Starting phenix.real_space_refine
on Thu Nov 14 16:52:38 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovx_17225/11_2024/8ovx_17225.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovx_17225/11_2024/8ovx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovx_17225/11_2024/8ovx_17225.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovx_17225/11_2024/8ovx_17225.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovx_17225/11_2024/8ovx_17225.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovx_17225/11_2024/8ovx_17225.cif"
  }
  resolution = 3.4
  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=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          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, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2}
          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, 'GLU:plan': 7, 'HIS:plan': 1, 'ASP:plan': 4}
          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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5}
          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: {'PHE:plan': 1, 'GLU:plan': 11, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 6}
          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: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 3, 'TYR:plan': 1, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 60
  Time building chain proxies: 4.44, per 1000 atoms: 0.66
  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: 1.67
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.70
  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: 2.13

  Time building geometry restraints manager: 1.94 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:             0.250
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     19.690
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.130
-------------------------------------------------------------------------------
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= 0.252
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.28), 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
 TRP   0.043   0.003   TRP P 215 
 HIS   0.003   0.001   HIS U 237 
 PHE   0.056   0.002   PHE P 207 
 TYR   0.024   0.003   TYR Z  43 
 ARG   0.012   0.001   ARG Z  49 

*********************** 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  : 0.900 
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: 0.2249
  time to fit residues: 36.2733
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  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 64 optimal weight:    0.6980
   chunk 35 optimal weight:   30.0000
   chunk 22 optimal weight:    0.0970
   chunk 43 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
O 231 ASN
U 288 ASN
U 294 HIS
** Y  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  80 GLN
Y 170 GLN
** Z   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z  47 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6995
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6845  Z= 0.167
  Angle     :  0.642   8.778   9236  Z= 0.330
  Chirality :  0.042   0.168   1116
  Planarity :  0.004   0.040   1159
  Dihedral  :  4.653  28.095    927
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.68 %
    Favored  : 87.75 %
  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: -0.09 (0.29), residues: 853
  helix:  0.77 (0.22), residues: 542
  sheet: -0.25 (0.52), residues: 105
  loop : -2.07 (0.44), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP P 215 
 HIS   0.002   0.000   HIS U 237 
 PHE   0.013   0.001   PHE Z  25 
 TYR   0.017   0.002   TYR Z  43 
 ARG   0.006   0.001   ARG O 227 

*********************** 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
  109 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.7609 (ptt) cc_final: 0.7113 (ptt)
REVERT: O  267 PHE cc_start: 0.7797 (t80) cc_final: 0.7388 (t80)
REVERT: P  262 ILE cc_start: 0.6603 (mm) cc_final: 0.6233 (mm)
REVERT: Q  331 GLU cc_start: 0.7963 (tt0) cc_final: 0.6895 (tm-30)
REVERT: U  299 MET cc_start: 0.7096 (mtm) cc_final: 0.6742 (mtt)
REVERT: Y  119 LYS cc_start: 0.8473 (mtmm) cc_final: 0.8091 (mtmm)
REVERT: Z    1 MET cc_start: 0.7638 (tmm) cc_final: 0.7079 (tpt)
  outliers start: 11
  outliers final: 9
  residues processed: 105
  average time/residue: 0.2145
  time to fit residues: 29.4086
Evaluate side-chains
  92 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
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  205 TYR
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 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 42 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 76 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
O 168 ASN
P 160 HIS
** 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: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6845  Z= 0.157
  Angle     :  0.639  11.551   9236  Z= 0.320
  Chirality :  0.041   0.166   1116
  Planarity :  0.003   0.036   1159
  Dihedral  :  4.404  28.172    927
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 13.39 %
    Favored  : 84.33 %
  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:  0.32 (0.30), residues: 853
  helix:  1.11 (0.23), residues: 544
  sheet: -0.06 (0.53), residues: 102
  loop : -2.00 (0.44), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP P 215 
 HIS   0.001   0.000   HIS U 294 
 PHE   0.016   0.001   PHE Z  22 
 TYR   0.013   0.001   TYR Z  43 
 ARG   0.005   0.000   ARG Z  52 

*********************** 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
  101 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.7845 (ptt) cc_final: 0.7181 (ptt)
REVERT: O  201 MET cc_start: 0.7665 (mmp) cc_final: 0.6565 (tpp)
REVERT: O  267 PHE cc_start: 0.8100 (t80) cc_final: 0.7588 (t80)
REVERT: P  262 ILE cc_start: 0.6637 (mm) cc_final: 0.6321 (mm)
REVERT: Q  331 GLU cc_start: 0.8110 (tt0) cc_final: 0.7232 (tm-30)
REVERT: U  299 MET cc_start: 0.6991 (mtm) cc_final: 0.6664 (mtt)
REVERT: Y  119 LYS cc_start: 0.8473 (mtmm) cc_final: 0.8100 (mtmm)
REVERT: Z    1 MET cc_start: 0.6840 (tmm) cc_final: 0.5702 (tpp)
  outliers start: 16
  outliers final: 12
  residues processed: 96
  average time/residue: 0.1468
  time to fit residues: 19.2858
Evaluate side-chains
  91 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
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  205 TYR
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 Y residue  173 SER
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 76 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 40 optimal weight:    8.9990
   chunk 8 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 82 optimal weight:   10.0000
   chunk 73 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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**
Z  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.2518

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= 0.169
  Angle     :  0.610   9.736   9236  Z= 0.309
  Chirality :  0.041   0.161   1116
  Planarity :  0.003   0.034   1159
  Dihedral  :  4.342  28.427    927
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 14.10 %
    Favored  : 82.62 %
  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:  0.53 (0.30), residues: 853
  helix:  1.31 (0.23), residues: 541
  sheet:  0.09 (0.52), residues: 107
  loop : -2.08 (0.43), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP P 215 
 HIS   0.002   0.000   HIS U 294 
 PHE   0.018   0.001   PHE O 234 
 TYR   0.012   0.001   TYR P 187 
 ARG   0.005   0.000   ARG Z  49 

*********************** 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
  112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.7799 (ptt) cc_final: 0.7151 (ptt)
REVERT: O  201 MET cc_start: 0.7792 (mmp) cc_final: 0.6557 (tpp)
REVERT: O  323 GLU cc_start: 0.7914 (tp30) cc_final: 0.7710 (mm-30)
REVERT: P  262 ILE cc_start: 0.6783 (mm) cc_final: 0.6489 (mm)
REVERT: Q  331 GLU cc_start: 0.8014 (tt0) cc_final: 0.7179 (tm-30)
REVERT: Q  374 MET cc_start: 0.6116 (ppp) cc_final: 0.5707 (ppp)
REVERT: U  299 MET cc_start: 0.7000 (mtm) cc_final: 0.6689 (mtt)
REVERT: Y  119 LYS cc_start: 0.8471 (mtmm) cc_final: 0.8151 (mtmt)
REVERT: Z    1 MET cc_start: 0.6925 (tmm) cc_final: 0.6402 (tpp)
REVERT: Z   15 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9335 (pp)
  outliers start: 23
  outliers final: 15
  residues processed: 105
  average time/residue: 0.1985
  time to fit residues: 28.1488
Evaluate side-chains
  96 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
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  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  117 VAL
Chi-restraints excluded: chain Y residue  120 LEU
Chi-restraints excluded: chain Y residue  150 LEU
Chi-restraints excluded: chain Y residue  173 SER
Chi-restraints excluded: chain Z residue   15 LEU
Chi-restraints excluded: chain Z residue   44 GLU
Chi-restraints excluded: chain Z residue   47 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 33 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0970
   chunk 0 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 73 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
Q 283 ASN
** Y  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6845  Z= 0.178
  Angle     :  0.642  10.525   9236  Z= 0.324
  Chirality :  0.041   0.193   1116
  Planarity :  0.003   0.032   1159
  Dihedral  :  4.312  28.879    927
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.52 %
    Favored  : 80.63 %
  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:  0.64 (0.30), residues: 853
  helix:  1.39 (0.23), residues: 540
  sheet:  0.23 (0.52), residues: 109
  loop : -2.08 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP P 326 
 HIS   0.001   0.000   HIS U 237 
 PHE   0.024   0.002   PHE O 267 
 TYR   0.012   0.001   TYR P 187 
 ARG   0.011   0.001   ARG Z  52 

*********************** 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
  109 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.7642 (ptt) cc_final: 0.7048 (ptt)
REVERT: O  201 MET cc_start: 0.7808 (mmp) cc_final: 0.6852 (tpp)
REVERT: P  262 ILE cc_start: 0.6703 (mm) cc_final: 0.6480 (mm)
REVERT: Q  331 GLU cc_start: 0.7923 (tt0) cc_final: 0.7149 (tm-30)
REVERT: Q  374 MET cc_start: 0.6156 (ppp) cc_final: 0.5711 (ppp)
REVERT: U  299 MET cc_start: 0.6863 (mtm) cc_final: 0.6545 (mtt)
REVERT: Y  119 LYS cc_start: 0.8420 (mtmm) cc_final: 0.8156 (mtmt)
REVERT: Z    1 MET cc_start: 0.6940 (tmm) cc_final: 0.6445 (tpp)
  outliers start: 20
  outliers final: 14
  residues processed: 101
  average time/residue: 0.1802
  time to fit residues: 25.0125
Evaluate side-chains
  98 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
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  203 MET
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  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 Y residue  173 SER
Chi-restraints excluded: chain Z residue   44 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 82 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 27 optimal weight:    1.9990
   chunk 43 optimal weight:    7.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
O 261 HIS
P 223 ASN
** U 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 124 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6845  Z= 0.324
  Angle     :  0.726  10.446   9236  Z= 0.374
  Chirality :  0.045   0.222   1116
  Planarity :  0.004   0.031   1159
  Dihedral  :  4.694  30.962    927
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 16.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 17.81 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (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:  0.29 (0.29), residues: 853
  helix:  1.05 (0.22), residues: 536
  sheet:  0.56 (0.58), residues: 96
  loop : -2.09 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P 326 
 HIS   0.003   0.001   HIS Z   8 
 PHE   0.018   0.002   PHE P 207 
 TYR   0.016   0.002   TYR Y 197 
 ARG   0.006   0.001   ARG Z  49 

*********************** 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: 23
    poor density    : 86
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.8068 (ptt) cc_final: 0.7586 (ptt)
REVERT: O  201 MET cc_start: 0.7597 (mmp) cc_final: 0.6840 (tpp)
REVERT: P  172 ARG cc_start: 0.6822 (mpp-170) cc_final: 0.6615 (tmt170)
REVERT: Q  338 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8377 (m-30)
REVERT: U  299 MET cc_start: 0.7127 (mtm) cc_final: 0.6764 (mtt)
REVERT: Z    1 MET cc_start: 0.7656 (tmm) cc_final: 0.7227 (tpp)
  outliers start: 23
  outliers final: 14
  residues processed: 98
  average time/residue: 0.2104
  time to fit residues: 27.4896
Evaluate side-chains
  93 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
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  203 MET
Chi-restraints excluded: chain P residue  205 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 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  120 LEU
Chi-restraints excluded: chain Y residue  150 LEU
Chi-restraints excluded: chain Z residue   44 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 69 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   chunk 50 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
P 223 ASN
** Z   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7071
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      :  0.003   0.038   6845  Z= 0.189
  Angle     :  0.679  12.699   9236  Z= 0.338
  Chirality :  0.042   0.183   1116
  Planarity :  0.003   0.029   1159
  Dihedral  :  4.507  30.966    927
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.66 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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 (0.30), residues: 853
  helix:  1.43 (0.23), residues: 525
  sheet:  0.24 (0.53), residues: 109
  loop : -1.91 (0.42), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP P 326 
 HIS   0.002   0.000   HIS U 294 
 PHE   0.020   0.001   PHE P 207 
 TYR   0.015   0.002   TYR O 170 
 ARG   0.003   0.000   ARG Z  52 

*********************** 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
  108 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.7805 (ptt) cc_final: 0.7411 (ptt)
REVERT: O  201 MET cc_start: 0.7593 (mmp) cc_final: 0.6820 (tpp)
REVERT: Q  336 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8369 (pp)
REVERT: Q  338 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8345 (m-30)
REVERT: Q  374 MET cc_start: 0.5663 (ppp) cc_final: 0.5349 (ppp)
REVERT: U  299 MET cc_start: 0.6947 (mtm) cc_final: 0.6702 (mtt)
REVERT: Y   80 GLN cc_start: 0.8353 (pp30) cc_final: 0.8127 (mm110)
REVERT: Y  119 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8092 (mtmm)
REVERT: Y  151 ILE cc_start: 0.6708 (OUTLIER) cc_final: 0.6216 (tp)
REVERT: Z    1 MET cc_start: 0.7120 (tmm) cc_final: 0.6491 (tpp)
  outliers start: 23
  outliers final: 14
  residues processed: 96
  average time/residue: 0.2135
  time to fit residues: 27.0633
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  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 Y residue  151 ILE
Chi-restraints excluded: chain Z residue   15 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 48 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 15 optimal weight:    8.9990
   chunk 52 optimal weight:    6.9990
   chunk 55 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 74 optimal weight:    6.9990
   chunk 78 optimal weight:    7.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** 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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6845  Z= 0.235
  Angle     :  0.696  11.597   9236  Z= 0.352
  Chirality :  0.042   0.172   1116
  Planarity :  0.003   0.030   1159
  Dihedral  :  4.492  31.172    927
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 20.09 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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 (0.30), residues: 853
  helix:  1.38 (0.23), residues: 528
  sheet:  0.23 (0.53), residues: 109
  loop : -1.84 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P 326 
 HIS   0.002   0.001   HIS P 164 
 PHE   0.022   0.002   PHE P 207 
 TYR   0.017   0.002   TYR O 170 
 ARG   0.005   0.001   ARG Q 347 

*********************** 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
  107 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.7908 (ptt) cc_final: 0.7475 (ptt)
REVERT: O  201 MET cc_start: 0.7591 (mmp) cc_final: 0.6806 (tpp)
REVERT: Q  277 MET cc_start: 0.4073 (tpp) cc_final: 0.3760 (mmp)
REVERT: Q  336 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8497 (pp)
REVERT: Q  338 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8400 (m-30)
REVERT: Q  374 MET cc_start: 0.5836 (ppp) cc_final: 0.5392 (ppp)
REVERT: U  299 MET cc_start: 0.7027 (mtm) cc_final: 0.6761 (mtt)
REVERT: U  314 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7661 (mm-30)
REVERT: Y  151 ILE cc_start: 0.6778 (OUTLIER) cc_final: 0.6276 (tp)
REVERT: Z    1 MET cc_start: 0.7728 (tmm) cc_final: 0.7200 (tpp)
REVERT: Z  125 MET cc_start: 0.9051 (ppp) cc_final: 0.8847 (ppp)
  outliers start: 22
  outliers final: 18
  residues processed: 98
  average time/residue: 0.2048
  time to fit residues: 26.8038
Evaluate side-chains
  98 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  165 LEU
Chi-restraints excluded: chain P residue  203 MET
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 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   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 Y residue  151 ILE
Chi-restraints excluded: chain Z residue   15 LEU
Chi-restraints excluded: chain Z residue   44 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 76 optimal weight:    0.8980
   chunk 78 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 59 optimal weight:    0.4980
   chunk 23 optimal weight:    0.7980
   chunk 68 optimal weight:   10.0000
   chunk 72 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
moved from start:          0.3529

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= 0.182
  Angle     :  0.693  11.627   9236  Z= 0.349
  Chirality :  0.042   0.209   1116
  Planarity :  0.003   0.030   1159
  Dihedral  :  4.410  31.123    927
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.80 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (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:  0.83 (0.30), residues: 853
  helix:  1.57 (0.23), residues: 525
  sheet:  0.21 (0.53), residues: 109
  loop : -1.79 (0.43), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P 326 
 HIS   0.001   0.000   HIS P 164 
 PHE   0.025   0.001   PHE P 207 
 TYR   0.015   0.001   TYR O 170 
 ARG   0.005   0.000   ARG Q 347 

*********************** 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
  111 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.7749 (ptt) cc_final: 0.7356 (ptt)
REVERT: O  201 MET cc_start: 0.7598 (mmp) cc_final: 0.6803 (tpp)
REVERT: Q  277 MET cc_start: 0.4331 (tpp) cc_final: 0.4121 (mmp)
REVERT: Q  336 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8361 (pp)
REVERT: Q  338 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8356 (m-30)
REVERT: Q  374 MET cc_start: 0.5639 (ppp) cc_final: 0.5202 (ppp)
REVERT: U  299 MET cc_start: 0.7107 (mtm) cc_final: 0.6851 (mtt)
REVERT: U  314 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7919 (mm-30)
REVERT: Y   80 GLN cc_start: 0.8322 (pp30) cc_final: 0.8094 (mm110)
REVERT: Y  151 ILE cc_start: 0.6611 (OUTLIER) cc_final: 0.6059 (tp)
REVERT: Y  162 SER cc_start: 0.8276 (m) cc_final: 0.8034 (m)
REVERT: Z    1 MET cc_start: 0.7226 (tmm) cc_final: 0.6628 (tpp)
REVERT: Z  125 MET cc_start: 0.8907 (ppp) cc_final: 0.8647 (ppp)
  outliers start: 21
  outliers final: 16
  residues processed: 100
  average time/residue: 0.2187
  time to fit residues: 28.8638
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  : 0.858 
-------------------------------------------------------------------------------
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  165 LEU
Chi-restraints excluded: chain P residue  203 MET
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   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 Y residue  151 ILE
Chi-restraints excluded: chain Z residue   15 LEU
Chi-restraints excluded: chain Z residue   44 GLU
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 49 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 56 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
U 243 GLN
** 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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7063
moved from start:          0.3645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6845  Z= 0.214
  Angle     :  0.708  11.306   9236  Z= 0.358
  Chirality :  0.041   0.184   1116
  Planarity :  0.003   0.030   1159
  Dihedral  :  4.402  31.205    927
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 20.09 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  0.78 (0.30), residues: 853
  helix:  1.53 (0.23), residues: 528
  sheet:  0.19 (0.53), residues: 109
  loop : -1.85 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P 326 
 HIS   0.002   0.000   HIS U 237 
 PHE   0.027   0.001   PHE P 207 
 TYR   0.015   0.001   TYR O 170 
 ARG   0.007   0.001   ARG Z  49 

********************** 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
  104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  172 MET cc_start: 0.7782 (ptt) cc_final: 0.7369 (ptt)
REVERT: O  201 MET cc_start: 0.7600 (mmp) cc_final: 0.6795 (tpp)
REVERT: P  165 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8437 (tp)
REVERT: Q  336 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7988 (pp)
REVERT: Q  338 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8399 (m-30)
REVERT: Q  374 MET cc_start: 0.5667 (ppp) cc_final: 0.5177 (ppp)
REVERT: U  299 MET cc_start: 0.6948 (mtm) cc_final: 0.6712 (mtt)
REVERT: Y   80 GLN cc_start: 0.8338 (pp30) cc_final: 0.8097 (mm110)
REVERT: Y  151 ILE cc_start: 0.6665 (OUTLIER) cc_final: 0.6124 (tp)
REVERT: Z    1 MET cc_start: 0.7739 (tmm) cc_final: 0.7224 (tpp)
  outliers start: 20
  outliers final: 14
  residues processed: 93
  average time/residue: 0.2214
  time to fit residues: 27.0285
Evaluate side-chains
  99 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  165 LEU
Chi-restraints excluded: chain P residue  203 MET
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   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 Y residue  151 ILE
Chi-restraints excluded: chain Z residue   15 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 67 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0670
   chunk 69 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 12 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    1.1122

-------------------------------------------------------------------------------
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**
Z  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.119553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.087254 restraints weight = 26078.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3772 rms_B_bonded: 5.74
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.3732

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= 0.217
  Angle     :  0.724  11.186   9236  Z= 0.369
  Chirality :  0.042   0.168   1116
  Planarity :  0.003   0.034   1159
  Dihedral  :  4.470  31.317    927
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 20.09 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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 (0.30), residues: 853
  helix:  1.45 (0.23), residues: 534
  sheet:  0.15 (0.53), residues: 109
  loop : -1.78 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP Z  42 
 HIS   0.002   0.000   HIS P 164 
 PHE   0.027   0.002   PHE P 207 
 TYR   0.018   0.002   TYR U 302 
 ARG   0.005   0.000   ARG Q 347 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1558.06 seconds
wall clock time: 35 minutes 35.86 seconds (2135.86 seconds total)