Starting phenix.real_space_refine
on Fri Aug 22 18:25:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ovx_17225/08_2025/8ovx_17225.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ovx_17225/08_2025/8ovx_17225.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ovx_17225/08_2025/8ovx_17225.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ovx_17225/08_2025/8ovx_17225.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ovx_17225/08_2025/8ovx_17225.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ovx_17225/08_2025/8ovx_17225.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.001 sd=   0.062
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      29      5.16       5
     C    4320      2.51       5
     N    1163      2.21       5
     O    1251      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6763
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "O"
      Number of atoms: 1347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 1347
          Classifications: {'peptide': 165}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 3, 'TRANS': 161}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "P"
      Number of atoms: 1564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1564
          Classifications: {'peptide': 199}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 5, 'TRANS': 193}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 88
          Unresolved non-hydrogen angles: 107
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 61
    Chain: "Q"
      Number of atoms: 732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 732
          Classifications: {'peptide': 99}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 84
          Unresolved non-hydrogen dihedrals: 56
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'HIS:plan': 1, 'GLU:plan': 7}
          Unresolved non-hydrogen planarities: 49
    Chain: "U"
      Number of atoms: 585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 585
          Classifications: {'peptide': 79}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "Y"
      Number of atoms: 1473
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1473
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 3, 'TRANS': 199}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 140
          Unresolved non-hydrogen angles: 170
          Unresolved non-hydrogen dihedrals: 113
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 6, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 76
    Chain: "Z"
      Number of atoms: 1062
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1062
          Classifications: {'peptide': 140}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 2, 'TRANS': 137}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 116
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 60
  Time building chain proxies: 1.90, per 1000 atoms: 0.28
  Number of scatterers: 6763
  At special positions: 0
  Unit cell: (97.468, 80.948, 123.9, 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      29     16.00
     O    1251      8.00
     N    1163      7.00
     C    4320      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.59
  Conformation dependent library (CDL) restraints added in 376.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1718

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 5 sheets defined
      64.5% alpha, 9.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'O' and resid 162 through 172
      removed outlier: 3.866A  pdb=" N   LEU O 166 " --> pdb=" O   ASP O 162 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 253 through 257
    Processing helix  chain 'O' and resid 260 through 291
      removed outlier: 3.549A  pdb=" N   ALA O 264 " --> pdb=" O   SER O 260 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 353 through 364
      removed outlier: 3.651A  pdb=" N   LEU O 357 " --> pdb=" O   ASP O 353 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   ASN O 360 " --> pdb=" O   GLU O 356 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   HIS O 361 " --> pdb=" O   LEU O 357 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 154 through 160
    Processing helix  chain 'P' and resid 226 through 231
      removed outlier: 3.986A  pdb=" N   GLN P 230 " --> pdb=" O   LEU P 226 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LEU P 231 " --> pdb=" O   LYS P 227 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 226 through 231'
    Processing helix  chain 'P' and resid 232 through 234
      No H-bonds generated for 'chain 'P' and resid 232 through 234'
    Processing helix  chain 'P' and resid 236 through 240
    Processing helix  chain 'P' and resid 244 through 263
    Processing helix  chain 'P' and resid 333 through 348
      removed outlier: 3.904A  pdb=" N   LEU P 337 " --> pdb=" O   ASN P 333 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 349 through 363
      removed outlier: 3.605A  pdb=" N   LEU P 354 " --> pdb=" O   VAL P 350 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 278 through 291
      removed outlier: 3.822A  pdb=" N   LYS Q 285 " --> pdb=" O   THR Q 281 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG Q 286 " --> pdb=" O   ASN Q 282 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 321 through 332
      removed outlier: 4.429A  pdb=" N   HIS Q 330 " --> pdb=" O   ARG Q 326 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU Q 331 " --> pdb=" O   ASN Q 327 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 349 through 357
    Processing helix  chain 'Q' and resid 358 through 380
      removed outlier: 4.085A  pdb=" N   GLU Q 362 " --> pdb=" O   PRO Q 358 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LYS Q 365 " --> pdb=" O   LYS Q 361 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   GLN Q 376 " --> pdb=" O   GLU Q 372 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   MET Q 377 " --> pdb=" O   THR Q 373 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 382 through 391
    Processing helix  chain 'U' and resid 234 through 266
      removed outlier: 3.805A  pdb=" N   ASN U 247 " --> pdb=" O   GLN U 243 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 286 through 299
      removed outlier: 3.753A  pdb=" N   LEU U 290 " --> pdb=" O   ASP U 286 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASP U 297 " --> pdb=" O   ALA U 293 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 305 through 321
      removed outlier: 3.898A  pdb=" N   ASN U 315 " --> pdb=" O   LYS U 311 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 2 through 31
    Processing helix  chain 'Y' and resid 35 through 50
    Processing helix  chain 'Y' and resid 51 through 54
      removed outlier: 3.717A  pdb=" N   MET Y  54 " --> pdb=" O   LYS Y  51 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Y' and resid 51 through 54'
    Processing helix  chain 'Y' and resid 55 through 86
      removed outlier: 3.671A  pdb=" N   ASP Y  60 " --> pdb=" O   ARG Y  56 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   GLY Y  86 " --> pdb=" O   MET Y  82 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 111 through 119
    Processing helix  chain 'Y' and resid 137 through 186
      removed outlier: 3.647A  pdb=" N   LYS Y 153 " --> pdb=" O   ASP Y 149 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLN Y 158 " --> pdb=" O   CYS Y 154 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   SER Y 169 " --> pdb=" O   SER Y 165 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER Y 185 " --> pdb=" O   ILE Y 181 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 189 through 194
      removed outlier: 3.552A  pdb=" N   TYR Y 193 " --> pdb=" O   ASP Y 189 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE Y 194 " --> pdb=" O   ILE Y 190 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Y' and resid 189 through 194'
    Processing helix  chain 'Y' and resid 196 through 219
    Processing helix  chain 'Y' and resid 221 through 238
      removed outlier: 4.175A  pdb=" N   GLU Y 235 " --> pdb=" O   LYS Y 231 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU Y 236 " --> pdb=" O   ILE Y 232 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   LYS Y 237 " --> pdb=" O   LEU Y 233 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 2 through 13
      removed outlier: 3.559A  pdb=" N   LEU Z   6 " --> pdb=" O   ASN Z   2 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 21 through 29
      removed outlier: 3.602A  pdb=" N   PHE Z  25 " --> pdb=" O   SER Z  21 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 37 through 71
      removed outlier: 4.126A  pdb=" N   HIS Z  41 " --> pdb=" O   GLN Z  37 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER Z  55 " --> pdb=" O   ALA Z  51 " (cutoff:3.500A)
      removed outlier: 5.138A  pdb=" N   GLU Z  58 " --> pdb=" O   THR Z  54 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ALA Z  59 " --> pdb=" O   SER Z  55 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ARG Z  60 " --> pdb=" O   GLU Z  56 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 88 through 126
      removed outlier: 4.239A  pdb=" N   ASP Z  92 " --> pdb=" O   GLU Z  88 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA Z  93 " --> pdb=" O   THR Z  89 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLN Z 103 " --> pdb=" O   ASP Z  99 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ILE Z 107 " --> pdb=" O   GLN Z 103 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU Z 108 " --> pdb=" O   ARG Z 104 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLU Z 114 " --> pdb=" O   ASP Z 110 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LYS Z 115 " --> pdb=" O   ALA Z 111 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 131 through 153
      Proline residue:  Z 137  - end of helix
    Processing sheet with id=AA1, first strand: chain 'O' and resid 175 through 179
      removed outlier: 6.923A  pdb=" N   TYR O 221 " --> pdb=" O   HIS O 238 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   HIS O 238 " --> pdb=" O   TYR O 221 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   LEU O 223 " --> pdb=" O   PHE O 236 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'O' and resid 297 through 298
      removed outlier: 3.540A  pdb=" N   SER O 307 " --> pdb=" O   ASP O 298 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'O' and resid 315 through 320
      removed outlier: 6.577A  pdb=" N   GLU O 316 " --> pdb=" O   CYS O 327 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   CYS O 327 " --> pdb=" O   GLU O 316 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   PHE O 318 " --> pdb=" O   VAL O 325 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'P' and resid 165 through 174
      removed outlier: 6.730A  pdb=" N   VAL P 184 " --> pdb=" O   GLN P 170 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   ARG P 172 " --> pdb=" O   VAL P 182 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   VAL P 182 " --> pdb=" O   ARG P 172 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE P 197 " --> pdb=" O   PHE P 189 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   GLU P 198 " --> pdb=" O   ILE P 220 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   ILE P 220 " --> pdb=" O   GLU P 198 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   GLN P 200 " --> pdb=" O   LEU P 218 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'P' and resid 270 through 273

    447 hydrogen bonds defined for protein.
    1308 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.01

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1585
        1.33 -     1.45: 1222
        1.45 -     1.57: 3989
        1.57 -     1.69: 1
        1.69 -     1.81: 48
  Bond restraints: 6845
  Sorted by residual:
  bond pdb=" CA  LEU Q 291 "
       pdb=" C   LEU Q 291 "
    ideal  model  delta    sigma   weight residual
    1.523  1.574 -0.051 1.34e-02 5.57e+03 1.44e+01
  bond pdb=" CA  MET Q 335 "
       pdb=" CB  MET Q 335 "
    ideal  model  delta    sigma   weight residual
    1.528  1.568 -0.040 1.51e-02 4.39e+03 6.96e+00
  bond pdb=" CB  GLU U 314 "
       pdb=" CG  GLU U 314 "
    ideal  model  delta    sigma   weight residual
    1.520  1.561 -0.041 3.00e-02 1.11e+03 1.85e+00
  bond pdb=" N   PHE P 207 "
       pdb=" CA  PHE P 207 "
    ideal  model  delta    sigma   weight residual
    1.456  1.472 -0.016 1.23e-02 6.61e+03 1.61e+00
  bond pdb=" C   PHE O 177 "
       pdb=" N   PHE O 178 "
    ideal  model  delta    sigma   weight residual
    1.331  1.311  0.021 1.63e-02 3.76e+03 1.59e+00
  ... (remaining 6840 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.93: 9035
        2.93 -     5.86: 162
        5.86 -     8.79: 30
        8.79 -    11.73: 8
       11.73 -    14.66: 1
  Bond angle restraints: 9236
  Sorted by residual:
  angle pdb=" C   ALA Z 135 "
        pdb=" N   ILE Z 136 "
        pdb=" CA  ILE Z 136 "
      ideal   model   delta    sigma   weight residual
     120.24  123.78   -3.54 6.30e-01 2.52e+00 3.15e+01
  angle pdb=" CA  ARG Z  52 "
        pdb=" CB  ARG Z  52 "
        pdb=" CG  ARG Z  52 "
      ideal   model   delta    sigma   weight residual
     114.10  124.73  -10.63 2.00e+00 2.50e-01 2.83e+01
  angle pdb=" C   PHE O 177 "
        pdb=" N   PHE O 178 "
        pdb=" CA  PHE O 178 "
      ideal   model   delta    sigma   weight residual
     121.61  128.35   -6.74 1.39e+00 5.18e-01 2.35e+01
  angle pdb=" C   THR Q 373 "
        pdb=" N   MET Q 374 "
        pdb=" CA  MET Q 374 "
      ideal   model   delta    sigma   weight residual
     122.37  115.64    6.73 1.54e+00 4.22e-01 1.91e+01
  angle pdb=" N   GLU Z  44 "
        pdb=" CA  GLU Z  44 "
        pdb=" CB  GLU Z  44 "
      ideal   model   delta    sigma   weight residual
     110.28  116.82   -6.54 1.55e+00 4.16e-01 1.78e+01
  ... (remaining 9231 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 3822
       17.86 -    35.72: 313
       35.72 -    53.59: 51
       53.59 -    71.45: 8
       71.45 -    89.31: 4
  Dihedral angle restraints: 4198
    sinusoidal: 1587
      harmonic: 2611
  Sorted by residual:
  dihedral pdb=" CA  LEU Q 334 "
           pdb=" C   LEU Q 334 "
           pdb=" N   MET Q 335 "
           pdb=" CA  MET Q 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.55   29.45     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  MET Q 374 "
           pdb=" C   MET Q 374 "
           pdb=" N   GLY Q 375 "
           pdb=" CA  GLY Q 375 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.41   22.59     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  ASN Z   2 "
           pdb=" C   ASN Z   2 "
           pdb=" N   SER Z   3 "
           pdb=" CA  SER Z   3 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.53  -20.47     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 4195 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 849
       0.056 -    0.111: 212
       0.111 -    0.167: 45
       0.167 -    0.222: 8
       0.222 -    0.278: 2
  Chirality restraints: 1116
  Sorted by residual:
  chirality pdb=" CG  LEU Y  26 "
            pdb=" CB  LEU Y  26 "
            pdb=" CD1 LEU Y  26 "
            pdb=" CD2 LEU Y  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.31   -0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CB  ILE Q 292 "
            pdb=" CA  ILE Q 292 "
            pdb=" CG1 ILE Q 292 "
            pdb=" CG2 ILE Q 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.89   -0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  ARG Z  52 "
            pdb=" N   ARG Z  52 "
            pdb=" C   ARG Z  52 "
            pdb=" CB  ARG Z  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1113 not shown)

  Planarity restraints: 1159
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE P 207 "   -0.017 2.00e-02 2.50e+03   2.47e-02 1.07e+01
        pdb=" CG  PHE P 207 "    0.056 2.00e-02 2.50e+03
        pdb=" CD1 PHE P 207 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 PHE P 207 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE1 PHE P 207 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE P 207 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE P 207 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP P 215 "   -0.013 2.00e-02 2.50e+03   1.62e-02 6.54e+00
        pdb=" CG  TRP P 215 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TRP P 215 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP P 215 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP P 215 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP P 215 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP P 215 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ2 TRP P 215 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP P 215 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP P 215 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE O 240 "   -0.034 5.00e-02 4.00e+02   5.16e-02 4.25e+00
        pdb=" N   PRO O 241 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO O 241 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO O 241 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1156 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 619
        2.75 -     3.29: 6915
        3.29 -     3.82: 11673
        3.82 -     4.36: 12687
        4.36 -     4.90: 21051
  Nonbonded interactions: 52945
  Sorted by model distance:
  nonbonded pdb=" OH  TYR U 302 "
            pdb=" OE2 GLU Y 183 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OG  SER O 210 "
            pdb=" OG1 THR O 213 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OD1 ASN Q 337 "
            pdb=" NH2 ARG U 284 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" O   PRO P 163 "
            pdb=" OH  TYR P 245 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" NZ  LYS P 229 "
            pdb=" OH  TYR U 302 "
     model   vdw
     2.313 3.120
  ... (remaining 52940 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.380
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.950
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
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      :  0.004   0.051   6845  Z= 0.201
  Angle     :  0.984  14.658   9236  Z= 0.518
  Chirality :  0.053   0.278   1116
  Planarity :  0.004   0.052   1159
  Dihedral  : 13.526  89.310   2480
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.04 (0.28), residues: 853
  helix: -0.11 (0.21), residues: 538
  sheet: -0.25 (0.51), residues: 103
  loop : -2.14 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG Z  49 
 TYR   0.024   0.003   TYR Z  43 
 PHE   0.056   0.002   PHE P 207 
 TRP   0.043   0.003   TRP P 215 
 HIS   0.003   0.001   HIS U 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6845)
  covalent geometry    : angle       0.98417 ( 9236)
  hydrogen bonds       : bond        0.12519 (  447)
  hydrogen bonds       : angle       6.14470 ( 1308)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: O  201 MET cc_start: 0.7283 (mmp) cc_final: 0.6624 (tpp)
REVERT: O  320 LYS cc_start: 0.9136 (mmpt) cc_final: 0.8907 (mmmt)
REVERT: P  262 ILE cc_start: 0.6820 (mm) cc_final: 0.6460 (mm)
REVERT: Z    1 MET cc_start: 0.7414 (tmm) cc_final: 0.6983 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0991
  time to fit residues: 16.2459
Evaluate side-chains
  87 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:   20.0000
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
P 160 HIS
** U 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 294 HIS
** Y  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  80 GLN
** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z  23 GLN
Z  47 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.120295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.088023 restraints weight = 26632.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 5.97
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6845  Z= 0.173
  Angle     :  0.678   8.253   9236  Z= 0.352
  Chirality :  0.044   0.172   1116
  Planarity :  0.004   0.038   1159
  Dihedral  :  4.766  29.091    927
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 11.40 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.29), residues: 853
  helix:  0.71 (0.22), residues: 538
  sheet: -0.29 (0.50), residues: 112
  loop : -2.21 (0.43), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG U 284 
 TYR   0.020   0.002   TYR U 302 
 PHE   0.014   0.002   PHE Y 194 
 TRP   0.015   0.002   TRP P 215 
 HIS   0.002   0.001   HIS O 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 6845)
  covalent geometry    : angle       0.67816 ( 9236)
  hydrogen bonds       : bond        0.04236 (  447)
  hydrogen bonds       : angle       4.75743 ( 1308)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.7914 (ptt) cc_final: 0.7271 (ptt)
REVERT: O  267 PHE cc_start: 0.8182 (t80) cc_final: 0.7646 (t80)
REVERT: P  262 ILE cc_start: 0.6962 (mm) cc_final: 0.6647 (mm)
REVERT: Q  338 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8225 (m-30)
REVERT: Q  377 MET cc_start: 0.7927 (tpp) cc_final: 0.7620 (mmt)
REVERT: Y  119 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8072 (mtmm)
REVERT: Z    1 MET cc_start: 0.7786 (tmm) cc_final: 0.6895 (tpp)
  outliers start: 12
  outliers final: 8
  residues processed: 100
  average time/residue: 0.0984
  time to fit residues: 12.7546
Evaluate side-chains
  89 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  165 VAL
Chi-restraints excluded: chain O residue  287 ASP
Chi-restraints excluded: chain P residue  303 THR
Chi-restraints excluded: chain Q residue  338 ASP
Chi-restraints excluded: chain Q residue  346 VAL
Chi-restraints excluded: chain U residue  257 ASN
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain Y residue   73 LEU
Chi-restraints excluded: chain Z residue   44 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
O 168 ASN
U 288 ASN
Y 170 GLN
** Z   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.120105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.092400 restraints weight = 26226.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 5.65
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6845  Z= 0.138
  Angle     :  0.646  11.422   9236  Z= 0.325
  Chirality :  0.042   0.194   1116
  Planarity :  0.003   0.035   1159
  Dihedral  :  4.525  28.581    927
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.25 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.30), residues: 853
  helix:  1.09 (0.23), residues: 537
  sheet: -0.05 (0.53), residues: 107
  loop : -2.13 (0.42), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG Z  52 
 TYR   0.014   0.002   TYR Z  43 
 PHE   0.018   0.001   PHE P 207 
 TRP   0.017   0.002   TRP P 215 
 HIS   0.002   0.001   HIS U 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6845)
  covalent geometry    : angle       0.64629 ( 9236)
  hydrogen bonds       : bond        0.03893 (  447)
  hydrogen bonds       : angle       4.47789 ( 1308)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.7914 (ptt) cc_final: 0.7358 (ptt)
REVERT: O  201 MET cc_start: 0.7673 (mmp) cc_final: 0.6639 (tpp)
REVERT: P  262 ILE cc_start: 0.6981 (mm) cc_final: 0.6649 (mm)
REVERT: Q  331 GLU cc_start: 0.8283 (tt0) cc_final: 0.7389 (tm-30)
REVERT: Q  338 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8171 (m-30)
REVERT: Q  341 LYS cc_start: 0.8182 (tppt) cc_final: 0.7960 (mmmt)
REVERT: Y  119 LYS cc_start: 0.8408 (mtmm) cc_final: 0.8146 (mtmt)
REVERT: Y  151 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6393 (tp)
REVERT: Z    1 MET cc_start: 0.7598 (tmm) cc_final: 0.6845 (tpp)
  outliers start: 18
  outliers final: 12
  residues processed: 95
  average time/residue: 0.0784
  time to fit residues: 10.1652
Evaluate side-chains
  92 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  165 VAL
Chi-restraints excluded: chain O residue  287 ASP
Chi-restraints excluded: chain O residue  355 LEU
Chi-restraints excluded: chain P residue  167 VAL
Chi-restraints excluded: chain P residue  205 TYR
Chi-restraints excluded: chain P residue  303 THR
Chi-restraints excluded: chain Q residue  338 ASP
Chi-restraints excluded: chain Q residue  343 THR
Chi-restraints excluded: chain Q residue  346 VAL
Chi-restraints excluded: chain U residue  257 ASN
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain Y residue   73 LEU
Chi-restraints excluded: chain Y residue  151 ILE
Chi-restraints excluded: chain Z residue   44 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 82 optimal weight:    9.9990
   chunk 11 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
U 288 ASN
** Z   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.120259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.088245 restraints weight = 26268.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 5.84
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6845  Z= 0.123
  Angle     :  0.622  10.830   9236  Z= 0.314
  Chirality :  0.041   0.189   1116
  Planarity :  0.003   0.032   1159
  Dihedral  :  4.407  29.367    927
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 15.24 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.30), residues: 853
  helix:  1.21 (0.23), residues: 540
  sheet:  0.11 (0.53), residues: 107
  loop : -2.20 (0.42), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG Z  49 
 TYR   0.013   0.001   TYR P 187 
 PHE   0.022   0.001   PHE O 267 
 TRP   0.010   0.001   TRP P 215 
 HIS   0.002   0.000   HIS U 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6845)
  covalent geometry    : angle       0.62159 ( 9236)
  hydrogen bonds       : bond        0.03743 (  447)
  hydrogen bonds       : angle       4.31079 ( 1308)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.8094 (ptt) cc_final: 0.7667 (ptt)
REVERT: O  201 MET cc_start: 0.7787 (mmp) cc_final: 0.6667 (tpp)
REVERT: P  262 ILE cc_start: 0.6836 (mm) cc_final: 0.6512 (mm)
REVERT: Q  331 GLU cc_start: 0.8100 (tt0) cc_final: 0.7293 (tm-30)
REVERT: Q  341 LYS cc_start: 0.8074 (tppt) cc_final: 0.7872 (mmmt)
REVERT: U  288 ASN cc_start: 0.6995 (OUTLIER) cc_final: 0.6769 (t0)
REVERT: U  299 MET cc_start: 0.7181 (mtm) cc_final: 0.6967 (mtt)
REVERT: Y  119 LYS cc_start: 0.8464 (mtmm) cc_final: 0.8182 (mtmt)
REVERT: Z    1 MET cc_start: 0.7903 (tmm) cc_final: 0.6933 (tpp)
  outliers start: 24
  outliers final: 13
  residues processed: 105
  average time/residue: 0.0760
  time to fit residues: 10.8727
Evaluate side-chains
  89 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  287 ASP
Chi-restraints excluded: chain O residue  355 LEU
Chi-restraints excluded: chain P residue  205 TYR
Chi-restraints excluded: chain P residue  303 THR
Chi-restraints excluded: chain Q residue  338 ASP
Chi-restraints excluded: chain Q residue  343 THR
Chi-restraints excluded: chain Q residue  346 VAL
Chi-restraints excluded: chain U residue  257 ASN
Chi-restraints excluded: chain U residue  288 ASN
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain Y residue   73 LEU
Chi-restraints excluded: chain Y residue  150 LEU
Chi-restraints excluded: chain Y residue  173 SER
Chi-restraints excluded: chain Z residue   44 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 3 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
O 168 ASN
** Z   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.118774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.086757 restraints weight = 26633.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3764 rms_B_bonded: 5.70
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6845  Z= 0.159
  Angle     :  0.638   9.595   9236  Z= 0.326
  Chirality :  0.042   0.162   1116
  Planarity :  0.003   0.031   1159
  Dihedral  :  4.468  29.824    927
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.24 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.30), residues: 853
  helix:  1.25 (0.23), residues: 540
  sheet:  0.13 (0.53), residues: 109
  loop : -2.30 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG Z  49 
 TYR   0.012   0.002   TYR O 163 
 PHE   0.021   0.002   PHE O 234 
 TRP   0.009   0.001   TRP P 326 
 HIS   0.002   0.000   HIS O 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6845)
  covalent geometry    : angle       0.63820 ( 9236)
  hydrogen bonds       : bond        0.03886 (  447)
  hydrogen bonds       : angle       4.34458 ( 1308)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  201 MET cc_start: 0.7752 (mmp) cc_final: 0.7365 (mmm)
REVERT: O  323 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7112 (mm-30)
REVERT: P  262 ILE cc_start: 0.7145 (mm) cc_final: 0.6895 (mm)
REVERT: Q  336 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8748 (pp)
REVERT: Q  338 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8327 (m-30)
REVERT: U  299 MET cc_start: 0.7420 (mtm) cc_final: 0.7191 (mtt)
REVERT: Y  119 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8268 (mtmt)
REVERT: Z    1 MET cc_start: 0.7943 (tmm) cc_final: 0.7151 (tpp)
  outliers start: 20
  outliers final: 15
  residues processed: 94
  average time/residue: 0.0964
  time to fit residues: 11.9895
Evaluate side-chains
  95 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  167 GLU
Chi-restraints excluded: chain O residue  287 ASP
Chi-restraints excluded: chain O residue  355 LEU
Chi-restraints excluded: chain P residue  203 MET
Chi-restraints excluded: chain P residue  205 TYR
Chi-restraints excluded: chain P residue  303 THR
Chi-restraints excluded: chain Q residue  336 LEU
Chi-restraints excluded: chain Q residue  338 ASP
Chi-restraints excluded: chain Q residue  343 THR
Chi-restraints excluded: chain Q residue  346 VAL
Chi-restraints excluded: chain U residue  257 ASN
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain Y residue   73 LEU
Chi-restraints excluded: chain Y residue  120 LEU
Chi-restraints excluded: chain Y residue  150 LEU
Chi-restraints excluded: chain Z residue   44 GLU
Chi-restraints excluded: chain Z residue   47 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 83 optimal weight:    9.9990
   chunk 59 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 74 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** Z   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z  23 GLN
Z 124 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.119348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.087246 restraints weight = 26628.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 5.70
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.3098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6845  Z= 0.136
  Angle     :  0.646  10.215   9236  Z= 0.327
  Chirality :  0.041   0.186   1116
  Planarity :  0.003   0.031   1159
  Dihedral  :  4.415  29.724    927
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 18.80 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.30), residues: 853
  helix:  1.32 (0.23), residues: 540
  sheet:  0.12 (0.53), residues: 109
  loop : -2.22 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Z  49 
 TYR   0.010   0.001   TYR Y 143 
 PHE   0.017   0.001   PHE P 207 
 TRP   0.009   0.001   TRP P 326 
 HIS   0.001   0.000   HIS U 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6845)
  covalent geometry    : angle       0.64631 ( 9236)
  hydrogen bonds       : bond        0.03814 (  447)
  hydrogen bonds       : angle       4.27662 ( 1308)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.7790 (ptt) cc_final: 0.7539 (ptt)
REVERT: O  201 MET cc_start: 0.7737 (mmp) cc_final: 0.7326 (mmm)
REVERT: P  172 ARG cc_start: 0.6891 (mpp-170) cc_final: 0.6649 (tmt170)
REVERT: P  242 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8062 (mm)
REVERT: P  262 ILE cc_start: 0.6939 (mm) cc_final: 0.6685 (mm)
REVERT: Q  336 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8426 (pp)
REVERT: Q  338 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8373 (m-30)
REVERT: U  299 MET cc_start: 0.7330 (mtm) cc_final: 0.7107 (mtt)
REVERT: Y  119 LYS cc_start: 0.8456 (mtmm) cc_final: 0.8174 (mtmt)
REVERT: Z    1 MET cc_start: 0.7808 (tmm) cc_final: 0.7043 (tpp)
  outliers start: 22
  outliers final: 16
  residues processed: 100
  average time/residue: 0.0946
  time to fit residues: 12.3042
Evaluate side-chains
  99 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  167 GLU
Chi-restraints excluded: chain O residue  276 VAL
Chi-restraints excluded: chain O residue  287 ASP
Chi-restraints excluded: chain O residue  355 LEU
Chi-restraints excluded: chain P residue  203 MET
Chi-restraints excluded: chain P residue  205 TYR
Chi-restraints excluded: chain P residue  242 LEU
Chi-restraints excluded: chain P residue  303 THR
Chi-restraints excluded: chain Q residue  336 LEU
Chi-restraints excluded: chain Q residue  338 ASP
Chi-restraints excluded: chain Q residue  343 THR
Chi-restraints excluded: chain Q residue  346 VAL
Chi-restraints excluded: chain Q residue  378 ILE
Chi-restraints excluded: chain U residue  257 ASN
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain Y residue   73 LEU
Chi-restraints excluded: chain Y residue  150 LEU
Chi-restraints excluded: chain Z residue   44 GLU
Chi-restraints excluded: chain Z residue   47 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 4 optimal weight:   10.0000
   chunk 81 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
Q 283 ASN
** U 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.119143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.091589 restraints weight = 26815.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 5.44
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.3266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6845  Z= 0.148
  Angle     :  0.649  10.603   9236  Z= 0.330
  Chirality :  0.041   0.184   1116
  Planarity :  0.003   0.031   1159
  Dihedral  :  4.429  29.821    927
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 19.23 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.30), residues: 853
  helix:  1.36 (0.23), residues: 531
  sheet:  0.14 (0.53), residues: 109
  loop : -1.96 (0.42), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y  50 
 TYR   0.010   0.001   TYR Y 143 
 PHE   0.014   0.001   PHE O 234 
 TRP   0.008   0.001   TRP P 326 
 HIS   0.002   0.000   HIS U 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6845)
  covalent geometry    : angle       0.64934 ( 9236)
  hydrogen bonds       : bond        0.03890 (  447)
  hydrogen bonds       : angle       4.28570 ( 1308)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.7912 (ptt) cc_final: 0.7452 (ptt)
REVERT: O  201 MET cc_start: 0.7623 (mmp) cc_final: 0.7234 (mmm)
REVERT: O  323 GLU cc_start: 0.8294 (tp30) cc_final: 0.8015 (mm-30)
REVERT: P  172 ARG cc_start: 0.7178 (mpp-170) cc_final: 0.6759 (tmt-80)
REVERT: Q  331 GLU cc_start: 0.7555 (tp30) cc_final: 0.7000 (tm-30)
REVERT: Q  336 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8627 (pp)
REVERT: Q  338 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8360 (m-30)
REVERT: U  299 MET cc_start: 0.7311 (mtm) cc_final: 0.7090 (mtt)
REVERT: Y   80 GLN cc_start: 0.8328 (pp30) cc_final: 0.8042 (mm110)
REVERT: Y  119 LYS cc_start: 0.8490 (mtmm) cc_final: 0.8247 (mtmt)
REVERT: Z    1 MET cc_start: 0.7670 (tmm) cc_final: 0.7022 (tpp)
  outliers start: 22
  outliers final: 17
  residues processed: 94
  average time/residue: 0.0872
  time to fit residues: 10.7567
Evaluate side-chains
  99 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  167 GLU
Chi-restraints excluded: chain O residue  276 VAL
Chi-restraints excluded: chain O residue  287 ASP
Chi-restraints excluded: chain O residue  355 LEU
Chi-restraints excluded: chain P residue  203 MET
Chi-restraints excluded: chain P residue  205 TYR
Chi-restraints excluded: chain P residue  303 THR
Chi-restraints excluded: chain P residue  348 TYR
Chi-restraints excluded: chain Q residue  336 LEU
Chi-restraints excluded: chain Q residue  338 ASP
Chi-restraints excluded: chain Q residue  343 THR
Chi-restraints excluded: chain Q residue  346 VAL
Chi-restraints excluded: chain U residue  257 ASN
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain Y residue   73 LEU
Chi-restraints excluded: chain Y residue  120 LEU
Chi-restraints excluded: chain Y residue  150 LEU
Chi-restraints excluded: chain Z residue   44 GLU
Chi-restraints excluded: chain Z residue   47 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 66 optimal weight:    0.2980
   chunk 33 optimal weight:    0.8980
   chunk 35 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0770
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** U 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.120768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.088486 restraints weight = 26545.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3805 rms_B_bonded: 5.88
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6845  Z= 0.117
  Angle     :  0.630  10.554   9236  Z= 0.317
  Chirality :  0.040   0.177   1116
  Planarity :  0.003   0.032   1159
  Dihedral  :  4.313  29.248    927
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 19.80 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.30), residues: 853
  helix:  1.48 (0.23), residues: 531
  sheet:  0.17 (0.54), residues: 109
  loop : -1.81 (0.43), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG Q 347 
 TYR   0.012   0.001   TYR Y 143 
 PHE   0.023   0.001   PHE P 207 
 TRP   0.008   0.001   TRP P 326 
 HIS   0.001   0.000   HIS U 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 6845)
  covalent geometry    : angle       0.62993 ( 9236)
  hydrogen bonds       : bond        0.03659 (  447)
  hydrogen bonds       : angle       4.12074 ( 1308)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.7871 (ptt) cc_final: 0.7311 (ptt)
REVERT: O  201 MET cc_start: 0.7685 (mmp) cc_final: 0.7223 (mmm)
REVERT: P  242 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7975 (mm)
REVERT: Q  331 GLU cc_start: 0.7600 (tp30) cc_final: 0.7227 (tm-30)
REVERT: Q  336 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8202 (pp)
REVERT: Q  338 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8394 (m-30)
REVERT: Y  162 SER cc_start: 0.8382 (m) cc_final: 0.8127 (m)
REVERT: Z    1 MET cc_start: 0.7759 (tmm) cc_final: 0.7019 (tpp)
  outliers start: 20
  outliers final: 13
  residues processed: 102
  average time/residue: 0.0892
  time to fit residues: 12.0618
Evaluate side-chains
  94 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  167 GLU
Chi-restraints excluded: chain O residue  276 VAL
Chi-restraints excluded: chain O residue  287 ASP
Chi-restraints excluded: chain O residue  355 LEU
Chi-restraints excluded: chain P residue  242 LEU
Chi-restraints excluded: chain P residue  303 THR
Chi-restraints excluded: chain P residue  348 TYR
Chi-restraints excluded: chain Q residue  336 LEU
Chi-restraints excluded: chain Q residue  338 ASP
Chi-restraints excluded: chain Q residue  343 THR
Chi-restraints excluded: chain Q residue  346 VAL
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain Y residue   73 LEU
Chi-restraints excluded: chain Y residue  120 LEU
Chi-restraints excluded: chain Y residue  150 LEU
Chi-restraints excluded: chain Z residue   47 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 22 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 63 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
U 288 ASN
** Z   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.119156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.086707 restraints weight = 26327.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 5.79
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.3527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   6845  Z= 0.160
  Angle     :  0.685  10.394   9236  Z= 0.354
  Chirality :  0.043   0.232   1116
  Planarity :  0.003   0.031   1159
  Dihedral  :  4.408  30.593    927
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.09 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.30), residues: 853
  helix:  1.45 (0.23), residues: 528
  sheet:  0.15 (0.54), residues: 109
  loop : -1.86 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG Q 347 
 TYR   0.014   0.002   TYR O 163 
 PHE   0.023   0.002   PHE U 295 
 TRP   0.009   0.001   TRP Z  42 
 HIS   0.004   0.001   HIS U 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6845)
  covalent geometry    : angle       0.68465 ( 9236)
  hydrogen bonds       : bond        0.04020 (  447)
  hydrogen bonds       : angle       4.37361 ( 1308)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.7913 (ptt) cc_final: 0.7409 (ptt)
REVERT: P  242 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7992 (mm)
REVERT: Q  331 GLU cc_start: 0.7725 (tp30) cc_final: 0.7341 (tm-30)
REVERT: Q  338 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8489 (m-30)
REVERT: Y   80 GLN cc_start: 0.8403 (pp30) cc_final: 0.8150 (mm110)
REVERT: Y  119 LYS cc_start: 0.8618 (mtmt) cc_final: 0.8278 (mtmm)
REVERT: Z    1 MET cc_start: 0.8230 (tmm) cc_final: 0.7596 (tpp)
  outliers start: 21
  outliers final: 16
  residues processed: 96
  average time/residue: 0.0941
  time to fit residues: 11.8116
Evaluate side-chains
  97 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  167 GLU
Chi-restraints excluded: chain O residue  276 VAL
Chi-restraints excluded: chain O residue  287 ASP
Chi-restraints excluded: chain O residue  355 LEU
Chi-restraints excluded: chain P residue  203 MET
Chi-restraints excluded: chain P residue  242 LEU
Chi-restraints excluded: chain P residue  303 THR
Chi-restraints excluded: chain P residue  348 TYR
Chi-restraints excluded: chain Q residue  338 ASP
Chi-restraints excluded: chain Q residue  343 THR
Chi-restraints excluded: chain Q residue  346 VAL
Chi-restraints excluded: chain U residue  257 ASN
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain Y residue   45 GLN
Chi-restraints excluded: chain Y residue   73 LEU
Chi-restraints excluded: chain Y residue  120 LEU
Chi-restraints excluded: chain Y residue  150 LEU
Chi-restraints excluded: chain Z residue   47 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0470
   chunk 15 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 72 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.9480

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.120368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.090011 restraints weight = 27132.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 5.45
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   6845  Z= 0.144
  Angle     :  0.693  10.553   9236  Z= 0.356
  Chirality :  0.043   0.212   1116
  Planarity :  0.003   0.032   1159
  Dihedral  :  4.401  30.989    927
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 20.23 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.30), residues: 853
  helix:  1.41 (0.23), residues: 534
  sheet:  0.16 (0.53), residues: 109
  loop : -1.78 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG Q 347 
 TYR   0.011   0.001   TYR O 170 
 PHE   0.032   0.002   PHE U 295 
 TRP   0.008   0.001   TRP P 326 
 HIS   0.001   0.000   HIS U 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6845)
  covalent geometry    : angle       0.69326 ( 9236)
  hydrogen bonds       : bond        0.04059 (  447)
  hydrogen bonds       : angle       4.36501 ( 1308)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.7919 (ptt) cc_final: 0.7370 (ptt)
REVERT: P  242 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7947 (mm)
REVERT: Q  331 GLU cc_start: 0.7666 (tp30) cc_final: 0.7259 (tm-30)
REVERT: Q  338 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8472 (m-30)
REVERT: Y   80 GLN cc_start: 0.8383 (pp30) cc_final: 0.8138 (mm110)
REVERT: Y  119 LYS cc_start: 0.8616 (mtmt) cc_final: 0.8286 (mtmm)
REVERT: Z    1 MET cc_start: 0.8259 (tmm) cc_final: 0.7686 (tpp)
  outliers start: 18
  outliers final: 15
  residues processed: 94
  average time/residue: 0.0952
  time to fit residues: 11.8216
Evaluate side-chains
  96 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  167 GLU
Chi-restraints excluded: chain O residue  276 VAL
Chi-restraints excluded: chain O residue  287 ASP
Chi-restraints excluded: chain O residue  355 LEU
Chi-restraints excluded: chain P residue  203 MET
Chi-restraints excluded: chain P residue  242 LEU
Chi-restraints excluded: chain P residue  303 THR
Chi-restraints excluded: chain P residue  348 TYR
Chi-restraints excluded: chain Q residue  338 ASP
Chi-restraints excluded: chain Q residue  343 THR
Chi-restraints excluded: chain Q residue  346 VAL
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain Y residue   45 GLN
Chi-restraints excluded: chain Y residue   73 LEU
Chi-restraints excluded: chain Y residue  120 LEU
Chi-restraints excluded: chain Y residue  150 LEU
Chi-restraints excluded: chain Z residue   47 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 1 optimal weight:    0.2980
   chunk 44 optimal weight:    7.9990
   chunk 28 optimal weight:    0.0370
   chunk 84 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 59 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0980
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    7.9990
   overall best weight:    0.3458

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.122239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.092241 restraints weight = 27187.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3838 rms_B_bonded: 5.74
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7124
moved from start:          0.3631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6845  Z= 0.125
  Angle     :  0.684  10.568   9236  Z= 0.348
  Chirality :  0.042   0.201   1116
  Planarity :  0.003   0.032   1159
  Dihedral  :  4.302  29.910    927
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 21.23 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.30), residues: 853
  helix:  1.50 (0.23), residues: 536
  sheet:  0.19 (0.53), residues: 109
  loop : -1.77 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG Q 347 
 TYR   0.012   0.001   TYR Y 143 
 PHE   0.025   0.002   PHE P 207 
 TRP   0.007   0.001   TRP P 326 
 HIS   0.001   0.000   HIS U 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6845)
  covalent geometry    : angle       0.68446 ( 9236)
  hydrogen bonds       : bond        0.03877 (  447)
  hydrogen bonds       : angle       4.23850 ( 1308)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1866.05 seconds
wall clock time: 32 minutes 36.54 seconds (1956.54 seconds total)