS cc_start: 0.9519 (tmmm) cc_final: 0.9271 (tptp)
REVERT: B  217 MET cc_start: 0.8467 (ppp) cc_final: 0.8131 (ppp)
REVERT: G   18 GLN cc_start: 0.8930 (tp40) cc_final: 0.8331 (tp40)
REVERT: G   32 LYS cc_start: 0.8640 (ttpp) cc_final: 0.8436 (tppp)
REVERT: N    5 GLN cc_start: 0.8404 (tp-100) cc_final: 0.8057 (tp40)
REVERT: N   43 LYS cc_start: 0.8002 (mmmm) cc_final: 0.7681 (tptt)
REVERT: N   53 GLN cc_start: 0.8034 (mp10) cc_final: 0.7666 (mp10)
REVERT: N   70 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8297 (pp)
REVERT: N   73 ASP cc_start: 0.7875 (t0) cc_final: 0.7385 (t0)
REVERT: N   87 LYS cc_start: 0.9120 (mttp) cc_final: 0.8737 (mttm)
  outliers start: 32
  outliers final: 16
  residues processed: 165
  average time/residue: 1.1517
  time to fit residues: 202.2212
Evaluate side-chains
  161 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
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  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 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   38 MET
Chi-restraints excluded: chain G residue   57 SER
Chi-restraints excluded: chain N residue   11 LEU
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:    0.9990
   chunk 93 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3630 r_free = 0.3630 target = 0.106057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.073544 restraints weight = 15573.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 3.60
r_work: 0.2890 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8321  Z= 0.219
  Angle     :  0.644  10.508  11260  Z= 0.330
  Chirality :  0.044   0.268   1266
  Planarity :  0.004   0.061   1440
  Dihedral  :  4.412  44.926   1141
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 21.58 %
    Favored  : 75.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.27), residues: 1015
  helix:  1.93 (0.26), residues: 409
  sheet:  0.67 (0.37), residues: 205
  loop : -1.31 (0.30), residues: 401

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 335 
 ARG   0.007   0.000   ARG G  13 

*********************** 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
  186 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 159
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
REVERT: R  170 ASN cc_start: 0.8402 (m110) cc_final: 0.8127 (m-40)
REVERT: R  293 LYS cc_start: 0.6741 (pptt) cc_final: 0.6427 (pptt)
REVERT: R  384 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7756 (tt0)
REVERT: R  396 ASN cc_start: 0.8202 (t0) cc_final: 0.7621 (t0)
REVERT: R  408 HIS cc_start: 0.8320 (m170) cc_final: 0.7982 (m-70)
REVERT: A   27 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8604 (mm-30)
REVERT: A  311 TYR cc_start: 0.7780 (m-10) cc_final: 0.7368 (m-10)
REVERT: A  356 ARG cc_start: 0.8130 (mtp-110) cc_final: 0.7601 (mtp-110)
REVERT: A  390 GLN cc_start: 0.8770 (tt0) cc_final: 0.8340 (tp-100)
REVERT: B    8 ARG cc_start: 0.9100 (mpt-90) cc_final: 0.8729 (mtt-85)
REVERT: B   12 GLU cc_start: 0.8990 (pp20) cc_final: 0.8739 (pp20)
REVERT: B   15 LYS cc_start: 0.9264 (mtmm) cc_final: 0.8812 (tmmt)
REVERT: B   23 LYS cc_start: 0.9530 (tmmm) cc_final: 0.9267 (tptp)
REVERT: B  217 MET cc_start: 0.8445 (ppp) cc_final: 0.8089 (ppp)
REVERT: G   13 ARG cc_start: 0.9305 (ptp-110) cc_final: 0.8909 (mtm110)
REVERT: G   17 GLU cc_start: 0.9564 (tp30) cc_final: 0.9195 (mm-30)
REVERT: G   18 GLN cc_start: 0.8891 (tp40) cc_final: 0.8295 (tp40)
REVERT: G   29 LYS cc_start: 0.8298 (mmtm) cc_final: 0.8073 (tppp)
REVERT: N    5 GLN cc_start: 0.8463 (tp-100) cc_final: 0.8134 (tp40)
REVERT: N   46 GLU cc_start: 0.8840 (pt0) cc_final: 0.8608 (pt0)
REVERT: N   53 GLN cc_start: 0.8072 (mp10) cc_final: 0.7696 (mp10)
REVERT: N   70 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8322 (pp)
REVERT: N   73 ASP cc_start: 0.7915 (t0) cc_final: 0.7409 (t0)
REVERT: N   76 LYS cc_start: 0.9466 (mmmm) cc_final: 0.9186 (mmmm)
REVERT: N   87 LYS cc_start: 0.9117 (mttp) cc_final: 0.8766 (mttm)
  outliers start: 27
  outliers final: 18
  residues processed: 171
  average time/residue: 1.0837
  time to fit residues: 197.9990
Evaluate side-chains
  165 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
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  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 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   38 MET
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 14 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 87 optimal weight:    6.9990
   chunk 3 optimal weight:    0.1980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3634 r_free = 0.3634 target = 0.106376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.074184 restraints weight = 15553.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 3.55
r_work: 0.2910 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8321  Z= 0.206
  Angle     :  0.654   9.931  11260  Z= 0.335
  Chirality :  0.044   0.228   1266
  Planarity :  0.004   0.062   1440
  Dihedral  :  4.472  46.349   1141
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 23.52 %
    Favored  : 73.74 %
  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:  0.69 (0.27), residues: 1015
  helix:  2.01 (0.26), residues: 405
  sheet:  0.63 (0.37), residues: 211
  loop : -1.31 (0.30), residues: 399

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   0.013   0.001   TYR R 141 
 ARG   0.006   0.000   ARG G  13 

*********************** 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
  176 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.937 
Fit side-chains
REVERT: R  170 ASN cc_start: 0.8395 (m110) cc_final: 0.8117 (m-40)
REVERT: R  293 LYS cc_start: 0.6703 (pptt) cc_final: 0.6374 (pptt)
REVERT: R  396 ASN cc_start: 0.8199 (t0) cc_final: 0.7552 (t0)
REVERT: R  408 HIS cc_start: 0.8314 (m170) cc_final: 0.7974 (m-70)
REVERT: A  311 TYR cc_start: 0.7808 (m-10) cc_final: 0.7368 (m-10)
REVERT: A  356 ARG cc_start: 0.8088 (mtp-110) cc_final: 0.7552 (mtp-110)
REVERT: A  390 GLN cc_start: 0.8748 (tt0) cc_final: 0.8330 (tp-100)
REVERT: B    8 ARG cc_start: 0.9053 (mpt-90) cc_final: 0.8681 (mtt-85)
REVERT: B   10 GLU cc_start: 0.8933 (pp20) cc_final: 0.8722 (pp20)
REVERT: B   12 GLU cc_start: 0.8997 (pp20) cc_final: 0.8788 (pp20)
REVERT: B   15 LYS cc_start: 0.9263 (mtmm) cc_final: 0.8808 (tmmt)
REVERT: B   23 LYS cc_start: 0.9529 (tmmm) cc_final: 0.9248 (tptp)
REVERT: B  217 MET cc_start: 0.8425 (ppp) cc_final: 0.8035 (ppp)
REVERT: G   13 ARG cc_start: 0.9358 (ptp-110) cc_final: 0.8962 (mtm110)
REVERT: G   17 GLU cc_start: 0.9563 (tp30) cc_final: 0.9266 (mm-30)
REVERT: G   18 GLN cc_start: 0.8882 (tp40) cc_final: 0.8336 (tp40)
REVERT: G   24 ASN cc_start: 0.9214 (p0) cc_final: 0.8989 (p0)
REVERT: G   28 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7981 (tp)
REVERT: G   29 LYS cc_start: 0.8278 (mmtm) cc_final: 0.8071 (tppp)
REVERT: G   47 GLU cc_start: 0.8721 (mp0) cc_final: 0.7740 (mp0)
REVERT: N    5 GLN cc_start: 0.8443 (tp-100) cc_final: 0.8118 (tp40)
REVERT: N   53 GLN cc_start: 0.8127 (mp10) cc_final: 0.7781 (mp10)
REVERT: N   70 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8285 (pp)
REVERT: N   73 ASP cc_start: 0.7924 (t0) cc_final: 0.7420 (t0)
REVERT: N   76 LYS cc_start: 0.9474 (mmmm) cc_final: 0.9199 (mmmm)
REVERT: N   87 LYS cc_start: 0.9115 (mttp) cc_final: 0.8769 (mttm)
REVERT: N  105 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8544 (mtm180)
  outliers start: 24
  outliers final: 15
  residues processed: 161
  average time/residue: 1.1467
  time to fit residues: 196.9189
Evaluate side-chains
  164 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
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  248 VAL
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 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   70 ILE
Chi-restraints excluded: chain N residue  105 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 43 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9990
   chunk 68 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 78 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3637 r_free = 0.3637 target = 0.106658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.074215 restraints weight = 15693.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 3.60
r_work: 0.2909 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.2582

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= 0.206
  Angle     :  0.672  10.826  11260  Z= 0.341
  Chirality :  0.045   0.315   1266
  Planarity :  0.004   0.064   1440
  Dihedral  :  4.464  45.825   1141
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 24.09 %
    Favored  : 73.17 %
  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:  0.69 (0.27), residues: 1015
  helix:  1.96 (0.26), residues: 407
  sheet:  0.60 (0.37), residues: 211
  loop : -1.27 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP R 287 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.021   0.001   PHE R 371 
 TYR   0.012   0.001   TYR R 141 
 ARG   0.005   0.000   ARG G  13 

*********************** 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
  177 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 153
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  170 ASN cc_start: 0.8396 (m110) cc_final: 0.8129 (m-40)
REVERT: R  293 LYS cc_start: 0.6709 (pptt) cc_final: 0.6376 (pptt)
REVERT: R  384 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7649 (tt0)
REVERT: R  396 ASN cc_start: 0.8131 (t0) cc_final: 0.7509 (t0)
REVERT: R  408 HIS cc_start: 0.8329 (m170) cc_final: 0.7997 (m-70)
REVERT: A   27 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8603 (mm-30)
REVERT: A  311 TYR cc_start: 0.7834 (m-10) cc_final: 0.7402 (m-10)
REVERT: A  356 ARG cc_start: 0.8115 (mtp-110) cc_final: 0.7567 (mtp-110)
REVERT: A  390 GLN cc_start: 0.8781 (tt0) cc_final: 0.8340 (tp-100)
REVERT: B    8 ARG cc_start: 0.8985 (mpt-90) cc_final: 0.8661 (mpt-90)
REVERT: B   12 GLU cc_start: 0.8985 (pp20) cc_final: 0.8733 (pp20)
REVERT: B   15 LYS cc_start: 0.9251 (mtmm) cc_final: 0.8813 (tmmt)
REVERT: B   23 LYS cc_start: 0.9523 (tmmm) cc_final: 0.9233 (tptp)
REVERT: B  217 MET cc_start: 0.8436 (ppp) cc_final: 0.8086 (ppp)
REVERT: G   13 ARG cc_start: 0.9362 (ptp-110) cc_final: 0.9134 (mtm110)
REVERT: G   18 GLN cc_start: 0.8784 (tp40) cc_final: 0.8254 (tp40)
REVERT: G   24 ASN cc_start: 0.9137 (p0) cc_final: 0.8886 (p0)
REVERT: G   28 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7980 (tp)
REVERT: G   29 LYS cc_start: 0.8261 (mmtm) cc_final: 0.8021 (tppp)
REVERT: N    5 GLN cc_start: 0.8435 (tp-100) cc_final: 0.8083 (tp40)
REVERT: N   53 GLN cc_start: 0.8142 (mp10) cc_final: 0.7794 (mp10)
REVERT: N   70 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8257 (pp)
REVERT: N   73 ASP cc_start: 0.7948 (t0) cc_final: 0.7443 (t0)
REVERT: N   76 LYS cc_start: 0.9480 (mmmm) cc_final: 0.9212 (mmmm)
REVERT: N   87 LYS cc_start: 0.9110 (mttp) cc_final: 0.8755 (mttm)
  outliers start: 24
  outliers final: 16
  residues processed: 162
  average time/residue: 1.1307
  time to fit residues: 194.9873
Evaluate side-chains
  164 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 145
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
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  213 LEU
Chi-restraints excluded: chain R residue  248 VAL
Chi-restraints excluded: chain R residue  270 PHE
Chi-restraints excluded: chain R residue  349 LEU
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 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 88 optimal weight:    0.0670
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 100 optimal weight:    0.6980
   chunk 70 optimal weight:    0.2980
   chunk 57 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0270
   chunk 78 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.3776

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

Flipped N/Q/H residues before XYZ refinement:
R 329 GLN
R 384 GLN
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 268 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.107410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.074989 restraints weight = 15808.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3093 rms_B_bonded: 3.62
r_work: 0.2925 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8321  Z= 0.185
  Angle     :  0.677  10.524  11260  Z= 0.342
  Chirality :  0.045   0.299   1266
  Planarity :  0.004   0.066   1440
  Dihedral  :  4.436  45.601   1141
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 24.09 %
    Favored  : 72.83 %
  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:  1.97 (0.26), residues: 407
  sheet:  0.61 (0.37), residues: 211
  loop : -1.34 (0.30), residues: 397

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   0.033   0.001   PHE N 103 
 TYR   0.012   0.001   TYR R 141 
 ARG   0.005   0.000   ARG G  13 

*********************** 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
  176 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 149
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
REVERT: R  164 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8474 (tmm-80)
REVERT: R  170 ASN cc_start: 0.8375 (m110) cc_final: 0.8086 (m-40)
REVERT: R  293 LYS cc_start: 0.6701 (pptt) cc_final: 0.6363 (pptt)
REVERT: R  335 TYR cc_start: 0.6741 (OUTLIER) cc_final: 0.6297 (m-10)
REVERT: R  396 ASN cc_start: 0.8149 (t0) cc_final: 0.7528 (t0)
REVERT: R  408 HIS cc_start: 0.8327 (m170) cc_final: 0.7995 (m-70)
REVERT: A   27 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8609 (mm-30)
REVERT: A  311 TYR cc_start: 0.7824 (m-10) cc_final: 0.7376 (m-10)
REVERT: A  356 ARG cc_start: 0.8098 (mtp-110) cc_final: 0.7545 (mtp-110)
REVERT: A  390 GLN cc_start: 0.8756 (tt0) cc_final: 0.8332 (tp-100)
REVERT: B    8 ARG cc_start: 0.8972 (mpt-90) cc_final: 0.8616 (mpt-90)
REVERT: B   10 GLU cc_start: 0.8905 (pp20) cc_final: 0.8672 (pp20)
REVERT: B   12 GLU cc_start: 0.8985 (pp20) cc_final: 0.8709 (pp20)
REVERT: B   15 LYS cc_start: 0.9255 (mtmm) cc_final: 0.8824 (tmmt)
REVERT: B   23 LYS cc_start: 0.9514 (tmmm) cc_final: 0.9214 (tptp)
REVERT: B  217 MET cc_start: 0.8439 (ppp) cc_final: 0.8120 (ppp)
REVERT: G   13 ARG cc_start: 0.9366 (ptp-110) cc_final: 0.9012 (mtm110)
REVERT: G   18 GLN cc_start: 0.8818 (tp40) cc_final: 0.8316 (tp40)
REVERT: G   24 ASN cc_start: 0.9140 (p0) cc_final: 0.8856 (p0)
REVERT: G   28 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.8009 (tp)
REVERT: G   29 LYS cc_start: 0.8224 (mmtm) cc_final: 0.8005 (tppp)
REVERT: G   47 GLU cc_start: 0.8489 (mp0) cc_final: 0.7802 (mp0)
REVERT: N    5 GLN cc_start: 0.8398 (tp-100) cc_final: 0.8034 (tp40)
REVERT: N   53 GLN cc_start: 0.8130 (mp10) cc_final: 0.7747 (mp10)
REVERT: N   70 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8202 (pp)
REVERT: N   73 ASP cc_start: 0.7933 (t0) cc_final: 0.7477 (t0)
REVERT: N   76 LYS cc_start: 0.9483 (mmmm) cc_final: 0.9216 (mmmm)
REVERT: N   87 LYS cc_start: 0.9112 (mttp) cc_final: 0.8740 (mttm)
  outliers start: 27
  outliers final: 15
  residues processed: 161
  average time/residue: 1.1371
  time to fit residues: 194.8633
Evaluate side-chains
  163 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
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  164 ARG
Chi-restraints excluded: chain R residue  213 LEU
Chi-restraints excluded: chain R residue  248 VAL
Chi-restraints excluded: chain R residue  270 PHE
Chi-restraints excluded: chain R residue  335 TYR
Chi-restraints excluded: chain R residue  349 LEU
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 B residue  317 CYS
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   28 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 67 optimal weight:    0.8980
   chunk 94 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.106604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.074066 restraints weight = 15510.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 3.58
r_work: 0.2905 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8321  Z= 0.214
  Angle     :  0.707  11.890  11260  Z= 0.356
  Chirality :  0.046   0.336   1266
  Planarity :  0.004   0.067   1440
  Dihedral  :  4.462  44.963   1141
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 25.11 %
    Favored  : 72.49 %
  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:  0.65 (0.27), residues: 1015
  helix:  1.96 (0.26), residues: 407
  sheet:  0.55 (0.37), residues: 213
  loop : -1.31 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP R 287 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.028   0.001   PHE N 103 
 TYR   0.011   0.001   TYR R 141 
 ARG   0.014   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
  165 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: R  157 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.7938 (tt)
REVERT: R  164 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8486 (tmm-80)
REVERT: R  170 ASN cc_start: 0.8413 (m110) cc_final: 0.8169 (m-40)
REVERT: R  293 LYS cc_start: 0.6662 (pptt) cc_final: 0.6354 (pptt)
REVERT: R  396 ASN cc_start: 0.8059 (t0) cc_final: 0.7417 (t0)
REVERT: R  408 HIS cc_start: 0.8344 (m170) cc_final: 0.8011 (m-70)
REVERT: A   27 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8599 (mm-30)
REVERT: A  311 TYR cc_start: 0.7905 (m-10) cc_final: 0.7458 (m-10)
REVERT: A  356 ARG cc_start: 0.8102 (mtp-110) cc_final: 0.7556 (mtp-110)
REVERT: A  390 GLN cc_start: 0.8774 (tt0) cc_final: 0.8345 (tp-100)
REVERT: B    8 ARG cc_start: 0.8905 (mpt-90) cc_final: 0.8589 (mpt-90)
REVERT: B   12 GLU cc_start: 0.8940 (pp20) cc_final: 0.8708 (pp20)
REVERT: B   15 LYS cc_start: 0.9263 (mtmm) cc_final: 0.8813 (tmmt)
REVERT: B   23 LYS cc_start: 0.9514 (tmmm) cc_final: 0.9218 (tptp)
REVERT: B  217 MET cc_start: 0.8436 (ppp) cc_final: 0.8115 (ppp)
REVERT: G   13 ARG cc_start: 0.9374 (ptp-110) cc_final: 0.9081 (mtm110)
REVERT: G   18 GLN cc_start: 0.8780 (tp40) cc_final: 0.8193 (tp40)
REVERT: G   24 ASN cc_start: 0.9145 (p0) cc_final: 0.8862 (p0)
REVERT: G   28 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7987 (tp)
REVERT: G   29 LYS cc_start: 0.8247 (mmtm) cc_final: 0.8036 (tppp)
REVERT: N    5 GLN cc_start: 0.8406 (tp-100) cc_final: 0.8053 (tp40)
REVERT: N   53 GLN cc_start: 0.8158 (mp10) cc_final: 0.7766 (mp10)
REVERT: N   70 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8313 (pt)
REVERT: N   73 ASP cc_start: 0.8143 (t0) cc_final: 0.7574 (t0)
REVERT: N   76 LYS cc_start: 0.9457 (mmmm) cc_final: 0.9179 (mmmm)
REVERT: N   87 LYS cc_start: 0.9129 (mttp) cc_final: 0.8762 (mttm)
  outliers start: 21
  outliers final: 14
  residues processed: 153
  average time/residue: 1.1564
  time to fit residues: 188.3508
Evaluate side-chains
  159 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
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  164 ARG
Chi-restraints excluded: chain R residue  248 VAL
Chi-restraints excluded: chain R residue  270 PHE
Chi-restraints excluded: chain R residue  349 LEU
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 N residue   11 LEU
Chi-restraints excluded: chain N residue   70 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 94 optimal weight:    6.9990
   chunk 84 optimal weight:    9.9990
   chunk 65 optimal weight:    0.4980
   chunk 85 optimal weight:    9.9990
   chunk 4 optimal weight:    0.7980
   chunk 80 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 70 optimal weight:    0.2980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.106424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.073878 restraints weight = 15758.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 3.61
r_work: 0.2901 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8321  Z= 0.211
  Angle     :  0.691  11.816  11260  Z= 0.351
  Chirality :  0.046   0.345   1266
  Planarity :  0.004   0.067   1440
  Dihedral  :  4.494  46.301   1141
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 25.00 %
    Favored  : 72.60 %
  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 (0.26), residues: 407
  sheet:  0.53 (0.37), residues: 213
  loop : -1.31 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP R 287 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.022   0.001   PHE N 103 
 TYR   0.011   0.001   TYR R 141 
 ARG   0.013   0.000   ARG R 326 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6194.69 seconds
wall clock time: 109 minutes 59.22 seconds (6599.22 seconds total)