Starting phenix.real_space_refine
on Wed Apr 30 17:07:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f24_31427/04_2025/7f24_31427.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f24_31427/04_2025/7f24_31427.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f24_31427/04_2025/7f24_31427.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f24_31427/04_2025/7f24_31427.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f24_31427/04_2025/7f24_31427.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f24_31427/04_2025/7f24_31427.cif"
  }
  resolution = 4.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3054 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      47      5.16       5
     C    4549      2.51       5
     N    1251      2.21       5
     O    1315      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7165
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1860
          Classifications: {'peptide': 226}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "F"
      Number of atoms: 2208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2208
          Classifications: {'peptide': 277}
          Link IDs: {'PTRANS': 9, 'TRANS': 267}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2629
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 341, 2605
          Classifications: {'peptide': 341}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
      Conformer: "B"
        Number of residues, atoms: 341, 2605
          Classifications: {'peptide': 341}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
          bond proxies already assigned to first conformer: 2624
    Chain: "D"
      Number of atoms: 425
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 425
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Unusual residues: {'LDP': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AASP B  27 " occ=0.45
      ... (14 atoms not shown)
      pdb=" OD2BASP B  27 " occ=0.55
  Time building chain proxies: 5.27, per 1000 atoms: 0.74
  Number of scatterers: 7165
  At special positions: 0
  Unit cell: (79.351, 94.569, 115.222, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      47     16.00
     P       3     15.00
     O    1315      8.00
     N    1251      7.00
     C    4549      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS F  96 " - pdb=" SG  CYS F 186 " distance=2.02

  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: 1.86
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 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:
      29 helices and 8 sheets defined
      50.4% alpha, 18.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 39
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 232 through 237
      removed outlier: 3.633A  pdb=" N   CYS A 237 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.589A  pdb=" N   PHE A 312 " --> pdb=" O   GLU A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 4.232A  pdb=" N   ARG A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.942A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 391
    Processing helix  chain 'F' and resid 21 through 51
    Processing helix  chain 'F' and resid 51 through 56
      removed outlier: 3.627A  pdb=" N   ARG F  55 " --> pdb=" O   PHE F  51 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 58 through 77
      removed outlier: 3.981A  pdb=" N   PHE F  62 " --> pdb=" O   VAL F  58 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   VAL F  63 " --> pdb=" O   THR F  59 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 77 through 88
    Processing helix  chain 'F' and resid 92 through 94
      No H-bonds generated for 'chain 'F' and resid 92 through 94'
    Processing helix  chain 'F' and resid 95 through 127
      removed outlier: 4.018A  pdb=" N   ILE F 111 " --> pdb=" O   SER F 107 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   SER F 127 " --> pdb=" O   TRP F 123 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 127 through 135
    Processing helix  chain 'F' and resid 136 through 161
      Proline residue:  F 158  - end of helix
    Processing helix  chain 'F' and resid 191 through 203
    Processing helix  chain 'F' and resid 203 through 237
    Processing helix  chain 'F' and resid 265 through 298
      Proline residue:  F 287  - end of helix
      Proline residue:  F 296  - end of helix
    Processing helix  chain 'F' and resid 309 through 332
      removed outlier: 3.659A  pdb=" N   SER F 324 " --> pdb=" O   GLY F 320 " (cutoff:3.500A)
      Proline residue:  F 328  - end of helix
    Processing helix  chain 'F' and resid 334 through 346
    Processing helix  chain 'B' and resid 2 through 25
      removed outlier: 3.899A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'D' and resid 9 through 24
    Processing helix  chain 'D' and resid 29 through 44
    Processing helix  chain 'D' and resid 45 through 48
    Processing helix  chain 'D' and resid 55 through 59
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 9.211A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.027A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.467A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.659A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.747A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.974A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.812A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ALA B 167 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.699A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.581A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.883A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.830A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)

    388 hydrogen bonds defined for protein.
    1131 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: 2.09

  Time building geometry restraints manager: 2.15 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2321
        1.34 -     1.46: 1562
        1.46 -     1.58: 3366
        1.58 -     1.69: 5
        1.69 -     1.81: 64
  Bond restraints: 7318
  Sorted by residual:
  bond pdb=" CA  SER F 110 "
       pdb=" C   SER F 110 "
    ideal  model  delta    sigma   weight residual
    1.524  1.495  0.029 1.24e-02 6.50e+03 5.37e+00
  bond pdb=" CB  TRP F 148 "
       pdb=" CG  TRP F 148 "
    ideal  model  delta    sigma   weight residual
    1.498  1.427  0.071 3.10e-02 1.04e+03 5.20e+00
  bond pdb=" CA  ASN A 371 "
       pdb=" C   ASN A 371 "
    ideal  model  delta    sigma   weight residual
    1.518  1.429  0.089 4.01e-02 6.22e+02 4.97e+00
  bond pdb=" CB  TRP F 318 "
       pdb=" CG  TRP F 318 "
    ideal  model  delta    sigma   weight residual
    1.498  1.432  0.066 3.10e-02 1.04e+03 4.51e+00
  bond pdb=" CB  PHE F  62 "
       pdb=" CG  PHE F  62 "
    ideal  model  delta    sigma   weight residual
    1.502  1.455  0.047 2.30e-02 1.89e+03 4.25e+00
  ... (remaining 7313 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 9390
        2.12 -     4.24: 473
        4.24 -     6.37: 53
        6.37 -     8.49: 9
        8.49 -    10.61: 4
  Bond angle restraints: 9929
  Sorted by residual:
  angle pdb=" C   PHE A 238 "
        pdb=" N   ASN A 239 "
        pdb=" CA  ASN A 239 "
      ideal   model   delta    sigma   weight residual
     121.18  128.28   -7.10 1.98e+00 2.55e-01 1.28e+01
  angle pdb=" C   PHE A 222 "
        pdb=" CA  PHE A 222 "
        pdb=" CB  PHE A 222 "
      ideal   model   delta    sigma   weight residual
     109.70  103.24    6.46 1.81e+00 3.05e-01 1.27e+01
  angle pdb=" N   HIS A  41 "
        pdb=" CA  HIS A  41 "
        pdb=" C   HIS A  41 "
      ideal   model   delta    sigma   weight residual
     108.41  114.07   -5.66 1.61e+00 3.86e-01 1.24e+01
  angle pdb=" C   LYS A 211 "
        pdb=" N   PHE A 212 "
        pdb=" CA  PHE A 212 "
      ideal   model   delta    sigma   weight residual
     122.29  116.69    5.60 1.65e+00 3.67e-01 1.15e+01
  angle pdb=" N   GLY B 131 "
        pdb=" CA  GLY B 131 "
        pdb=" C   GLY B 131 "
      ideal   model   delta    sigma   weight residual
     113.18  121.12   -7.94 2.37e+00 1.78e-01 1.12e+01
  ... (remaining 9924 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.37: 4253
       34.37 -    68.74: 85
       68.74 -   103.11: 8
      103.11 -   137.48: 1
      137.48 -   171.85: 2
  Dihedral angle restraints: 4349
    sinusoidal: 1707
      harmonic: 2642
  Sorted by residual:
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -118.88 -171.85     1      2.00e+01 2.50e-03 4.78e+01
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -50.08  154.67     1      2.00e+01 2.50e-03 4.57e+01
  dihedral pdb=" O3A GTP A 401 "
           pdb=" O3B GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PG  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.21   56.51 -112.72     1      2.00e+01 2.50e-03 3.33e+01
  ... (remaining 4346 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 613
       0.039 -    0.078: 336
       0.078 -    0.117: 128
       0.117 -    0.155: 38
       0.155 -    0.194: 10
  Chirality restraints: 1125
  Sorted by residual:
  chirality pdb=" CB  ILE F 308 "
            pdb=" CA  ILE F 308 "
            pdb=" CG1 ILE F 308 "
            pdb=" CG2 ILE F 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.44e-01
  chirality pdb=" CA  ILE B 120 "
            pdb=" N   ILE B 120 "
            pdb=" C   ILE B 120 "
            pdb=" CB  ILE B 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.38e-01
  chirality pdb=" CA  HIS B 311 "
            pdb=" N   HIS B 311 "
            pdb=" C   HIS B 311 "
            pdb=" CB  HIS B 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.14e-01
  ... (remaining 1122 not shown)

  Planarity restraints: 1256
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA F 109 "   -0.040 2.00e-02 2.50e+03   7.93e-02 6.28e+01
        pdb=" C   ALA F 109 "    0.137 2.00e-02 2.50e+03
        pdb=" O   ALA F 109 "   -0.051 2.00e-02 2.50e+03
        pdb=" N   SER F 110 "   -0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 327 "   -0.047 5.00e-02 4.00e+02   7.19e-02 8.26e+00
        pdb=" N   PRO A 328 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO A 328 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 328 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 338 "   -0.013 2.00e-02 2.50e+03   2.63e-02 6.91e+00
        pdb=" C   LYS A 338 "    0.045 2.00e-02 2.50e+03
        pdb=" O   LYS A 338 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   TYR A 339 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1253 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 188
        2.64 -     3.21: 7498
        3.21 -     3.77: 11822
        3.77 -     4.34: 15850
        4.34 -     4.90: 25209
  Nonbonded interactions: 60567
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 260 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.076 3.040
  nonbonded pdb=" OG BSER B 227 "
            pdb=" OG  SER B 245 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" O   HIS B  54 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OG1 THR B 321 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" OG ASER B 227 "
            pdb=" OG  SER B 245 "
     model   vdw
     2.178 3.040
  ... (remaining 60562 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.38 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.600
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
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      :  0.009   0.089   7319  Z= 0.426
  Angle     :  1.045  10.612   9931  Z= 0.611
  Chirality :  0.056   0.194   1125
  Planarity :  0.007   0.079   1256
  Dihedral  : 15.531 171.855   2628
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 24.77
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.09 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 10.64 %
    Favored  : 88.72 %
  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: -2.40 (0.24), residues: 890
  helix: -1.64 (0.21), residues: 409
  sheet: -0.83 (0.36), residues: 184
  loop : -1.68 (0.31), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP F 318 
 HIS   0.015   0.003   HIS A 357 
 PHE   0.040   0.003   PHE A 238 
 TYR   0.018   0.003   TYR F 218 
 ARG   0.006   0.001   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15020 (  388)
  hydrogen bonds       : angle       7.19435 ( 1131)
  SS BOND              : bond        0.00748 (    1)
  SS BOND              : angle       1.06531 (    2)
  covalent geometry    : bond        0.00888 ( 7318)
  covalent geometry    : angle       1.04529 ( 9929)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 212
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.7824 (mttp) cc_final: 0.7483 (tttt)
REVERT: A  360 TYR cc_start: 0.9093 (OUTLIER) cc_final: 0.7726 (m-10)
REVERT: F  105 MET cc_start: 0.9125 (ttp) cc_final: 0.8647 (tmm)
REVERT: F  289 PHE cc_start: 0.8119 (m-80) cc_final: 0.7681 (m-80)
REVERT: F  333 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.8036 (p90)
REVERT: B    6 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7587 (mm-40)
REVERT: B   52 ARG cc_start: 0.7499 (mtt-85) cc_final: 0.7286 (mtt90)
REVERT: B   61 MET cc_start: 0.8636 (ppp) cc_final: 0.8178 (ppp)
REVERT: B   70 LEU cc_start: 0.7371 (pt) cc_final: 0.7037 (mp)
REVERT: B   78 LYS cc_start: 0.6658 (mmmt) cc_final: 0.6117 (tppt)
REVERT: B   85 TYR cc_start: 0.8582 (m-10) cc_final: 0.8369 (m-80)
REVERT: B  209 LYS cc_start: 0.7814 (mttp) cc_final: 0.7560 (mttp)
REVERT: B  295 ASN cc_start: 0.6510 (m110) cc_final: 0.6124 (t0)
REVERT: B  297 TRP cc_start: 0.6352 (m100) cc_final: 0.5755 (m100)
REVERT: B  335 PHE cc_start: 0.7217 (m-80) cc_final: 0.6521 (m-80)
REVERT: D   32 LYS cc_start: 0.8578 (tptp) cc_final: 0.8333 (tptt)
  outliers start: 3
  outliers final: 0
  residues processed: 214
  average time/residue: 0.2031
  time to fit residues: 57.0633
Evaluate side-chains
  163 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 161
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 66 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 68 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
A 371 ASN
F  60 ASN
F 327 ASN
B  62 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.130475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.099353 restraints weight = 59151.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.104286 restraints weight = 33237.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.104876 restraints weight = 17617.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3463
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3462
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7319  Z= 0.147
  Angle     :  0.653   7.693   9931  Z= 0.348
  Chirality :  0.046   0.224   1125
  Planarity :  0.005   0.056   1256
  Dihedral  :  9.497 156.431   1003
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.11 %
    Favored  : 96.63 %
  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: -0.45 (0.26), residues: 890
  helix:  0.25 (0.23), residues: 401
  sheet:  0.08 (0.40), residues: 146
  loop : -1.00 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 169 
 HIS   0.009   0.002   HIS A 357 
 PHE   0.020   0.002   PHE F 333 
 TYR   0.019   0.002   TYR B  59 
 ARG   0.008   0.001   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04972 (  388)
  hydrogen bonds       : angle       5.17038 ( 1131)
  SS BOND              : bond        0.00289 (    1)
  SS BOND              : angle       0.85104 (    2)
  covalent geometry    : bond        0.00307 ( 7318)
  covalent geometry    : angle       0.65317 ( 9929)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 251
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.7608 (mttp) cc_final: 0.7276 (tttt)
REVERT: A  277 TRP cc_start: 0.8784 (t-100) cc_final: 0.8238 (t-100)
REVERT: A  283 ARG cc_start: 0.7637 (mtp85) cc_final: 0.7174 (mmt-90)
REVERT: A  343 ASP cc_start: 0.8089 (p0) cc_final: 0.7674 (m-30)
REVERT: A  378 ASP cc_start: 0.8913 (m-30) cc_final: 0.8703 (m-30)
REVERT: A  386 MET cc_start: 0.7904 (tmm) cc_final: 0.7472 (tpp)
REVERT: F   35 LEU cc_start: 0.9325 (mt) cc_final: 0.9060 (mt)
REVERT: F   70 ASP cc_start: 0.9050 (m-30) cc_final: 0.8704 (m-30)
REVERT: F  105 MET cc_start: 0.8796 (ttp) cc_final: 0.8512 (tmm)
REVERT: F  222 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7466 (pm20)
REVERT: F  289 PHE cc_start: 0.7935 (m-80) cc_final: 0.7501 (m-80)
REVERT: F  321 TRP cc_start: 0.9095 (m-10) cc_final: 0.8768 (m-10)
REVERT: F  324 SER cc_start: 0.8692 (m) cc_final: 0.8286 (m)
REVERT: F  327 ASN cc_start: 0.8647 (m110) cc_final: 0.7953 (m110)
REVERT: F  337 PHE cc_start: 0.8075 (m-80) cc_final: 0.7829 (m-80)
REVERT: B   52 ARG cc_start: 0.7715 (mtt-85) cc_final: 0.7321 (mtm110)
REVERT: B   85 TYR cc_start: 0.8746 (m-10) cc_final: 0.8266 (m-80)
REVERT: B   88 ASN cc_start: 0.7743 (t0) cc_final: 0.7422 (t0)
REVERT: B   91 HIS cc_start: 0.8065 (m90) cc_final: 0.7731 (m-70)
REVERT: B  105 TYR cc_start: 0.6854 (t80) cc_final: 0.6500 (t80)
REVERT: B  110 ASN cc_start: 0.7938 (t0) cc_final: 0.7418 (t0)
REVERT: B  124 TYR cc_start: 0.8460 (m-10) cc_final: 0.8198 (m-10)
REVERT: B  171 ILE cc_start: 0.8948 (pt) cc_final: 0.8739 (pt)
REVERT: B  172 GLU cc_start: 0.8671 (tp30) cc_final: 0.8046 (tm-30)
REVERT: B  228 ASP cc_start: 0.8041 (m-30) cc_final: 0.7434 (m-30)
REVERT: B  229 ILE cc_start: 0.8271 (mt) cc_final: 0.8033 (tp)
REVERT: B  284 LEU cc_start: 0.8482 (tp) cc_final: 0.8271 (tp)
REVERT: B  289 TYR cc_start: 0.6451 (m-80) cc_final: 0.6216 (m-80)
REVERT: B  297 TRP cc_start: 0.6345 (m100) cc_final: 0.5831 (m100)
REVERT: B  313 ASN cc_start: 0.7262 (t0) cc_final: 0.6797 (m-40)
REVERT: B  335 PHE cc_start: 0.7283 (m-80) cc_final: 0.6665 (m-80)
REVERT: D   32 LYS cc_start: 0.8766 (tptp) cc_final: 0.8432 (tptt)
  outliers start: 1
  outliers final: 0
  residues processed: 251
  average time/residue: 0.1746
  time to fit residues: 59.2420
Evaluate side-chains
  192 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 191
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 65 optimal weight:   10.0000
   chunk 27 optimal weight:    0.4980
   chunk 2 optimal weight:    3.9990
   chunk 84 optimal weight:   20.0000
   chunk 82 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 66 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 119 ASN
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.129996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.099925 restraints weight = 54752.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.103348 restraints weight = 41920.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.106085 restraints weight = 17609.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3483
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3483
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7319  Z= 0.151
  Angle     :  0.629  11.955   9931  Z= 0.329
  Chirality :  0.044   0.207   1125
  Planarity :  0.004   0.048   1256
  Dihedral  :  9.287 149.817   1003
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.20 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.27), residues: 890
  helix:  0.97 (0.24), residues: 396
  sheet:  0.19 (0.40), residues: 142
  loop : -0.69 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.006   0.001   HIS B  54 
 PHE   0.023   0.002   PHE F 333 
 TYR   0.018   0.002   TYR B  59 
 ARG   0.006   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04541 (  388)
  hydrogen bonds       : angle       4.92844 ( 1131)
  SS BOND              : bond        0.00808 (    1)
  SS BOND              : angle       0.81895 (    2)
  covalent geometry    : bond        0.00332 ( 7318)
  covalent geometry    : angle       0.62861 ( 9929)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.7539 (mttp) cc_final: 0.7195 (tttt)
REVERT: A  277 TRP cc_start: 0.8792 (t-100) cc_final: 0.8363 (t-100)
REVERT: A  283 ARG cc_start: 0.7576 (mtp85) cc_final: 0.7309 (mmt-90)
REVERT: A  291 LEU cc_start: 0.9126 (mt) cc_final: 0.8608 (mt)
REVERT: A  343 ASP cc_start: 0.8072 (p0) cc_final: 0.7706 (m-30)
REVERT: F  105 MET cc_start: 0.8826 (ttp) cc_final: 0.8502 (tmm)
REVERT: F  289 PHE cc_start: 0.7688 (m-80) cc_final: 0.7473 (m-80)
REVERT: F  324 SER cc_start: 0.8773 (m) cc_final: 0.8495 (m)
REVERT: F  336 ASP cc_start: 0.8444 (p0) cc_final: 0.8192 (p0)
REVERT: F  337 PHE cc_start: 0.8029 (m-80) cc_final: 0.7825 (m-80)
REVERT: B   61 MET cc_start: 0.8635 (ppp) cc_final: 0.8323 (ppp)
REVERT: B   85 TYR cc_start: 0.8700 (m-10) cc_final: 0.8096 (m-80)
REVERT: B   88 ASN cc_start: 0.7667 (t0) cc_final: 0.7466 (t0)
REVERT: B   99 TRP cc_start: 0.7141 (m-90) cc_final: 0.6420 (m-90)
REVERT: B  110 ASN cc_start: 0.7836 (t0) cc_final: 0.7285 (t0)
REVERT: B  142 HIS cc_start: 0.7266 (m-70) cc_final: 0.6914 (m-70)
REVERT: B  156 GLN cc_start: 0.7600 (tp40) cc_final: 0.7381 (mm110)
REVERT: B  172 GLU cc_start: 0.8582 (tp30) cc_final: 0.7903 (tm-30)
REVERT: B  228 ASP cc_start: 0.8110 (m-30) cc_final: 0.7405 (m-30)
REVERT: B  297 TRP cc_start: 0.5789 (m100) cc_final: 0.5501 (m100)
REVERT: B  308 LEU cc_start: 0.8068 (mp) cc_final: 0.7781 (mp)
REVERT: D   32 LYS cc_start: 0.8771 (tptp) cc_final: 0.8447 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 0.1712
  time to fit residues: 53.7093
Evaluate side-chains
  181 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 38 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 8 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 83 optimal weight:   20.0000
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
B 156 GLN
** D  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.128510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.098952 restraints weight = 58996.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.101598 restraints weight = 49078.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.104965 restraints weight = 19979.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3457
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3457
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7319  Z= 0.167
  Angle     :  0.622  11.255   9931  Z= 0.328
  Chirality :  0.045   0.207   1125
  Planarity :  0.004   0.048   1256
  Dihedral  :  9.291 148.951   1003
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.37 %
    Favored  : 96.50 %
  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:  0.27 (0.28), residues: 890
  helix:  1.11 (0.25), residues: 393
  sheet: -0.04 (0.41), residues: 143
  loop : -0.70 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP F 321 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.022   0.002   PHE F 333 
 TYR   0.017   0.002   TYR B  59 
 ARG   0.003   0.000   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04434 (  388)
  hydrogen bonds       : angle       4.92888 ( 1131)
  SS BOND              : bond        0.00700 (    1)
  SS BOND              : angle       0.76325 (    2)
  covalent geometry    : bond        0.00370 ( 7318)
  covalent geometry    : angle       0.62221 ( 9929)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.8527 (mtmt) cc_final: 0.7875 (mmtt)
REVERT: A   34 LYS cc_start: 0.7774 (mttp) cc_final: 0.7532 (tttt)
REVERT: A  279 ASN cc_start: 0.8943 (t0) cc_final: 0.8719 (t0)
REVERT: A  283 ARG cc_start: 0.7625 (mtp85) cc_final: 0.7275 (mmt-90)
REVERT: A  291 LEU cc_start: 0.9168 (mt) cc_final: 0.8806 (mt)
REVERT: A  343 ASP cc_start: 0.7977 (p0) cc_final: 0.7611 (m-30)
REVERT: F   70 ASP cc_start: 0.8906 (m-30) cc_final: 0.8568 (m-30)
REVERT: F  105 MET cc_start: 0.8880 (ttp) cc_final: 0.8500 (tmm)
REVERT: F  289 PHE cc_start: 0.7707 (m-80) cc_final: 0.7504 (m-80)
REVERT: F  321 TRP cc_start: 0.9117 (m-10) cc_final: 0.8915 (m-10)
REVERT: F  324 SER cc_start: 0.8866 (m) cc_final: 0.8133 (m)
REVERT: F  327 ASN cc_start: 0.8626 (m110) cc_final: 0.8071 (m110)
REVERT: B   52 ARG cc_start: 0.7464 (ptp-170) cc_final: 0.7257 (mtm110)
REVERT: B   61 MET cc_start: 0.8742 (ppp) cc_final: 0.8328 (ppp)
REVERT: B   85 TYR cc_start: 0.8663 (m-10) cc_final: 0.8134 (m-80)
REVERT: B   88 ASN cc_start: 0.7694 (t0) cc_final: 0.7383 (t0)
REVERT: B   99 TRP cc_start: 0.6744 (m-90) cc_final: 0.5255 (m-90)
REVERT: B  110 ASN cc_start: 0.7647 (t0) cc_final: 0.7203 (t0)
REVERT: B  156 GLN cc_start: 0.7983 (tp-100) cc_final: 0.7700 (mm110)
REVERT: B  172 GLU cc_start: 0.8487 (tp30) cc_final: 0.7866 (tm-30)
REVERT: B  176 GLN cc_start: 0.6811 (mp10) cc_final: 0.6585 (mp10)
REVERT: B  228 ASP cc_start: 0.8252 (m-30) cc_final: 0.7583 (m-30)
REVERT: B  297 TRP cc_start: 0.5648 (m100) cc_final: 0.5419 (m100)
REVERT: D   32 LYS cc_start: 0.8679 (tptp) cc_final: 0.8425 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1759
  time to fit residues: 52.0538
Evaluate side-chains
  176 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 57 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 73 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 65 optimal weight:    6.9990
   chunk 78 optimal weight:    7.9990
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 323 ASN
B  62 HIS
** D  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  59 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.127031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.096465 restraints weight = 60521.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.099341 restraints weight = 41507.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.102792 restraints weight = 16744.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3445
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3445 r_free = 0.3445    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3445 r_free = 0.3445    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3445
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7319  Z= 0.178
  Angle     :  0.636  13.159   9931  Z= 0.332
  Chirality :  0.045   0.214   1125
  Planarity :  0.004   0.048   1256
  Dihedral  :  9.261 148.389   1003
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.08 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.28), residues: 890
  helix:  1.12 (0.25), residues: 393
  sheet: -0.07 (0.43), residues: 137
  loop : -0.64 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  99 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.021   0.002   PHE F 333 
 TYR   0.031   0.002   TYR B  59 
 ARG   0.005   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04388 (  388)
  hydrogen bonds       : angle       4.85136 ( 1131)
  SS BOND              : bond        0.00730 (    1)
  SS BOND              : angle       0.75682 (    2)
  covalent geometry    : bond        0.00394 ( 7318)
  covalent geometry    : angle       0.63610 ( 9929)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 209
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.8450 (mtmt) cc_final: 0.7826 (mmtt)
REVERT: A   34 LYS cc_start: 0.7938 (mttp) cc_final: 0.7721 (tttt)
REVERT: A  209 GLU cc_start: 0.6947 (mm-30) cc_final: 0.5870 (mm-30)
REVERT: A  279 ASN cc_start: 0.8945 (t0) cc_final: 0.8717 (t0)
REVERT: A  283 ARG cc_start: 0.7652 (mtp85) cc_final: 0.7270 (mmt-90)
REVERT: A  291 LEU cc_start: 0.9151 (mt) cc_final: 0.8849 (mt)
REVERT: A  343 ASP cc_start: 0.8084 (p0) cc_final: 0.7709 (m-30)
REVERT: A  390 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8034 (tm-30)
REVERT: F   70 ASP cc_start: 0.9025 (m-30) cc_final: 0.8715 (m-30)
REVERT: F  105 MET cc_start: 0.8820 (ttp) cc_final: 0.8388 (tmm)
REVERT: F  222 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7706 (pm20)
REVERT: F  324 SER cc_start: 0.8864 (m) cc_final: 0.8214 (m)
REVERT: F  327 ASN cc_start: 0.8919 (m110) cc_final: 0.8219 (m110)
REVERT: B   52 ARG cc_start: 0.7522 (ptp-170) cc_final: 0.7300 (mtm110)
REVERT: B   61 MET cc_start: 0.8733 (ppp) cc_final: 0.8214 (ppp)
REVERT: B   70 LEU cc_start: 0.7321 (pt) cc_final: 0.6895 (mp)
REVERT: B   85 TYR cc_start: 0.8567 (m-10) cc_final: 0.8124 (m-80)
REVERT: B  156 GLN cc_start: 0.7797 (tp-100) cc_final: 0.7483 (mm110)
REVERT: B  172 GLU cc_start: 0.8488 (tp30) cc_final: 0.7886 (tm-30)
REVERT: B  176 GLN cc_start: 0.6688 (mp10) cc_final: 0.6352 (mp10)
REVERT: B  228 ASP cc_start: 0.8110 (m-30) cc_final: 0.7466 (m-30)
REVERT: B  297 TRP cc_start: 0.5776 (m100) cc_final: 0.5500 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 210
  average time/residue: 0.1740
  time to fit residues: 49.8139
Evaluate side-chains
  174 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 173
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 50 optimal weight:    7.9990
   chunk 32 optimal weight:    0.4980
   chunk 5 optimal weight:    8.9990
   chunk 39 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 7 optimal weight:    9.9990
   chunk 3 optimal weight:    0.4980
   chunk 18 optimal weight:    4.9990
   chunk 69 optimal weight:    9.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
** D  11 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 = 0.3861 r_free = 0.3861 target = 0.128652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.098978 restraints weight = 56627.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.100697 restraints weight = 45221.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.104168 restraints weight = 20367.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3459
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3459 r_free = 0.3459    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3459 r_free = 0.3459    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3459
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.4012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7319  Z= 0.137
  Angle     :  0.612  12.121   9931  Z= 0.322
  Chirality :  0.044   0.200   1125
  Planarity :  0.004   0.050   1256
  Dihedral  :  9.118 146.889   1003
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.82 %
    Favored  : 98.05 %
  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:  0.38 (0.28), residues: 890
  helix:  1.15 (0.25), residues: 399
  sheet: -0.11 (0.44), residues: 136
  loop : -0.54 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.078   0.003   TRP B  99 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.026   0.002   PHE B 292 
 TYR   0.029   0.002   TYR B  59 
 ARG   0.002   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04244 (  388)
  hydrogen bonds       : angle       4.80674 ( 1131)
  SS BOND              : bond        0.00565 (    1)
  SS BOND              : angle       0.62220 (    2)
  covalent geometry    : bond        0.00299 ( 7318)
  covalent geometry    : angle       0.61218 ( 9929)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.8470 (mtmt) cc_final: 0.7881 (mmtt)
REVERT: A   34 LYS cc_start: 0.7845 (mttp) cc_final: 0.7540 (tttt)
REVERT: A  283 ARG cc_start: 0.7617 (mtp85) cc_final: 0.7271 (mmt-90)
REVERT: A  291 LEU cc_start: 0.9094 (mt) cc_final: 0.8773 (mt)
REVERT: A  343 ASP cc_start: 0.8035 (p0) cc_final: 0.7659 (m-30)
REVERT: F   61 PHE cc_start: 0.7159 (m-80) cc_final: 0.6926 (m-80)
REVERT: F   70 ASP cc_start: 0.8932 (m-30) cc_final: 0.8622 (m-30)
REVERT: F  324 SER cc_start: 0.8865 (m) cc_final: 0.8221 (m)
REVERT: F  327 ASN cc_start: 0.9023 (m110) cc_final: 0.8272 (m110)
REVERT: B   61 MET cc_start: 0.8746 (ppp) cc_final: 0.8176 (ppp)
REVERT: B   70 LEU cc_start: 0.7384 (pt) cc_final: 0.7088 (mp)
REVERT: B   85 TYR cc_start: 0.8535 (m-10) cc_final: 0.8122 (m-80)
REVERT: B  110 ASN cc_start: 0.7353 (t0) cc_final: 0.6574 (t0)
REVERT: B  156 GLN cc_start: 0.7884 (tp-100) cc_final: 0.7564 (mm110)
REVERT: B  172 GLU cc_start: 0.8464 (tp30) cc_final: 0.7869 (tm-30)
REVERT: B  176 GLN cc_start: 0.6711 (mp10) cc_final: 0.6436 (mp10)
REVERT: B  228 ASP cc_start: 0.8211 (m-30) cc_final: 0.7570 (m-30)
REVERT: B  284 LEU cc_start: 0.8247 (tp) cc_final: 0.8037 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 219
  average time/residue: 0.1689
  time to fit residues: 51.0484
Evaluate side-chains
  178 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0010
   chunk 5 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 65 optimal weight:   20.0000
   chunk 6 optimal weight:    0.8980
   chunk 50 optimal weight:    7.9990
   chunk 85 optimal weight:   10.0000
   overall best weight:    1.1790

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  11 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 = 0.3881 r_free = 0.3881 target = 0.129844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.100394 restraints weight = 53507.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.104666 restraints weight = 38896.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.105795 restraints weight = 16294.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3497
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3496
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.4314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7319  Z= 0.130
  Angle     :  0.614  13.557   9931  Z= 0.319
  Chirality :  0.044   0.216   1125
  Planarity :  0.004   0.052   1256
  Dihedral  :  9.044 145.801   1003
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.82 %
    Favored  : 98.05 %
  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:  0.36 (0.28), residues: 890
  helix:  1.15 (0.25), residues: 410
  sheet: -0.22 (0.43), residues: 133
  loop : -0.59 (0.35), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP B  99 
 HIS   0.006   0.001   HIS A  64 
 PHE   0.024   0.002   PHE A 222 
 TYR   0.027   0.002   TYR B  59 
 ARG   0.004   0.000   ARG D  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04156 (  388)
  hydrogen bonds       : angle       4.72908 ( 1131)
  SS BOND              : bond        0.00465 (    1)
  SS BOND              : angle       0.57073 (    2)
  covalent geometry    : bond        0.00283 ( 7318)
  covalent geometry    : angle       0.61440 ( 9929)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.8371 (mtmt) cc_final: 0.7812 (mmtt)
REVERT: A   34 LYS cc_start: 0.7829 (mttp) cc_final: 0.7569 (tttt)
REVERT: A   37 TYR cc_start: 0.8064 (t80) cc_final: 0.7780 (t80)
REVERT: A  283 ARG cc_start: 0.7549 (mtp85) cc_final: 0.7102 (mmt-90)
REVERT: A  291 LEU cc_start: 0.9075 (mt) cc_final: 0.8857 (mt)
REVERT: A  343 ASP cc_start: 0.8089 (p0) cc_final: 0.7725 (m-30)
REVERT: A  364 THR cc_start: 0.8551 (p) cc_final: 0.8325 (p)
REVERT: F   61 PHE cc_start: 0.7194 (m-80) cc_final: 0.6970 (m-80)
REVERT: F  105 MET cc_start: 0.8704 (ttp) cc_final: 0.8188 (tmm)
REVERT: F  324 SER cc_start: 0.8925 (m) cc_final: 0.8657 (m)
REVERT: B   52 ARG cc_start: 0.7249 (ptp-170) cc_final: 0.7013 (mtm110)
REVERT: B   61 MET cc_start: 0.8733 (ppp) cc_final: 0.8197 (ppp)
REVERT: B   70 LEU cc_start: 0.7493 (pt) cc_final: 0.7067 (mp)
REVERT: B   85 TYR cc_start: 0.8507 (m-10) cc_final: 0.8055 (m-80)
REVERT: B   99 TRP cc_start: 0.6273 (m100) cc_final: 0.4830 (m100)
REVERT: B  101 MET cc_start: 0.8407 (mpp) cc_final: 0.7800 (mpp)
REVERT: B  110 ASN cc_start: 0.7164 (t0) cc_final: 0.6462 (t0)
REVERT: B  156 GLN cc_start: 0.7860 (tp-100) cc_final: 0.7532 (mm110)
REVERT: B  172 GLU cc_start: 0.8416 (tp30) cc_final: 0.7878 (tm-30)
REVERT: B  176 GLN cc_start: 0.6647 (mp10) cc_final: 0.6394 (mp10)
REVERT: B  228 ASP cc_start: 0.8169 (m-30) cc_final: 0.7609 (m-30)
REVERT: B  263 THR cc_start: 0.8105 (m) cc_final: 0.7450 (m)
REVERT: B  313 ASN cc_start: 0.7062 (t0) cc_final: 0.6794 (m-40)
REVERT: B  329 THR cc_start: 0.8265 (t) cc_final: 0.7884 (m)
REVERT: B  331 SER cc_start: 0.8531 (t) cc_final: 0.8278 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 218
  average time/residue: 0.1540
  time to fit residues: 46.9344
Evaluate side-chains
  180 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 17 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 82 optimal weight:    7.9990
   chunk 81 optimal weight:    9.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
** D  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.130132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.100518 restraints weight = 53305.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.103146 restraints weight = 43987.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.105728 restraints weight = 18648.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3500
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3500 r_free = 0.3500    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3500 r_free = 0.3500    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3500
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.4504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7319  Z= 0.130
  Angle     :  0.623  12.590   9931  Z= 0.326
  Chirality :  0.045   0.206   1125
  Planarity :  0.004   0.052   1256
  Dihedral  :  8.950 142.011   1003
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.69 %
    Favored  : 98.18 %
  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:  0.28 (0.28), residues: 890
  helix:  1.05 (0.25), residues: 418
  sheet: -0.14 (0.43), residues: 134
  loop : -0.67 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B  99 
 HIS   0.005   0.001   HIS D  44 
 PHE   0.034   0.002   PHE B 292 
 TYR   0.025   0.002   TYR B  59 
 ARG   0.003   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04098 (  388)
  hydrogen bonds       : angle       4.82477 ( 1131)
  SS BOND              : bond        0.00533 (    1)
  SS BOND              : angle       0.50401 (    2)
  covalent geometry    : bond        0.00285 ( 7318)
  covalent geometry    : angle       0.62331 ( 9929)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.8347 (mtmt) cc_final: 0.7730 (tptt)
REVERT: A   34 LYS cc_start: 0.7764 (mttp) cc_final: 0.7503 (tttt)
REVERT: A   37 TYR cc_start: 0.8039 (t80) cc_final: 0.7698 (t80)
REVERT: A  283 ARG cc_start: 0.7560 (mtp85) cc_final: 0.7108 (mmt-90)
REVERT: A  291 LEU cc_start: 0.9036 (mt) cc_final: 0.8814 (mt)
REVERT: A  343 ASP cc_start: 0.8050 (p0) cc_final: 0.7755 (m-30)
REVERT: A  390 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8053 (tm-30)
REVERT: F   61 PHE cc_start: 0.7089 (m-80) cc_final: 0.6782 (m-80)
REVERT: F   70 ASP cc_start: 0.9042 (m-30) cc_final: 0.8681 (m-30)
REVERT: F  105 MET cc_start: 0.8669 (ttp) cc_final: 0.8450 (ttp)
REVERT: F  204 TYR cc_start: 0.7827 (m-80) cc_final: 0.7573 (m-80)
REVERT: F  324 SER cc_start: 0.8903 (m) cc_final: 0.8177 (m)
REVERT: F  327 ASN cc_start: 0.9007 (m110) cc_final: 0.8342 (m110)
REVERT: B   52 ARG cc_start: 0.7190 (ptp-170) cc_final: 0.6968 (mtm110)
REVERT: B   61 MET cc_start: 0.8706 (ppp) cc_final: 0.8126 (ppp)
REVERT: B   85 TYR cc_start: 0.8434 (m-10) cc_final: 0.8057 (m-80)
REVERT: B  110 ASN cc_start: 0.7142 (t0) cc_final: 0.6487 (t0)
REVERT: B  156 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7497 (mm110)
REVERT: B  172 GLU cc_start: 0.8365 (tp30) cc_final: 0.7897 (tm-30)
REVERT: B  176 GLN cc_start: 0.6730 (mp10) cc_final: 0.6499 (mp10)
REVERT: B  204 CYS cc_start: 0.7159 (m) cc_final: 0.6709 (m)
REVERT: B  228 ASP cc_start: 0.8203 (m-30) cc_final: 0.7667 (m-30)
REVERT: B  263 THR cc_start: 0.8147 (m) cc_final: 0.7603 (m)
REVERT: B  296 VAL cc_start: 0.8140 (t) cc_final: 0.7918 (t)
REVERT: B  297 TRP cc_start: 0.4744 (m100) cc_final: 0.4261 (m100)
REVERT: B  329 THR cc_start: 0.8186 (t) cc_final: 0.7854 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 226
  average time/residue: 0.1669
  time to fit residues: 52.1631
Evaluate side-chains
  182 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 51 optimal weight:   50.0000
   chunk 77 optimal weight:   10.0000
   chunk 75 optimal weight:    7.9990
   chunk 16 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 35 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    2.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
A 377 ASN
** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 323 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  11 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 = 0.3848 r_free = 0.3848 target = 0.127135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.096630 restraints weight = 51292.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.099344 restraints weight = 35182.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.101001 restraints weight = 18792.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3411
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3411 r_free = 0.3411    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3411 r_free = 0.3411    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3411
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.4513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7319  Z= 0.186
  Angle     :  0.669  14.728   9931  Z= 0.349
  Chirality :  0.047   0.207   1125
  Planarity :  0.004   0.052   1256
  Dihedral  :  9.038 144.223   1003
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.52 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.12 (0.28), residues: 890
  helix:  0.89 (0.25), residues: 418
  sheet: -0.14 (0.46), residues: 120
  loop : -0.73 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP B  99 
 HIS   0.005   0.001   HIS D  44 
 PHE   0.024   0.002   PHE A 340 
 TYR   0.027   0.002   TYR B  59 
 ARG   0.003   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04448 (  388)
  hydrogen bonds       : angle       4.98323 ( 1131)
  SS BOND              : bond        0.00769 (    1)
  SS BOND              : angle       0.57238 (    2)
  covalent geometry    : bond        0.00417 ( 7318)
  covalent geometry    : angle       0.66897 ( 9929)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.8406 (mtmt) cc_final: 0.7778 (tptt)
REVERT: A   34 LYS cc_start: 0.7717 (mttp) cc_final: 0.7492 (tttt)
REVERT: A   37 TYR cc_start: 0.8180 (t80) cc_final: 0.7809 (t80)
REVERT: A  239 ASN cc_start: 0.8067 (p0) cc_final: 0.7493 (t0)
REVERT: A  279 ASN cc_start: 0.8821 (t0) cc_final: 0.8430 (t0)
REVERT: A  282 LEU cc_start: 0.9173 (mt) cc_final: 0.8361 (mt)
REVERT: A  283 ARG cc_start: 0.7711 (mtp85) cc_final: 0.7200 (mmt-90)
REVERT: A  343 ASP cc_start: 0.8256 (p0) cc_final: 0.7788 (m-30)
REVERT: F   61 PHE cc_start: 0.7014 (m-80) cc_final: 0.6724 (m-80)
REVERT: F  105 MET cc_start: 0.8943 (ttp) cc_final: 0.8669 (tmm)
REVERT: F  324 SER cc_start: 0.9118 (m) cc_final: 0.8893 (m)
REVERT: B   85 TYR cc_start: 0.8576 (m-10) cc_final: 0.8107 (m-80)
REVERT: B   91 HIS cc_start: 0.8109 (m90) cc_final: 0.7470 (m90)
REVERT: B  156 GLN cc_start: 0.8094 (tp-100) cc_final: 0.7813 (mm110)
REVERT: B  172 GLU cc_start: 0.8502 (tp30) cc_final: 0.7997 (tm-30)
REVERT: B  204 CYS cc_start: 0.7298 (m) cc_final: 0.7017 (m)
REVERT: B  228 ASP cc_start: 0.8228 (m-30) cc_final: 0.7664 (m-30)
REVERT: B  263 THR cc_start: 0.8176 (m) cc_final: 0.7537 (m)
REVERT: B  297 TRP cc_start: 0.4676 (m100) cc_final: 0.4199 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.1606
  time to fit residues: 46.3419
Evaluate side-chains
  176 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 64 optimal weight:    0.0020
   chunk 37 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 80 optimal weight:    8.9990
   chunk 38 optimal weight:    0.8980
   chunk 77 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.9392

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.130475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.098997 restraints weight = 59826.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.103732 restraints weight = 40178.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.105011 restraints weight = 18366.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3461
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3461 r_free = 0.3461    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3461 r_free = 0.3461    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3461
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.4767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7319  Z= 0.128
  Angle     :  0.638  14.101   9931  Z= 0.330
  Chirality :  0.045   0.200   1125
  Planarity :  0.004   0.054   1256
  Dihedral  :  8.937 142.763   1003
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.52 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.28), residues: 890
  helix:  1.17 (0.25), residues: 400
  sheet: -0.07 (0.46), residues: 121
  loop : -0.74 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP B  99 
 HIS   0.006   0.001   HIS B 142 
 PHE   0.027   0.002   PHE B 292 
 TYR   0.022   0.002   TYR B  59 
 ARG   0.003   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04161 (  388)
  hydrogen bonds       : angle       4.80261 ( 1131)
  SS BOND              : bond        0.00367 (    1)
  SS BOND              : angle       0.34257 (    2)
  covalent geometry    : bond        0.00286 ( 7318)
  covalent geometry    : angle       0.63801 ( 9929)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.8447 (mtmt) cc_final: 0.7811 (tptt)
REVERT: A   34 LYS cc_start: 0.7689 (mttp) cc_final: 0.7443 (tttt)
REVERT: A   37 TYR cc_start: 0.8162 (t80) cc_final: 0.7788 (t80)
REVERT: A  239 ASN cc_start: 0.8086 (p0) cc_final: 0.7645 (t0)
REVERT: A  283 ARG cc_start: 0.7614 (mtp85) cc_final: 0.7066 (mmt-90)
REVERT: A  343 ASP cc_start: 0.8140 (p0) cc_final: 0.7789 (m-30)
REVERT: F   61 PHE cc_start: 0.7169 (m-80) cc_final: 0.6866 (m-80)
REVERT: F   70 ASP cc_start: 0.9117 (m-30) cc_final: 0.8639 (m-30)
REVERT: F  324 SER cc_start: 0.8893 (m) cc_final: 0.8258 (m)
REVERT: F  327 ASN cc_start: 0.8859 (m110) cc_final: 0.8279 (m110)
REVERT: F  337 PHE cc_start: 0.7432 (m-80) cc_final: 0.7140 (m-80)
REVERT: B   85 TYR cc_start: 0.8492 (m-10) cc_final: 0.8197 (m-80)
REVERT: B   91 HIS cc_start: 0.8175 (m90) cc_final: 0.7548 (m90)
REVERT: B  110 ASN cc_start: 0.7387 (t0) cc_final: 0.6740 (t0)
REVERT: B  156 GLN cc_start: 0.8028 (tp-100) cc_final: 0.7646 (mm110)
REVERT: B  172 GLU cc_start: 0.8470 (tp30) cc_final: 0.8030 (tm-30)
REVERT: B  228 ASP cc_start: 0.8113 (m-30) cc_final: 0.7510 (m-30)
REVERT: B  263 THR cc_start: 0.8078 (m) cc_final: 0.7429 (m)
REVERT: B  297 TRP cc_start: 0.4604 (m100) cc_final: 0.4095 (m100)
REVERT: D   36 ASP cc_start: 0.9024 (p0) cc_final: 0.8758 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1553
  time to fit residues: 46.2995
Evaluate side-chains
  169 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 68 optimal weight:    9.9990
   chunk 77 optimal weight:    7.9990
   chunk 64 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 3 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.128067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.097415 restraints weight = 57190.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.099508 restraints weight = 43557.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.102522 restraints weight = 21254.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3426
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3426
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.4779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7319  Z= 0.174
  Angle     :  0.664  14.525   9931  Z= 0.345
  Chirality :  0.046   0.212   1125
  Planarity :  0.005   0.054   1256
  Dihedral  :  8.964 143.430   1003
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 15.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.65 %
    Favored  : 99.22 %
  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:  0.18 (0.28), residues: 890
  helix:  1.09 (0.25), residues: 400
  sheet: -0.12 (0.47), residues: 120
  loop : -0.82 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP B  99 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.024   0.002   PHE A 340 
 TYR   0.024   0.002   TYR A  37 
 ARG   0.013   0.000   ARG B 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04336 (  388)
  hydrogen bonds       : angle       4.93251 ( 1131)
  SS BOND              : bond        0.00634 (    1)
  SS BOND              : angle       0.40825 (    2)
  covalent geometry    : bond        0.00396 ( 7318)
  covalent geometry    : angle       0.66449 ( 9929)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2680.62 seconds
wall clock time: 47 minutes 6.09 seconds (2826.09 seconds total)